[chimerax-users] Time-efficient python code for obtaining coordinates of atoms

[Tom Goddard]

Hi Shubham,

  Here is example Python code to lookup residues by chain identifier and residue numbers.

	https://rbvi.github.io/chimerax-recipes/residues/residues.html <https://rbvi.github.io/chimerax-recipes/residues/residues.html>

  Tom


> On Aug 1, 2022, at 10:39 PM, Shubham Devesh Ramgoolam via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Ok. Thank you, Eric.
> I appreciate it,
> Shubham
>  
> Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for Windows
>  
> From: Eric Pettersen <mailto:pett at cgl.ucsf.edu>
> Sent: Tuesday, August 2, 2022 5:34
> To: Shubham Devesh Ramgoolam <mailto:sdramgoolam at uwaterloo.ca>
> Cc: chimerax-users at cgl.ucsf.edu <mailto:chimerax-users at cgl.ucsf.edu>
> Subject: Re: [chimerax-users] Time-efficient python code for obtaining coordinates of atoms
>  
> Hi Shubham,
> First off, 'getcrd' really should return the coordinates in addition to logging them, so I have fixed that and the fix will be in tonight's daily build.
> But I don't think that really helps you because atom-spec parsing in ChimeraX is relatively slow, and I assume you would need to provide the same (long) atom spec to getcrd that you were using with "sel".  We want to improve the speed and reliability of atom-spec parsing, but achieving that is quite aways off at this point and so won't help with your current situation.
> I assume that which residues you need coordinates from are changing frequently, otherwise the cost of selecting them once wouldn't be that big a deal.  Depending on what criteria you are using to choose the residues, maybe you could loop through chimerax.atomic.all_structures(session).residues and get the coordinates of the residues that meet your criteria.
>  
> --Eric
>  
> Eric Pettersen
> UCSF Computer Graphics Lab
>  
> 
> 
> On Aug 1, 2022, at 2:32 AM, Shubham Devesh Ramgoolam via ChimeraX-users <chimerax-users at cgl.ucsf.edu <mailto:chimerax-users at cgl.ucsf.edu>> wrote:
>  
> Hi all,
> I hope you are doing well.
> I am looking for a time-efficient way of obtaining the coordinates of specified residues.
> I cannot use the command getcrd as I need these coordinates in a python script for defining geometric objects (getcrd prints the output to the log).
>  
> My attempt at this consisted of selecting all of the specified residues via run(session, ‘sel ...’), accessing that selection using selected_residues(session), and then, extracting the coordinates using .atoms.coords.
> The issue here is that run(session, ‘sel ...’) slows down if there are lots of specified residues.
>  
> I tried bypassing the command ‘sel’ by first importing AtomSpecArg from chimerax.core.commands.atomspec and then using AtomSpecArg.parse('my residue_ID', session)[0].evaluate(session).atoms[0]. However, this is even slower.
>  
> Regards,
> Shubham
>  
>  
> Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for Windows
>  
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