There are several possibilities to open a mass spectra file in TRANSPEC-Format:
Click on File|Open... to get to the Open File-dialogue and select the desired spectra file.
Use the 
-Icon
to get to the Open File-dialogue.
Click File to select a spectra file from the recent file list.
Drag & Drop the desired file from the Explorer or anywhere else into the MOLGEN-MS main window.
Hint: By double click onto a TRANSPEC-file you start a new MOLGEN-MS session with the chosen file.
Besides the TRANSPEC-Format MOLGEN-MS also supports JCAMP-DX mass spectra files as used in Chemical Concept's SpecInfo system. You can import JCAMP-DX files by clicking FILE|Import... . Then just select the desired spectra file.
Attention: As there are no strict standards for JCAMP-DX mass spectra file format, be aware that the file import fails. In such cases please send a detailed bug report to your MOLGEN-MS vendor.
Your mass spectra file will usually contain several mass
spectra. The number of mass spectra contained in the current file is
displayed in the status bar under the topic Spectra. You can go to
the next spectrum by clicking View|Next or the
-Icon of the toolbar. You
get to the previous spectrum by choosing View|Previous or the
-button.
You can display the masses of the highest peaks of each
peakgroup if you select View|Peak Masses or the
-Button:
If you click View|Peak Masses or the
-Button again, the
masses display disappears.
There is a possibility to store the compound name, the
CAS-number, the molecular mass, the molecular formula and the structural
formula in the TRANSPEC-files. You can display this data -
supposed it is available - by clicking View|Solution or the
-button:
If you click View|Solution or the
-button again, the
solution data disappears.
There is a possibility to store GC or AES-Data in the TRANSPEC-files. You can display this data - supposed it is available - by clicking View|AES Data or View|GC Data, respectively. By clicking the same menu item again, the according display disappears.
For a given molecular formula a matchvalue can be
computed which shows how good this formula fits the experimental spectrum.
By clicking View|Matchvalue or the 
-button
the following dialogue appears:
Here you enter the molecular formula you want to examine. Do this by entering the element symbols followed by the number of atoms of this element. Don't use any blanks. Press Return or the Enter-button to start the computation. This may take several minutes, depending on the number of peaks in the spectrum and the number of atoms in the molecular formula. When the computation is finished the matchvalue and the optimized theoretical spectrum is displayed in the MOLGEN-MS main window:
The intensities that can be explained by the molecular
formula are displayed green. Intensities
that keep unexplained or missing intensities are displayed
red. In the above example nearly all
intensities are marked green; C6H12O2
is the correct molecular formula. Nevertheless we have a little red stroke
at m/z=75. The reason is that the experimental isotope peak at m/z=75 is
too low. If you View|Matchvalue or the
-button again, the
matchvalue display and the according dialogue will disappear.
A first tool to compute all molecular formulae according
to a given mass interval is offered by the MolForm-dialogue, that
is obtained by Tools|MolForm or the 
-button.
Just enter the minimum and the maximum mass for the mass interval and press the Enter-button to compute all molecular formulae with molecular mass within the desired interval. For example if you enter 78 as lower and upper bound for the mass interval, you get the following result:
There exist altogether 251 molecular formula with molecular mass 78. 85 of them belong to ions, i.e. they have a non-negative sum of double bond equivalents. These 53 divide into odd electron ions and even electron ions. The odd electron ions have an integer sum of double bond equivalents. These are exactly the same molecular formulae, for which molecular graphs exist. Such molecular formulae are called graphical. The other 32 belong to even electron ions. These have a non-integer sum of double-bond equivalents. The radio-buttons in the Result-field show, which formulae will be displayed. In order to display the formulae you have to enable the View-checkbox in the Display-field:
Now after clicking the Enter-button up to 100 formulae are displayed in the dialogues listcontrol. You can select the order by which the computed formulae will be displayed in the Ranking-field. You can choose a ranking by the distance to molecular mass or similarity to isotope pattern.
Let's look for a (graphical) molecular formula with mass between 77 and 79 and exact molecular mass 78.047. At first enter the mass interval and enable the High Resolution-checkbox.
Then choose distance to molecular mass in the Ranking-Field and enter the experimental mass:
On clicking the Enter-Button you'll get the following result:
C6H6 is the elemental composition with molecular mass closest to 78.047. The matchvalue is the difference between the desired molecular mass 78.047 and the sum of atom masses of C6H6, which is 78.0468. Therefore we have 0.0002 as matchvalue.
