Frequently Asked Questions
- How do I get started using Rasmol and designing a model?
- How do I save a pdb file?
- How do I open a pdb file in Rasmol?
- How do I save a script file?
- How do I open my script file?
- How do I work from another computer?
- How do I add sidechains without adding backbone atoms?
- What sizes should I use for the backbone and the sidechains?
- How do I add hydrogen bonds?
- How do I remove hydrogen bonds?
- Where do I add monitor lines?
- How do I add monitor lines?
Q.
How do I get started using RasMol and designing a model?
A.
First, make a folder on your computer labeled as "SMART Team Folder". Paste a copy of RasMol in this folder. Save your pdb files in this folder. Each time you open RasMol, do so from this folder. Rasmol saves files to the folder in which the program was opened. Next, you will need to download your pdb file of interest (see How do I save a pdb file?). We recommend that you make a separate folder for each pdb file, and save a copy of RasMol in each folder. This will help you to keep your projects organized.
Q.
How do I save a pdb file?A.
Begin by going to the Protein Data Bank.Find the "Enter PDB ID or Keyword" box (circled in the picture below) and enter the pdb ID.
To download the file, click on Download Files on the side menu (indicated by the red box below), then click on PDB File to save your file (indicated by the red arrow below). Make sure to save the pdb file in your SMART Team Folder that has a copy of Rasmol.
Q.
How do I open a pdb file in RasMol?
A.
Launch RasMol from your "SMART Team Folder". Find "Open," in the top menu bar and click it. A window will open to find the file you wish to open. If you have launched RasMol from your SMART Team Folder, this is where the "Open" window will initially look for the pdb file; your file should be in this folder.
Q.
How do I save a script file?A.
At the command prompt, type "save script filename.spt"
Example: RasMol> save script test.spt
Common Errors
- Not including "script" before your filename.
Example: RasMol> save test.spt
By not including "script" before your filename, RasMol will not generate a script file. You will see test.spt in your folder, but it will not be saved in the correct format that RasMol needs in order to open the file. If you open this file, you will see a long list of commands go flying by on the RasMol command screen.
- Not including ".spt" extension at the end of the filename.
Example: RasMol> save script test
This will not create a file that RasMol can use. You will see the file appear in your folder, but if you try to open the file, it will not be recognized by RasMol. It will list the file type as "File". A correctly saved script file will show "RasMol RasWin Script" under the File Type in the folder.
Q.
How do I open my script file?
A.
At the command prompt, type "script filename.spt"
Example: RasMol> script test.spt
Common Errors
- Not including ".spt" extension at the end of the filename.
Example: RasMol> script test
If you forget to put the .spt at the end of your filename, RasMol will give you the error message of "cannot open script file ‘test’."
- Not launching RasMol from the folder you have your script file located.
Q.
I want to work on my design at home, but my script file is saved on the school computer. You said that we need to launch RasMol from our SMART Team folder since that is where our script files are located. How do I work at another computer?
A.
In order to open script files that were generated by one computer on a different computer, you will need to change the pathname.
On the new computer, make a new folder. In this folder, place a copy of RasMol, your pdb file and your current script file. Open the script file with MS Word or WordPad.
The first part of your script file will look like this:
#!rasmol -script
# File: test.spt
# Creator: RasMol Version 2.6
zap
load pdb "C:\Documents and Settings\SMART Team 2008\1FQY.pdb"
background [255,255,255]
set ambient 40
set specular off
You will need to change the pathname of the script file (the blue portion of the red text above). Note that the pathname will not be identical to the name above, but the format will be similar. In order to open the script file on the new computer, make the following change (replace the blue text portion above with the period, below):
#!rasmol -script
# File: test.spt
# Creator: RasMol Version 2.6
zap
load pdb ".\1FQY.pdb"
background [255,255,255]
set ambient 40
set specular off
Rather than having the long pathname of "C:\Documents, etc…", replace that with a period (.). This will indicate to RasMol that there is no specified pathname to follow and it will allow you to use your script file in a new location. You must also be sure to include the original pdb file in the folder with the script file on the new computer.
Q.
How do I add sidechains without adding the backbone atoms ("clean backbones")?
A.
