[chimerax-users] Your message to ChimeraX-users awaits moderator approval

[Krishnan Raman]

Hi Elaine,
Thanks for the quick reply.
I think I was not clear about the first request.
I have an sdf file with structure and some aasay value(numeric) associated with each structure. . The sdf option to open files brought up the structures in 2D in chimerax but none of the associated numbers. Hence the question.
Also is there a way to covert 3d structures into 3d molecules in chimerax with a plugin perhaps?
Regards
Krish


-----Original Message-----
From: Elaine Meng <meng at cgl.ucsf.edu>
Sent: Thursday, February 2, 2023 12:47 PM
To: Krishnan Raman <RKrishnan at BIOCRYST.com>
Cc: ChimeraX Users Help <chimerax-users at cgl.ucsf.edu>
Subject: Re: [chimerax-users] Your message to ChimeraX-users awaits moderator approval

[EXTERNAL]

Hi Krish,
(1) getting data associated with a structure into ChimeraX.  If there are specific values you want to assign to atoms or residues, you can do it with "attribute definition format" -- a simple plain-text file described here:

<https://link.edgepilot.com/s/0135ec44/fimMJLKy0UmmxsiSc5nMzg?u=https://rbvi.ucsf.edu/chimerax/docs/user/formats/defattr.html>

The assigned attributes can be used for coloring, or selecting atoms/residues with values in specific ranges, etc.
<https://link.edgepilot.com/s/1f7cc291/git0pEihikG9TH_xdQKJgw?u=https://rbvi.ucsf.edu/chimerax/docs/user/attributes.html>

Or if you mean something like density map or electrostatic potential map, or sequences and sequence alignments, there are number of formats that ChimeraX reads in addition to atomic coordinates:
<https://link.edgepilot.com/s/0ae80330/Nb2xJEwhtUWYXSpRHZjCPA?u=https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html%23formats>

(2) I don't know how (or whether it is possible) to start multiple instances of chimerax from an HTML file.  Somebody else will have to elaborate on that.

My experience with HTML with the special command-execution links is that you start ChimeraX yourself and then can click the links to execute commands in the existing instance.
<https://link.edgepilot.com/s/b1e84e4d/DNTmcaDwa0uwsSRpqo12Wg?u=https://rbvi.ucsf.edu/chimerax/docs/user/tools/helpviewer.html>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Feb 2, 2023, at 10:04 AM, Eric Pettersen via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
>
>> Begin forwarded message:
>>
>> From: Krishnan Raman
>> Subject: RE: Your message to ChimeraX-users awaits moderator approval
>> Date: February 2, 2023 at 9:47:12 AM PST
>> To: "chimerax-users-owner at cgl.ucsf.edu" <chimerax-users-owner at cgl.ucsf.edu>
>>
>> Hi guys
>>
>> is there a way to get structures + other numerical data into chimerax?
>> I get the structures using a sdf file. I want to get in someother data associated each structure.
>>
>> How to start multiple instances of chimerax from a html-commands file?
>> Thanks
>> Krish
>>



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