Say we have the following peakgroup measured with a low resolution mass spectrometer:
| m/z | Int |
|---|---|
| 72 | 0.4 |
| 73 | 1.0 |
| 74 | 3.9 |
| 75 | 2.2 |
| 76 | 7.0 |
| 77 | 15.0 |
| 78 | 100.0 |
| 79 | 6.8 |
| 80 | 0.2 |
We are searching for molecular formulae with mass 78, that fit this peakgroup best. Therefore we have to enter for the mass interval 78 as lower and as upper border, disable the High Resolution-checkbox and choose similarity to isotope pattern in the Ranking-field. Now the edit-control for the molecular mass becomes insensitive and the other controls in the Ranking-field are enabled. So you are able to to enter the peakgroup step by step. For every peak you have to enter its mass (Mass-edit-control) and its intensity (Intens-edit-control) and then click the Add-button. If your entry is allowed, it will be displayed in the listbox aside. Allowed are 1 to 10 peaks with integer masses between 1 and 999 and intensities between 0.0001 and 100. Otherwise an error message occurs. When you have inserted all peaks, click the Enter-button to obtain the result:
C6H6 is the elemental composition that fits the given peakgroup best. Here the matchvalue is the intensity amount (in percent) of the given peakgroup that keeps unexplained by the theoretical isotope pattern of the candidate formula. So if we had a candidate that can't explain any of the given peaks, we would get a matchvalue of 100. For the first entry in the list the matchvalue of 0.45776 is quite good. If we would allow more than five hydrogen losses it would become even better. If you like to, you can enter 6 losses. Then you'll get a matchvalue of 0.23416, because now also the peak at m/z=72 can be explained. Reset the number of allowed H-losses to the default value by clicking the Reset-button.
Hints:
The number of molecular formulae grows very fast for increasing masses. As the calculation of the matchvalue by similarity to isotope pattern applies an optimization algorithm and is therefore quite time consuming, try to keep the number of candidates small. If you know anything about the elemental composition in question, like present or absent elements or an interval for the number of atoms of an element, use the Edit-button to input this information. This additional information will then be shown in the Intervals-field.
Using the Molin-button you can directly proceed to the Molin-dialogue. The computed candidates are copied to the Molecular Formula-combobox.
At the beginning the MolForm-dialogue is initialized with the first peakgroup of the actual spectrum in MOLGEN-MS, assumed there is a spectrum loaded. So usually you do not have to input the peakgroup manually.
To save the computed candidates as text file, click the left mouse button on the Candidate-listbox.
To sort the computed candidates by their mass or their matchvalue, click the according column of the Candidate-listbox.
A frequent task for people treating with mass spectra is
the calculation of theoretical isotope patterns. From the MOLGEN-MS
main window you can reach a tool that calculates theoretical isotope
patterns for a given molecular formula. Call the IsoPat-dialogue
by clicking Tools|Isopat or the 
-button.
Input a molecular formula (element symbols followed by the according number of atoms, no blanks) and click the Enter-button. The theoretical isotope pattern is displayed as graphic and as peak list. The most intense peak is normalized to 100. Additionally the nominal molecular mass, the exact molecular mass and the ion type are displayed.
To start the mass spectra classification select Programs|MSclass
or click the 
-button.
If there is no spectrum loaded the program will answer with an error
message. The further descriptions refer to the first spectrum of the file
tra-demo.tra. Now if you start MSclass a dialogue similar
to the following appears on the screen.
In the Input-field you see the filename of the used classifier-file which is 160-9609.mcb, the number of classifiers that are contained in the classifier file and the treshold for the precision of the result answer for all classifiers, that is by default 95%. In the Output-field the number of found classifier answers with precision at least 95%, among which 5 gave answer yes, and 63 answer no. In the listbox the detailed classifier results of all 68 found classifiers are displayed. Each row contains the information of one classifier. In the first column there is the classifier name. As you see, some classifier names differ only in the last number, for instance non ar /1 and non ar /2. These classifiers belong to the same SP respectively, but have different classification algorithms. In the next column there is the answer type (yes or no) followed by the answer precision, the value of the discriminant variable and a short description of the SP associated with the classifier. The last indicates the classification method: There are two entries possible: LDA or RBF. LDA-classifiers use a linear discriminant function, based on principal component analysis and linear discriminant analysis. RBF-classifiers use a non-linear classification function, based on a neural network with radial basis functions.
To change the treshold for the precision, use the spin-boxes beside the Precision-edit-field:
The lower the precision is, the more classifier answers are found. For example at 90% you get 95 answers, among which are 9 times YES. To execute this, adjust the precision 90 and click the Classify-button. Of course the risk of getting wrong answers is higher at a lower precision. If you choose a higher precision, you'll get less classifier answers, with lower risk of wrong classification results vice versa.
