Suppose that I have measured distances between positive and negative sides and all of the proteins are in cartoon format. Now, I want to hide the whole proteins except the charged chains. I mean, I want to show the residues as sticks and hide the rest of the proteins but using a command not by hand.
What is your recommendation?
Thanks!
If you have your selection of negative and positive charges:
select negative, (resn ASP+Glu and name OD*+OE*)
select positive, (resn Lys and name NZ) or (resn arg and name NE+NH*)
you can display the whole residues as "stick" by
show sticks, br. (negative or positive)
(br. means "by residue")
if you use this together with a cartoon representation of the backbone, you might want
to specify:
set cartoon_side_chain_helper, on
This way, only Calpha and the side chain atoms are shown, and the cartoon goes exactly through the Calpha atoms
Dear Annemarie,
It works!
Thank you!
I have a new question:
How can I tell pymol to show only residues which are in 4 Ans distance from my central protein?
Suppose that some residues from surrounding proteins have only 4 Ang distance form my central protein, how can I tell pymol to show this residues in sticks and hide the rest of the proteins?
Thank you.
Maryam
You should select a central atom/residue and in the selection interface panel "Action" (on the right of the window ASHLC choose A), then in the "modify" option You'll see next tool "expand". There You can select atoms or residues in ... angs around the previously selected central entry.
I have posted the slides to my course in macromolecular visualization with PyMOL, under "Intermediate PyMOL", you get information on how to such things as the above examples.
See:
https://www.researchgate.net/publication/313877004_Introduction_to_PyMOL
https://www.researchgate.net/publication/313877009_Intermediate_PyMOL
https://www.researchgate.net/publication/313877075_Advanced_PyMOL
To find out more about the syntax of individual commands, refer to the PyMOL wiki:
https://pymolwiki.org/index.php/Main_Page
Presentation Introduction to PyMOL
Presentation Intermediate PyMOL
Presentation Advanced PyMOL
Dear Annemarie, it's a great work! Can You explain me if it is possible to mark several entries (residues, chains) with similar method (for example cartoons or sticks) but in different way (distinct thikness of sticks for entries, or alternative level of transparancy)? It is very uncomfortable to use wiki... It would be better to find a python/pymol manual, but I didn't...
Yes, you can set these properties at selection level, e.g.
https://pymolwiki.org/index.php/Stick_radius
set_bond stick_radius, ''size'', selection
set transparency, F, selection
where F is a value between 0 and 1
I actually find the wiki quite comfortable, much easier than having to leaf through a printed manual.
trick: just google what you want to know, together with "pymolwiki"
pymolwiki stick radius
pymolwiki transparency
to find the appropriate entry directly
There usually are examples showing the effect of typical parameters, not only the generic syntax. You can just copy/paste the command to your script file, then replace the parameters you want to alter.
Yes, I'm usually applying such operations, but I didn't explain my question properly. Is it possible to set several different representation features in the same workspace? for example, sticks of the ligands should be thicker than other sticks!
Yes, that is meant by using a selection:
for example (just paste the following into the command line of an empty pymol session)
load http://www.rcsb.org/pdb/files/1mbo.pdb
hide all
show sticks
set_bond stick_radius, 0.1, polymer
set_bond stick_radius, 0.5, organic
Oxygen, iron and the sulfate keep the default stick radius
"polymer" is the generic selector for protein/DNA/RNA, "organic" for small organic molecules. You may replace these for a selection expression specific to your molecule
In my example, i could have used "resn HEM" instead of "organic", and "chain A" instead of "polymer"
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