Good evening, I am actually using ChimeraX and I am trying to figure out a command that can show me all the contacts of my ligand below 3.0A with my protein. Unfortunately, I have not found anything clear enough to do so. Is there a way to do this? Another doubt is, if I have labelled 2 contacts (i.e 2.576A and 3.149A) but I am interested in only showing the label " 2.576A", I try deleting the other contact label (" 3.149A") by selecting it and typing the "label del" command, but this will delete my label of interest as well. Is there a way of only deleting specific labels from the contacts? Any help is appreciated. Best regards, Manuel
Hi Manuel, (1) Yes you can do that, it is not hard. For example: open 2gbp hide atoms contacts protein restrict ligand distanceOnly 3 reveal true See the "contacts" help page for the comand usage and the possible options (whether to write output to a file, specify color of lines, etc.) <https://rbvi.ucsf.edu/chimerax/docs/user/commands/clashes.html> If "ligand" does not specify the ligand in your structure, you could specify it some other way, such as by residue name, for example: contacts protein restrict :BGC distanceOnly 3 reveal true See "command-line specification" for how to use residue names, chain ID, residue number etc. in command line <https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html> You can use the menu and GUIs instead of a command: first select the ligand, and then use menu Select... Contacts, then in the dialog choose "Atomic" section, and then specify "center-center distance" ... see the help for this dialog: <https://rbvi.ucsf.edu/chimerax/docs/user/selectcontacts.html> Using the dialog shows the corresponding command in the Log, to help everybody learn the commands. (2) You can select the pseudobond that has the label you want to hide by Ctrl-click on the pseudobond. Then, use command ~label sel See "label" help <https://rbvi.ucsf.edu/chimerax/docs/user/commands/label.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 4, 2024, at 7:49 PM, Manuel Ospina via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Good evening,
I am actually using ChimeraX and I am trying to figure out a command that can show me all the contacts of my ligand below 3.0A with my protein. Unfortunately, I have not found anything clear enough to do so. Is there a way to do this?
Another doubt is, if I have labelled 2 contacts (i.e 2.576A and 3.149A) but I am interested in only showing the label " 2.576A", I try deleting the other contact label (" 3.149A") by selecting it and typing the "label del" command, but this will delete my label of interest as well. Is there a way of only deleting specific labels from the contacts?
Any help is appreciated.
Best regards, Manuel
Hi all, On a related note, what commands would I enter to display contacts between two separate chains in the same model? Specifically, if I have two separate chains (ie, #1/A and #1/B) what command displays contacts less than 4Å? Thanks, Jamie
On Aug 5, 2024, at 8:49 AM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Manuel, (1) Yes you can do that, it is not hard. For example:
open 2gbp hide atoms contacts protein restrict ligand distanceOnly 3 reveal true
See the "contacts" help page for the comand usage and the possible options (whether to write output to a file, specify color of lines, etc.) <https://rbvi.ucsf.edu/chimerax/docs/user/commands/clashes.html>
If "ligand" does not specify the ligand in your structure, you could specify it some other way, such as by residue name, for example:
contacts protein restrict :BGC distanceOnly 3 reveal true
See "command-line specification" for how to use residue names, chain ID, residue number etc. in command line <https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html>
You can use the menu and GUIs instead of a command: first select the ligand, and then use menu Select... Contacts, then in the dialog choose "Atomic" section, and then specify "center-center distance" ... see the help for this dialog: <https://rbvi.ucsf.edu/chimerax/docs/user/selectcontacts.html>
Using the dialog shows the corresponding command in the Log, to help everybody learn the commands.
(2) You can select the pseudobond that has the label you want to hide by Ctrl-click on the pseudobond. Then, use command
~label sel
See "label" help <https://rbvi.ucsf.edu/chimerax/docs/user/commands/label.html>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 4, 2024, at 7:49 PM, Manuel Ospina via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Good evening,
I am actually using ChimeraX and I am trying to figure out a command that can show me all the contacts of my ligand below 3.0A with my protein. Unfortunately, I have not found anything clear enough to do so. Is there a way to do this?
Another doubt is, if I have labelled 2 contacts (i.e 2.576A and 3.149A) but I am interested in only showing the label " 2.576A", I try deleting the other contact label (" 3.149A") by selecting it and typing the "label del" command, but this will delete my label of interest as well. Is there a way of only deleting specific labels from the contacts?
Any help is appreciated.
Best regards, Manuel
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
Hi Jamie, You could use your powers of generalization, as it is very similar to my previous response. contacts #1/A restrict #1/B distanceOnly 4 reveal true [various other options that you might want] Please see my previous reply for the links to help pages for the "contacts" command, how to specify chains etc., and using the Select Contacts GUI if you cannot yet figure out the command. The distanceOnly option uses atomic center distances only. However, it may be "smarter" without that option, taking into account the different sizes of different types of atoms. Again, please see the help... we wrote it so that we don't have to explain it all in emails...
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/clashes.html>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 5, 2024, at 10:30 AM, Jamie Shaum <jshaum@scripps.edu> wrote:
Hi all, On a related note, what commands would I enter to display contacts between two separate chains in the same model? Specifically, if I have two separate chains (ie, #1/A and #1/B) what command displays contacts less than 4Å?
Thanks, Jamie
On Aug 5, 2024, at 8:49 AM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Manuel, (1) Yes you can do that, it is not hard. For example:
open 2gbp hide atoms contacts protein restrict ligand distanceOnly 3 reveal true
See the "contacts" help page for the comand usage and the possible options (whether to write output to a file, specify color of lines, etc.) <https://rbvi.ucsf.edu/chimerax/docs/user/commands/clashes.html>
If "ligand" does not specify the ligand in your structure, you could specify it some other way, such as by residue name, for example:
contacts protein restrict :BGC distanceOnly 3 reveal true
See "command-line specification" for how to use residue names, chain ID, residue number etc. in command line <https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html>
You can use the menu and GUIs instead of a command: first select the ligand, and then use menu Select... Contacts, then in the dialog choose "Atomic" section, and then specify "center-center distance" ... see the help for this dialog: <https://rbvi.ucsf.edu/chimerax/docs/user/selectcontacts.html>
Using the dialog shows the corresponding command in the Log, to help everybody learn the commands.
(2) You can select the pseudobond that has the label you want to hide by Ctrl-click on the pseudobond. Then, use command
~label sel
See "label" help <https://rbvi.ucsf.edu/chimerax/docs/user/commands/label.html>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 4, 2024, at 7:49 PM, Manuel Ospina via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Good evening,
I am actually using ChimeraX and I am trying to figure out a command that can show me all the contacts of my ligand below 3.0A with my protein. Unfortunately, I have not found anything clear enough to do so. Is there a way to do this?
Another doubt is, if I have labelled 2 contacts (i.e 2.576A and 3.149A) but I am interested in only showing the label " 2.576A", I try deleting the other contact label (" 3.149A") by selecting it and typing the "label del" command, but this will delete my label of interest as well. Is there a way of only deleting specific labels from the contacts?
Any help is appreciated.
Best regards, Manuel
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
participants (3)
-
Elaine Meng -
Jamie Shaum -
Manuel Ospina