Attention: Classification techniques implemented in MSclass are mainly based on multivariate statistics. It is inherent to statistical methods, that no guarantee can be given for a particular classification result to be correct.
Hints:
You can change the classifier file by clicking the Open-button. Then an Open File-dialogue appears, where you can choose the new classifier file. Classifier files have suffixes .mcl (ascii file) or .mcb (binary file). This feature is important if new or improved classifiers are available (look out for updates) or if you just want to consider a special selection of classifiers.
Using the Molin-button you can directly proceed to the Molin-Dialogue.
If you leave MSclass the actual precision is stored and will be the start setting at your next call of MSclass.
Click the left mouse button on the Classifier-listbox, if you want to save the classification results to file.
To sort the found classifiers by their answer type, their answer precision, their description etc., click the according column of the Classifier-listbox.
This Program has to transform the classifier answers
into substructure information that can be processed by a structure
generator. The Molin-Dialogue allows the user to adjust tresholds
for precisions of classifier answers and to interact at the selection of
structure information. The Molin-dialogue can be opened from by
Programs|Molin or by clicking the 
-button.
In the Substructures-field there are three listboxes. One for prescribed SPs (Yes), one for forbidden SPs (No) and the big one for the remaining SPs. The SPs have names related to the classifier names. You get the SPs names from the classifier names by discarding the last two digits. In the current version we have 85 structures. They are already distributed into the three listboxes in accordance to the classification results, i.e. 2 prescribed and 40 forbidden SPs and 43 unclassified SPs. There are different methods implemented to decide, which SPs are prescribed/forbidden.
In the Classifier Precision-field, there are two editboxes named Yes and No that contain the minimum precision for Yes and No answers. For each SP all associated classifiers are taken into account. If there are contradicting answers above the treshold the considered SP will not be selected. If at least one classifier is above the treshold and the other associated classifiers give no contradicting result, the according substructure will be marked as prescribed/forbidden.
Let's have a look at two (fictive) examples that treat with the substructure me-est. There exist four classifiers for this substructure: me-est /1, me-est /2, me-est /3 and me-est /4. The treshold is 95% for both, Yes and No answers. The classification results are:
| Classifier | Y/N | Precision |
|---|---|---|
| me-est /1 | Y | 95 |
| me-est /2 | N | 94 |
| me-est /3 | N | 94 |
| me-est /4 | N | 94 |
In this case me-est would be chosen as prescribed substructure. In the other example
| Classifier | Y/N | Precision |
|---|---|---|
| me-est /1 | Y | 99 |
| me-est /2 | Y | 99 |
| me-est /3 | Y | 99 |
| me-est /4 | N | 95 |
me-est is neither selected as prescribed nor as forbidden substructure. These decisions seem not to be very clever. But no worries: for most substructures only two classifiers exist.
Not all SP supply useful structural information for the structure generator. For instance hydr carb (hydrocarbon) or non ar (non aromatic). On the other hand it is very important for the structure generation to have at least one substructure in the goodlist, because otherwise the number becomes too large. Therefore the Additional Goodlist-field is available, which is activated by unchecking Disable.
Here you can select the number of Entries for the goodlist. You have to specify another precision treshold, that is by default 90%. The above configuration means: Select the best classified substructure for the goodlist. The precision for an associated classifier must be at least 90%. Of course substructures with contradicting classifier answers are not regarded. Let's have a look at the following (fictive) example:
| Classifier | Y/N | Precision |
|---|---|---|
| non ar /1 | Y | 99 |
| me-est /1 | Y | 98 |
| me-est /2 | N | 95 |
| et-est /1 | Y | 92 |
| C quart ch /1 | Y | 91 |
With the above settings we have non ar in the Yes-list. me-est is not in the Yes-list, because there are contradicting classification results. As additional goodlist is enabled, but non ar is no substructure, the next best classified substructure will be chosen for the Yes-list. This is et-est. No further SPs will be added to the Yes-list , because Entries is set to 1.
If you enable check consistency to molecular formula, the edit-box in the molecular formula-field becomes activated. Now you can enter a molecular formula (element symbols followed by the according number of atoms, no blanks). Update the display by clicking the Enter-button. Now only SPs that do not contradict to the molecular formula will be added to the Yes- and the No-list. For instance without specification of a molecular formula, spectrum no. 4 of tra-demo.tra yields the following yes-list:
After entering
we obtain
The wrong substructure CH3-COOCH is deleted, because it has two oxygen atoms.
Select items from the list of unclassified SPs by clicking on them. The corresponding items become marked. To add them to the Yes/No-list click the corresponding Add-button. Otherwise if you want to delete SPs from the Yes/No-list, select them with mouseclick and use the Remove-button.
