[chimerax-users] values associated with structures; 2D to 3D?

[Krishnan Raman]

Hi Elaine,
That answered my question accurately. Id id find that reading *.mol files containing 3d coordinates works in chimerax.
Let me think about adding numerical values with each structure.
Thanks
Krish

-----Original Message-----
From: Elaine Meng <meng at cgl.ucsf.edu>
Sent: Thursday, February 2, 2023 2:58 PM
To: Krishnan Raman <RKrishnan at BIOCRYST.com>
Cc: Tianming Qu via ChimeraX-users <chimerax-users at cgl.ucsf.edu>
Subject: values associated with structures; 2D to 3D?

[EXTERNAL]

Hi Krish,
If I understand correctly, the SDF files that you have do not contain 3D atomic coordinates.  They only contain 2D "chemical diagrams" -- so they can't be used like real structures.  ChimeraX tries to apply chemical detection based on bond lengths and angles, which does not work on these chemical diagrams, since they are typically different in scale as well as being totally flat.  Sorry, there is no option to make them into real 3D molecules.

To get 3D structures of the compounds you would instead need to start with something like a SMILES string or a PubChem identifier and use those types of fetches (SMILES or PubChem3D) instead of your SDF files.  These types of fetches are done with the "open" command:
<https://link.edgepilot.com/s/61c9495d/aVeQcBTcUU2_ELnxB5JPKg?u=https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html%23fetch>

There is no automatic way to read arbitrary values from SDF files.  Instead you would need to open all the structures somehow, then create an attribute assignment file to assign the values.   Or, you would need to write a custom python script that reads the values from your files.  Somebody else would have to advise on that, as I don't know python.

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 12:24 PM, Krishnan Raman via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
>
> 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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