Decide which sidechains you wish to display. For example, if you wish to display the sidechain for ala218, you would type in the following:
RasMol> select ala218 and (sidechain or alpha)
RasMol> spacefill 275
RasMol> wireframe 225
If you do not include the "and (sidechain or alpha)", you will display each atom in the amino acid, including the nitrogen and the carbonyl oxygen atom. This will result in a bumpy backbone. If you have a sidechain with a bumpy backbone, you have to go through several commands to remove the bumpy backbone. For example, if you have a bumpy backbone for lys142, you would type the following:
RasMol> select lys142
RasMol> spacefill off
RasMol> wireframe off
RasMol> select lys142 and (sidechain or alpha)
RasMol> spacefill 275
RasMol> wireframe 225
Q.
What sizes should I use for the backbone and the sidechains?
A.
We typically recommend a backbone value of 300. For sidechains we typically use 275 for spacefill and 225 for wireframe.
Q.
How do I add hydrogen bonds?
A.
We normally add hydrogen bonds in proteins to the beta sheet structures. To do this:
RasMol> select sheets
RasMol> hbond on
At this point, you will notice that hydrogen bonds appear, but they are dotted lines and they do not attach to the backbone. To increase the size of the bonds and to attach them to the backbone:
RasMol> set hbond backbone
RasMol> hbond 225
Q.
How do I remove hydrogen bonds?
A.
If you want to remove all of the hydrogen bonds in a specific area, select the area and then type in the command, "hbonds off".
Example:
RasMol> select helices
RasMol> hbond off If you want to remove a specific hydrogen bond, you will need to identify the amino acids that the hydrogen bond is connecting.
The arrow points to a hydrogen bond that we refer to as a "triangle bond". These are bonds that are connecting amino acid n and amino acid n+2; for example, amino acid 2 and amino acid 4. We frequently remove these hydrogen bonds since they can clutter the model with unnecessary bonds.
To remove these "triangle bonds," you need to identify which amino acids are connected via the hydrogen bond. To do this:
Click on the amino acid displayed on the RasMol screen. Make sure that you click on the correct amino acids. The best way to check this is to make sure that they are 2 numbers apart (ie Trp 73 and Ala 75).
RasMol> select trp73 or ala75
RasMol> hbond off
This will remove the hydrogen bond between these two amino acids. If you look closely at the image above, you will see that there are several "triangle bonds." Each one will have to be removed individually. Keep track of the bonds that you have removed, in case something happens to the file and you need to start over.
Q.
Where do I add monitor lines?
A.
Remember that the function of monitor lines is to stabilize the protein. You will need to add monitor lines to the regions of the protein that look like they might be able to squeeze together. A good example of this: If you look at the image to the right, you can see the alpha helices are colored in magenta. These helices are stable from top to bottom, but they do have the tendency to flex from side to side. By adding monitor lines in between the helices, you will increase the stability of this protein. This is what we call the "squeeze test." When looking at the image on the computer screen, can you see where helices might be able to be squeezed together? If so, then you need to add monitor lines to prevent this "squeezing" from occurring. It is usually sufficient to add a monitor line to the top and bottom of each helix to stabilize it. Some loops (grey in the model shown) may also need to be stabilized. Monitor lines should not exceed 9 Ångstroms.
Q.
How do I add monitor lines?
A.
Click on one of the atoms you want to connect with the monitor line. The identity of the atom will appear in your command box.
Atom: CA 4201 Group: ALA 175 Chain: C
In our example, we have identified atom number 4201, which is the central alpha carbon (CA) of amino acid 175 (which is Ala) on chain C.
Click on the second atom in the same way.
Atom: CA 4125 Group: ARG 166 Chain: C
The command to add a monitor line between these two atoms requires you to list the two atom numbers. In this example, the command is:
RasMol> monitor 4201, 4125
If you accidentally clicked on the wrong atom, and the monitor line is longer than 9 Ångstroms, you can simply erase the monitor line by repeating the command. It is a good idea to make a list of the monitor lines you add in case you have to redesign your model.
Tip: We recommend that all monitor lines be shorter than 9 Ångstroms (the number appears on the screen after you have drawn in the monitor line will indicate the length of the monitor line).