Hints
If you have specified a molecular formula you can proceed directly to the structure generator by using the MOLGEN-button.
If there is no molecular formula entered, you can proceed to the elemental composition computation using the ElCoCo-button.
If you leave Molin the actual settings are stored and will be the start settings at your next call of Molin.
The program ElCoCo computes suggestions for the molecular formula of the unknown compound. There are several ways to get to the ElCoCo-dialogue:
Select Programs|ElCoCo from the MOLGEN-MS main window.
Click the 
-button
in the MOLGEN-MS main window.
Click the ElCoCo-button in the Molin-dialogue.
A window similar to the following will appear:
On the left side there is the Intervals-field, where classification results are displayed, that concern the computation of the molecular formula. In the above example there was me-est, i.e. a functional group methyl ester indicated as prescribed substructure. This substructure consists of 2 carbon, 3 hydrogen and 2 oxygen atoms. Therefore we have a minimum of 2 C, 3 H and 2 O atoms in the molecular formula. the upper bound 255 is a default value. As methyl ester has one double bond, the molecular formula must have at least one double bond equivalent (DBE). The intervals 0-0 for P and Si result from classifiers concerning the presence or absence of elements P and Si. If there are further intervals specified using the Edit-button, they will also be displayed in the Intervals-field.
The first decision for the computation is the choice of the molecular mass. In the Molecular Mass-field the user can select between different methods for this choice.
Statistic based: As the molecular ion peak is not visible in some electron impact mass spectra we have to consider several candidates for the molecular mass. Beginning at the mass of the most intense peak of the first peak group, which is 101 in the above example, most probable suggestions for the molecular mass are now made. According to frequently observed losses from the molecular ion several further masses are added to the list of candidates. In the above example these are 102 (loss 1, an H-atom) and 116 (loss 15, a CH3-group). The number of candidates depends on the precision for the molecular mass, which is 98% in the above example case. This treshold means that for at least 98% of the reference spectra the correct molecular mass would be among the candidates. The higher we chose this precision, the more candidates for the mass must be considered: At precision 99% in addition the masses 119 and 132 had to be recognized.
On the other hand if we only prescribe precision 90%, only mass 101 needs to be regarded.
The precision is can be chosen between 90% and 99.9% in steps of 0.1%.
User Input: Choose this option, if you know the molecular mass or if you want to try what's the algorithm's output at a special mass.
Solution Data: Choose this option if you want to use the mass that is read from file.
The next decision concerns the treshold for the matchvalue and the maximum number of candidates for the molecular formula. The matchvalue says how good the experimental spectrum can be explained by a given molecular formula. The smaller the matchvalue is, the better the molecular formula in question fits the experimental data. Let's have a look at the Precision-field, where the parameters for these settings can be changed. There are four configurations possible:
min Prec disabled, max Cand disabled: This is the most simple mode. The candidates with the smallest matchvalues are computed and displayed (up to 50 for each mass).
In our example we obtain 15 candidates as result. This number is displayed in the Result Candidates-editbox.
max Cand enabled, min Prec disabled: The candidates with the 10 smallest matchvalues are computed and displayed.
The maximum number of candidates can be changed using the spin controls besides the max Cand-editbox. The range for this number is from 1 to 50.
max Cand disabled, min Prec enabled: The program computes a set of candidates that contains the correct molecular formula with a minimum precision of 95%.
The precision can be changed using the spin controls besides the min Prec-editbox. The range for this precision is from 50 to 99. In our example we received 14 candidates. The result precision is the probability of the correct molecular formula being among the 14 candidates.
max Cand enabled, min Prec enabled: The program computes a set of at most 10 candidates that contains the correct molecular formula with a minimum precision of 95%. If such a set cannot be found, i.e. you would have to consider more than 10 formulae to achieve the desired precision, the program answers with a warning message and 0 result candidates:
If we choose a smaller precision, for instance 50% we get the following result:
This means that 9 formulae were computed among which the correct one is with probability 54%.
Hints
Depending on the molecular mass and the experimental data the computation will take several minutes. The progress bar tells you, how the computation proceeds.
During the computation, the Abort-button becomes sensitive. Use this button if you want to cancel the calculation. It can take several seconds until cancelation is executed.
Use the MOLGEN-button to proceed to the MOLGEN-dialogue. This can only be done if at least one molecular formula is found.
To save the computed candidates as text file, click the left mouse button on the Candidate-listbox.
To sort the computed candidates by their mass or their matchvalue, click the according column of the Candidate-listbox.
Attention
Of course the precisions used in ElCoCo are only valid with regard to the reference spectra used during the development of ElCoCo.
