PS: that "contacts" command just selects the contacting atoms, not their whole residues. To promote the selection to whole residues you would add another command "sel up" afterward, for example: contacts /A restrict /B distanceOnly 4 reveal true make false select true sel up style sel stick color sel yellow target a ~select If you want to draw lines between the interacting atoms, you would remove the "make false'" from the contacts command. E.g. contacts /A restrict /B distanceOnly 4 reveal true select true There are many other options, such as what color to make the dashed lines. You should read the help pages so that you can understand the options. As for deadlines, my advice is to always start early especially if you are learning a new program or method. Again, there are many other ways you could do it instead, such as the zone specifications which can be by atom or by whole residue. Elaine
On Jun 30, 2024, at 8:41 AM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Rashmi, there are probably 10 different ways you could do it, but here is a concise way with commands since it is easier for me to type it into an email:
contacts /A restrict /B distanceOnly 4 reveal true make false select true style sel stick color sel yellow target a ~select
See the command help pages for explanations of their options: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/clashes.html> <https://rbvi.ucsf.edu/chimerax/docs/user/index.html#commands>
You could also have used the Contacts tool, or menu Select... Contacts, or the "select" command with command-line zone specifiers, or the "interfaces" command... <https://rbvi.ucsf.edu/chimerax/docs/user/tools/clashes.html> <https://rbvi.ucsf.edu/chimerax/docs/user/selectcontacts.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html#zones> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/interfaces.html>
Since ChimeraX is a different program Pymol, you wouldn't necessarily do each step in the same way, but you would get to basically the same end result. 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 Jun 29, 2024, at 11:50 AM, Rashmi Aggarwal via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear UCSF ChimeraX Support Team,
My name is Rashmi, and I am currently working on molecular docking studies as part of my research. I have been using UCSF ChimeraX version 1.8 for visualizing and analyzing protein structures.
I am facing difficulties in performing the following tasks related to identifying interacting residues between chains A and B within 4 angstroms, similar to what I have previously done in PyMOL:
• Select residues in chain A that are within 4 angstroms of chain B:
select interactA, byres ((chain A) within 4 of (chain B)) • Select residues in chain B that are within 4 angstroms of chain A:
select interactB, byres ((chain B) within 4 of (chain A)) • Combine the selections for interacting residues:
select interaction_residues, interactA or interactB • Show interacting residues in stick representation and color them yellow:
show sticks, interaction_residues
color yellow, interaction_residues
Despite attempting various commands and exploring the graphical user interface, I have been unable to achieve the desired results using UCSF ChimeraX. Could you please provide guidance on the correct commands or steps to accomplish this task in ChimeraX? Any assistance or advice would be greatly appreciated, as I have a pending deadline for my project.
Thank you very much for your attention to this matter. I look forward to your prompt response.
Best regards,
Rashmi