GMOL Walkthrough
GMOL Walkthrough
This is a guided walkthrough to help you get started with GMOL. This walkthrough assumes you have downloaded and installed GMOL along with the necessary sample data files.
Viewing Models
Starting GMOL and opening files
Open GMOL by double-clicking the gmol_x.x.jar file. If you are familiar with Jmol you will notice that the GMOL interface is very similar. Start by opening the sample data that you previously downloaded. To do this select “File -> Open” and browse to “WHERE_DATA_WAS_EXTRACTED\human_with_seq\global\genome.gs.gss”. You can also open files by clicking on the green folder icon on the toolbar at the top of the window. The file you just opened is the entire genome structure and should look like what is pictured below. Each point in the model represents a chromosome.
Opening the console
Often times it is easier to type commands into the console rather than clicking through the various menus. To open the console select “File -> Console...”. The console window should open up and can be moved to wherever you want.
Moving, rotating, and scaling the model
GMOL allows you to move, rotate, and scale models so that they can be viewed in any way you desire. The following table lists the ways in which the model may be manipulated. Experiment with them until you are comfortable with adjusting the model.
Manipulating Models|
------------------------------- | -------------------------------
Rotation about the x and y axes | Click and drag the mouse.
| Left-right causes rotation about the y-axis
| Up-down cause rotation about the x-axis
Rotation about the x-axis | Shift-key, click and drag left-right
Zooming in and out | Shift-key, click and drag up-down
Moving the model in the x-y plane | Shift-key, double-click & hold and drag
Center model and expand to fill screen| Shift-key and double-click on background
*Credit to http://www.chem.uwec.edu/JmolTut/pages/page2.html
Functions
Measurement
By using the measurement function you can measure the distance between two points in the model, the angle between three points, and the dihedral angle between four points. To measure, type “measure a b c d” into the console, where ‘a’ ‘b’ ‘c’ ‘d’ are the indexes of the points. GMOL will automatically change the type of measurement based upon how many points you give. Start by measuring the distance between two chromosomes, for instance 1 and 5. To do this simply type “measure 1 5” into the console and hit enter. Now measure the angle between three chromosomes. We chose chromosomes 10 13 and 20 in the example. Finally measure the dihedral angle between 4 chromosomes. The units can be changed by going to “Tools -> Distance Units” and selecting nanometers, angstroms, or picometers. You can also view a table of all current measurements by selecting “Tools -> Measurements” or clicking the ruler icon on the toolbar.

Measurements can also be made with the mouse by clicking on the desired points. To do this first make sure you are in measuring mode by clicking on the ruler icon on the toolbar. Next, right-click in the empty background space, go to the “Measurements” menu, and select the type of measurement you want to make. You can then click on the units you want to measure and the measurement lines will be drawn between them, just like when entering the command into the console.
Selection types, Scaleup/Scaledown, and getting genome sequence
GMOL utilizes three different types of selection (select, gselect, sselect) and allows you to scale up or down between the different levels of the genome structure. In the next few examples you will learn how to use the three different selection types and how to scale the model up and down.
First, select chromosome 1 by entering “select 1” into the console. Now scale the structure down (zoom in) by either typing “scaledown” into the console or by clicking the blue downward pointing arrow on the toolbar. You are now viewing the structure of the first chromosome where each point represents loci.

Next, select loci 7 by typing “select 7” into the console and then scale it down again. The structure of loci 7 of chromosome 1 is now displayed and each point is a fiber within that loci.
This time select fiber 23 by entering “select 23” into the console and then scale down. This is the structure of fiber 23 of loci 7 of chromosome 1. At this scale each point represents a nucleosome. Finally, select nucleosome 2 by entering “select 2” into the console and again scale down. This scale is as far as GMOL allows you to zoom in. The structure being displayed is nucleosome 2 of fiber 23 of loci 7 of chromosome 1. As you can see, the select command selects units by index in the currently displayed structure. It is also possible to select multiple units with the select command by typing “select a b” into the console where ‘a’ is the starting index and ‘b’ is the ending index. For example, entering “select 1 3” at the genome scale (least detailed) would select chromosomes 1 through 3.

Now, scale the structure up (zoom out) until it is back at the genome scale. This can be achieved by either typing “scaleup” into the console or by clicking the blue upward pointing arrow on the toolbar. You should end up at the genome structure you started with. Once you have reached the initial structure, scale the structure down without any units selected. This will expand each point in the genome structure into its actual chromosome structure. In other words, it is the entire genome structure zoomed to the chromosome scale.
What if you wanted to select the entire first chromosome from this scale? Simply entering “select 1” would not work because it would only select the first loci in the structure. With the gselect command however, you can select based on scale information. To use it enter “gselect a,b,c,d” into the console where ‘a’ is the index of chromosome scale, ‘b’ is the index of loci scale, ‘c’ is the index of fiber scale, and ‘d’ is the index of nucleosome scale. Setting any of the variables to 0 means that it is unspecified and all indices on that scale will qualify. Now try to select the first chromosome by typing “gselect 1,0,0,0”. You should notice that all 101 units were selected. To highlight them enter “color red”.

The last type of selection that can be used in GMOL, sselect, lets you select units based upon genome sequence information. It can be used by typing “sselect X,a,b” into the console where ‘X’ is the chromosome number, ‘a’ is the starting position on the genome sequence, and ‘b’ is the ending position on the genome sequence. For example, try “sselect 1,1,111111111”. This will select units within chromosome 1 starting from the first location on the genome sequence up until location 111111111 on the genome sequence. Enter “color blue” to highlight the newly selected units. As you can see, This selection did not include all of the chromosome 1 because its genome sequence is longer than 111111111 units.

Additionally, GMOL allows you to get the genome sequence of a selected unit. Select the index of the first loci by entering “select 1” and then scaledown. Select the first fiber, again with “select 1” and scaledown again. You should now be at fiber 1 of loci 1 of chromosome 1, pictured below.
Now select the first nucleosome with “select 90” and then go to “Tools -> Genome Sequence”. From here you can choose to load the genome sequence of the selected unit from either the local database or from Ensembl. Once the sequence has finished loading it will appear in the console, unknown part of sequences will be shown as "N". You can load the genome sequence for any unit at any scale, however higher scales such as genome and chromosome will take several minutes for the sequence to load.
Besides, you can also transcribe or get the sequence properties the sequence by clicking “Tools -> Genome Sequence -> Choose Function”, where you can click “Sequence Transcribe” or “Sequence Properties ” after selecting a unit or region like the Figure shown above.
Gmol can also perform Blast search (Basic Local Alignment Search Tool) for structures selected. By click “Tools -> Genome Sequence -> Choose Function”, where you can click “NCBI_Blast”. The process takes several minutes and the result will be returned as a file saved locally like the Figure shown above.
Since blast search will take a long time, you can run other commands with Blast running at the background. Also, you can stop the Blast if you do not want the result anymore, just right click on the screen and go to “Thread -> kill Thread”. The message of the blast progress being stopped will show in the console.
At last, Gmol allows you to analyze the gene information on the structure you selected. You can do this by clicking “Tools -> Genome Sequence -> Choose Function”, where you can click “Exons Introns”. The process takes 1 minute and the result will be shown in the console and the screen like the Figure shown above.
Conclusion
This walkthrough has covered all of the functions vital to GMOL. However, functions from Jmol have also been integrated. For more information on Jmol functions see the Jmol user guide here. For an overview of the GMOL commands covered in this guide, please check out the Using GMOL page.

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