The program MOLGEN is able to compute all connectivity-isomers, that correspond to the molecular formulae calculated by ElCoCo and which fulfill the substructure restrictions obtained from MSclass. There are several possibilities to get to the MOLGEN-dialogue:
Select Programs|MOLGEN from the MOLGEN-MS main window.
Click the 
-button
in the MOLGEN-MS main window.
Click the MOLGEN-button in the Molin-dialogue.
Click the MOLGEN-button in the ElCoCo-dialogue.
A window similar to the following will appear:
In this listbox there are all prescribed substructures, i.e. the names of the MOLGEN substructure files that describe the substructures. Substructures in different rows are combined with a logical and. New rows can be added using the Add-button. A Open File-dialogue appears
where you can choose the substructure that will be added to the goodlist.
The new row is highlighted. To highlight another row simply mouse click on it. There is also the possibility to combine substructures with logical or. Substructures that are combined with logical or appear in the same row separated by a |. You can add alternatives to the highlighted row by clicking the Alternative-button. Again an Open File-dialogue appears. Select the substructure that will be joined. The goodlist will look as follows:
To read the complete row just double click on it:
Logical or has higher priority than logical and. This means for the above example the substructure funcme-est must appear and either a func(ch2)-co or a func(ch2)6-co. The highlighted line can be deleted by clicking the Delete-button.
Forbidden substructures are displayed in this listbox. Each row contains the filename of a MOLGEN substructure file. To add a new substructure click the Add-button. An Open File-dialogue appears on the screen where you can select a substructure. To delete a substructure from the badlist, highlight the according row by clicking on it and push the Delete-button. The Permbad-button allows to fill in automatically several badlist structures, the so-called permanent badlist. This permanent badlist contains substructures that were not found in the Beilstein-database. You can change this list for your own requirements by adding or deleting substructures to the permanent badlist-directory. The location of this directory can be found (and changed) in the Files&Folders-dialogue.
The Molecular Formulae-listbox contains all elemental compositions for which structural formulae will be computed. This list can be extended using the Add-button. The following dialogue appears:
Now you can enter a molecular formula by typing the element symbols followed by the number of atoms of this element. Don't use any blanks. If there is no number specified, one atom is assumed.
As long as the formula is displayed red, you have not entered a valid molecular formula. This means that there doesn't exist any molecular graphs with tis elemental composition. Valid formulae are displayed black.
Click the OK-button or simply hit return to finish your input and add the new formula to the list. Push the Cancel-button if you don't want a new formula to be added. A new formula is displayed highlighted in the listbox. You can change the highlighted item by clicking on another formula. In order to delete the highlighted formula, click the Delete-button. If you choose the Edit-button, the selected formula can be changed in the Edit Molecular Formula-dialogue.
In order to start the structure generation, push the Generate-button. All controls except the Abort- and the View-button become insensitive. During the generation the number of molecules already constructed together with the cpu-time needed is displayed in the Structural Formulae-field.
The currently considered molecular formula is highlighted. If you have have several molecular formulae in the list, you can see how far the generation has already proceeded. You may interrupt the generator at any time by pressing the Abort-button. In order to start the molecule viewer, push the View-button. When the computation is finished, a message box will appear on the screen and the Structural Formulae-Field will look like this:
There were 167 structural formulae computed and 21.4 seconds were needed to do these calculations.
Hints:
There are two different generation methods implemented in the current MOLGEN version. By default canonical labeling is set. This method is very well adapted to purposes of structure elucidation, because structural restrictions can be considered already during the generation process. This mode must store all molecules and is therefore limited by the available system memory. But even on 64 MB machines it is possible to generate more than 50.000 structures - an amount that is already much to huge for structure elucidation. Nevertheless, if you want to compute very big numbers of isomers, for instance without any structural restrictions you should use orderly generation, that can be enabled by clicking the menu item Options|Orderly Generation in the MOLGEN-MS main window. Using this mode you will still be able to view the generated formulae.
If you check Options|Disable Storing, you will no longer be able to view the generated formulae. Use this Option only, if you are just interested in the size of the solution space.
The molecule viewer 2DV is started by pushing the View-button in the MOLGEN-dialogue. A 2-dimensional placement of the structures is computed now, and several structures are displayed in the 2DV-window.
Since normally not all of them fit into the 3x2 grid shown above, you can scroll through them, using the scrollbar at the very right side of the window. Now you should regard every single structure as one object of the solution. You have a lot of possibilities to manipulate these objects. Clicking on one of the structures, a popup-menu will occur.
The Copy-option copies the selected structure to the clipboard - either as metafile or as bitmap. This is useful, if you want to import structures into other programs. The Name-option will open the following dialogue:
Every single structure can be named now. Clicking on MOLED will extract the structure out of the set of solutions into a temporary file. Now, you can manipulate and save this structure using MOLED. You might think about taking a certain part of a solution as a new substructure to decrease the number of computed isomers. MOLVIEW will compute a 3-dimensional representation of this single structure. The Representation-option opens a dialog window.
As you see, some options for drawing the isomer can be changed to make the structure look the way you like it. This dialog is also offered when clicking 2D View|Options|Representation in the 2DV-menu. Note, that changing the look here will only change the representation of a single molecule and not the one of all structures. But this can also be done and is described later in this section. The Select-option in the popup-menu will change the background color of the single molecule. Its number is registered now and you can use it to select only a few of them for printing or exporting into MDL/MOLFILE format. These were the actions that can be taken on one single molecule.
Apart from this, it is also possible to manipulate the whole solution set. To do this, click on the Menu shown in the 2DV-window. Selecting 2D View|Options|Grid from the menu enables you to change the number of structures that are displayed in the result window. The size suitable for you depends on the resolution of your screen. Note that big numbers in rows and columns may take the screen a while to display all molecules. The 2D View|Options|Representation-dialogue is known from before, but this time changes affect the whole number of structures displayed. Checking the 2D View|Options|Mix-entry mixes all structures saved to give you an overview over the different types of molecules generated. This may be useful since the algorithm for the generation produces similar structures close to each other. Choosing this option once again reverses the mixing. The dialog opened with the 2D View|Options|Go to-option lets you jump directly to a desired structure without scrolling through the window.
The File|Export to|Molfile Format-entry of the 2DV-main menu offers you the possibility to export selected structures from the solution generated by MOLGEN-MS into a file having the MDL/MOLFILE format.
In the Filename-field you can enter the name of the file, the structures should be saved to. If you don't know where this should be, you can select one by using the Search-button, which will open a standard system Save As-dialogue to select the appropriate filename. You can also easily select the structures to be saved inside the Select molecules-field. Behind the All-radiobutton, the total number of structures saved on the disk is displayed. They are all written, when this option is chosen. The Current Page-option saves only the structures currently displayed in your result window. Their number depends on the grid you have chosen. If you have selected single molecules in the result window, their number will be displayed in the edit-field behind the Selected-option. As described in the window, you can either enter the number of single structures, separated by a semicolon, or a certain interval where the lower and upper limit have to be separated by a "-" - character. In the Options-field it is possible to disable the computation of the 2-dimensional coordinates by clicking on the Include 2-D Coordinates in File-checkbox. This will save some time during the storing process and is useful if you do not need the placement for further data manipulation.
The File|Print-menu-entry opens a dialog very similar to the one for MOLFILE export.
The Printer-field shows the name of the printer the system is currently using as default printer. In order to change it, you can use the Printer-button that leads you to the system specific dialog that allows you to change this default printer. The Options-button is used for changing printer-dependent options like for example, the resolution. The Select molecules-field is used for selecting exactly the structures you want to print. The All/Current Page/Selected-options have the same function as described for export. In addition to that, it is possible to enter a new Grid for the print. By default, the grid shown on the screen is used, but often printers offer a much higher resolution than displays and so you can change the grid here again. Rows and Columns are used in respect to the smaller and larger side of the paper, so if you do not print in landscape mode and you entered more columns than rows, their values are exchanged automatically.
Attention:
There are several situations, when the 2DV cannot be started and an error message occurs:
You have already a 2DV running. There may only one 2DV be started at the same time.
There were no molecules generated or the Disable Storing-option is active.
There is a blank in the pathname of the 2DV. You can see the pathname by clicking Options|Files&Folders-button.
If you want to execute MSclass/Molin, ElCoCo and MOLGEN at one step, select Programs|Expert Mode from the MOLGEN-MS main window. The Expert Mode-dialogue appears on your screen:
In the MSclass/Molin-field you see the settings of Molin for the classifier selection. The numbers behind Precision YES and Precision NO are equivalent to the entries of the Classifier Precision-field of the Molin-dialogue and those behind Precision ADD and Number ADD correspond to the entries of the Additional Goodlist-field of the Molin-dialogue. In the above screenshot there are just blanks behind Precision ADD and Number ADD, what means, that the Additional Goodlist option is disabled.
In order to run the programs, click the Start-button. At first MSclass is executed. There appear additional values in the MSclass/Molin-field, which show the classification results:
Classifiers YES and Classifiers NO denote the numbers of found classifiers above the prescribed tresholds for YES- and NO answers. These numbers are similar to those of the MSclass-dialogue's Output-field. Substr. YES and Substr. NO show the numbers of prescribed and forbidden SP's. These numbers correspond to those above the YES- and NO-listbox of the Molin-dialogue.
In the ElCoCo-field we have in the left column the settings for ElCoCo. The value behind Prec. Masses shows the precision for the choice of candidates for the molecular mass (cf. ElCoCo, The Molecular Mass, Statistic based), Prec. ElCoCo denotes the minimum precision for the matchvalue (cf. ElCoCo, The Precision for the Matchvalue) and Cand. ElCoCo the maximum number of candidates for the molecular formula. If there is no number displayed behind Cand. ElCoCo, as in the screenshot below, there is no maximum number of candidates specified.
The left columns shows the results of ElCoCo: The number of proposed molecular masses, the result precision, and the number of candidates for the molecular formula. Again, these numbers are equal to the corresponding entries of the ElCoCo-dialogue.
After the computation of the elemental composition the structure generation is started. You can observe the progress of MOLGEN in the MOLGEN-field. The number of molecules generated and the elapsed time since the start of the generator are displayed.
When the generation is finished a message box appears on the screen. The result structures can be displayed by clicking the View-button.
Hints:
The settings for the execution of MSclass/Molin and ElCoCo cannot be changed in the Expert Mode-dialogue, because this dialogue is designed for users without any expert knowlege. Instead the Expert Mode-dialogue assumes the settings of the last calls of the Molin- and the ElCoCo-dialogue or their default settings respectively.
You can abort the execution of the Expert Mode anytime, if you push the Abort-button. However it can take several seconds until the program recognizes the command, depending on the size of the elucidation problem. Please be patient.
The following two features are not immediately involved in a typical MOLGEN-MS elucidation process. But nevertheless similar programs could become an important tool for automatic structure elucidation. The first one, MS Jena, uses GC-data in addition to the mass spectrum for the determination of structural properties of the unknown. The second special, AES/MS allows a combined evaluation of MS and AES (atom emission spectrum) for the computation of the molecular formula. This method is particular interesting, as both, the mass spectrometer and the atom emission detector can be coupled with a gas chromatograph and therefore can use its unique advantages.
If you want to reproduce the following examples, please open the TRANSPEC file unde.tra, that is also part of the MOLGEN-MS installation.
MS Jena is an algorithm that is devoted to the
recognition of alkane chains. For best results it needs GC-data,
but these are mostly not available. MS Jena is executed by
choosing Specials|MS Jena or clicking the
-button in the MOLGEN-MS
main window. As this program was only available as command line version,
the output is just (german language) ascii text.
The explanation of the Exit-button may be left as an exercise for the user.
An atom emission detector can be very useful for the
determination of the molecular formula. An atom emission
spectrum provides information about the presence or absence of the
chemical elements in the unknown compound and furthermore an estimation
for the relative ratios of the occuring elements. From the MS you can
approximate the molecular mass. These two informations, element ratios
together with the molecular mass, determine the molecular formula. If the
result is ambiguous, several candidates are given. To call the AES/MS
dialogue, select Specials|AES/MS in the menu of the MOLGEN-MS
main window or push the 
-button.
In the Element Ratios-field, for every element X detected by the AED, the ratio of X-atoms in relation to the number of C-atoms is displayed in the upper left list box. In our example, we have detected the elements C and H, and there was measured an amount of 2.09 as much H-atoms than C-atoms. The number 2.09 is averaged over several measurements, the second value 0.17 is the standard deviation. The pie chart illustrates the experimental element ratios. In the precision field, you can adjust several parameters concerning the computation of the molecular formula(e). To start the computation, push the Enter-button. The result is displayed in the listbox at the bottom of the dialogue:
In the above example, four candidates for the elemental composition were suggested. For each candidate the molecular mass and a matchvalue is displayed. The matchvalue reports, how good the formula fits the experimental element ratios. The lower the matchvalue is, the better the experimental ratios are fulfilled. For C11H24 the current ratio 24/11 differs from the experimental ratio 2.09 by 0.54 times the standard deviation 0.17. Let's have a look at the precision field. As like as in the ElCoCo-dialogue, in the Masses-editbox, you can select a precision between 90 an 99.9% for the choice of considered masses of the molecular ion. For a detailed description, see section ElCoCo, The Molecular Mass, Statistic based. If we reduce the masses precision to 98%, there remain only three masses to be considered, which are displayed in the listbox of the precision field. The Match-editbox contains the upper bound for the matchvalue. Candidates with Matchvalues above this border are neglected. The entry of the Cand-editbox limits the total number of candidates to be output. By default this number is 10. Now let's have another program run with masses precision 98% and matchvalue limit 5:
With these parameters only one solution remains. C11H24 is in fact the correct molecular formula!
Hints:
Click the Molin-button, and you will directly proceed to the Molin-dialogue. The computed candidates are copied to the Molecular Formula-combobox:
To save the computed candidates as text file, click the left mouse button on the Candidate-listbox. A Save file-dialogue appears and asks for the location to save your result. The content the file looks as follows:
C11H24 IONTYPE:OEI MASS:156 VALUE:0.542797
C13H18 IONTYPE:OEI MASS:174 VALUE:4.11921
C12H12 IONTYPE:OEI MASS:156 VALUE:6.36842
C14H6 IONTYPE:OEI MASS:174 VALUE:9.71011
To sort the computed candidates by their mass or their matchvalue, click the according column of the Candidate-listbox.
Select Options|Files & Folders ... to get to the Files & Folders-dialogue.
Locations of files and folders which are needed for the MOLGEN-MS data transfer are displayed and can be changed.
The MSclass classifier file contains the specification for the classifiers of MSclass. By changing this file, you can supply other classifiers to the program. For instance, if new classifiers are developed they will be distributed as such a file. Classifier files have suffixes .mcb (binary) or .mcl (ascii). Your installation will contain the classifier file 160-9609.mcb.
The Molin classifier info file describes the relations between classifiers, substructures, element- and RDB-intervals and provides necessary information for Molin. Molin classifier info files have suffix .mci. By default, this file is 160-0299.mci. This is an ascii-file and could be edited by the experienced user. A description of the file format can be obtained from the author.
The Elcoco matchvalue learn file supplies the scaling for the ElCoCo matchvalues. It could be useful to adapt this file to the precision of your mass spectrometer.
The default TRANSPEC spectra file and
the MOLGEN-MS settings file are not used in the current version.
The MOLGEN-MS main directory is equal to the installation directory and cannot be changed.
The MOLGEN-MS binary directory contains the executables and several tables that cannot be changed. The exception is atoms.tab, which must be changed, if you want to add further elements. The default elements are H, C, N, O, F, S, P, Cl, Br and I. For a specification of the file format contact the author.
The MOLGEN-MS temporary directory is used for storing temporary data as error- and warning-messages or the output of the structure generator. In the current version this directory cannot be changed.
The Molin substructure directory contains all the MOLGEN substructure files that occur in 160-0299.mci and that are necessary for the graphical description of the classifiers structural information.
The MOLGEN permanent badlist directory contains the MOLGEN substructures for the permanent badlist. Change this directory if you want to use another set of substructures for the permanent badlist.
To change files or folders, click the according
-button.
A standard system Open File- or Browse for Folder-dialogue
will appear. To assume the changes and close the File & Folders-dialogue,
push the OK-button. If you hit the Apply-button, the
changes are also assumed, but the window is not closed. Push the Reset-button,
if you want to have settings after opening the File & Folders-dialogue,
or after the last use of the Apply-button respectively. Hit the
Cancel-button to close the dialogue without assuming changes
For each element you can specify intervals for the numbers of atoms that may occur in the molecular formula. You can start the Elements & Intervals -dialogue by selecting Options|Elements & Intervals... from the MOLGEN-MS main window or by pushing the Edit-button in the MolForm-, the ElCoCo- or the AES/MS-dialogue.
In the dialogues listbox there is one row for each element. In each row, we have at first the element-symbol, followed by the minimum and the maximum number of atoms of this element. By default this interval is from 0 to 255 for each element. To change the interval for several elements, select the desired elements in the listbox. The symbols appear in the Elements-editbox of the Limits-field. Now you can change the minimum and the maximum number of atoms in the according editboxes. To accept your changes, click the Enter-button. The new bounds will be displayed in the listbox. Four instance in the above screenshot the intervals for Br and Cl were changed to a minimum and maximum of 0 atoms. This means that these two elements are disabled for the following computations. If you want to allow only C, H, N and O atoms, simply push the C,H,N,O only-button. For all other elements the lower and the upper bound is set to 0. The Set all 0-button changes all intervals to 0-0. Push the Reset-button, if you want to restore the default settings. The Exit-button closes the dialogue.
To enable one of the following options, just click the
according menue item, and a 
will appear on the right side of the menu item. This checker marks the
option as active.
Check Options|MOLGEN Inputfile, if the inputfile molgen.inp shall be written to the MOLGEN-MS temporary directory before each start of the structure generator.
Check Options|Orderly Generation, if MOLGEN shall use this generation strategy. Orderly Generation is faster, if you have no structural restrictions.
Check Options|Disable Storing, if you don't want to store the result structures on your disc. This saves time and disc space, but you won't be able to view the result structures.
To disable a checked option, click the according menu item one more time.