[chimerax-users] Coordset command not working in nogui mode

Thu May 26 09:15:08 PDT 2022

Hi Anthony,

I understand it now.

Thank you so much for the help,
Shubham

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From: Anthony James Schaefer<mailto:tony.schaefer at uga.edu>
Sent: Thursday, May 26, 2022 19:48
To: Shubham Devesh Ramgoolam<mailto:sdramgoolam at uwaterloo.ca>
Cc: ChimeraX Users Help<mailto:chimerax-users at cgl.ucsf.edu>
Subject: Re: [chimerax-users] Coordset command not working in nogui mode

Shubham,

session.models is a manager that keeps track of all the models in your session. You'll want to get a specific atomic structure from session.models. There's a couple ways to do this, but here's two:

# list all models that are atomic structures
from chimerax.atomic import AtomicStructure
session.models.list(type=AtomicStructure)

# iterate through all models
for m in session.models:
    print(m.name, m.atomspec)

With either of these, you'll have to pick out which model you want.

You should also be able to use the AtomicStructures list that was returned from your first 'open' command. As far as I know, the extra coordinate sets should be added to that structure after you open the trajectory file.

Best,

Tony

From: ChimeraX-users <chimerax-users-bounces at cgl.ucsf.edu> on behalf of Shubham Devesh Ramgoolam via ChimeraX-users <chimerax-users at cgl.ucsf.edu>
Sent: Thursday, May 26, 2022 11:17 AM
To: ChimeraX Users Help <chimerax-users at cgl.ucsf.edu>
Subject: Re: [chimerax-users] Coordset command not working in nogui mode

[EXTERNAL SENDER - PROCEED CAUTIOUSLY]

Hi Eric,

The ‘wait 1’ command is very helpful. Thank you so much!

I have also tried the other method but it is not working for me.

{Some background: My topology file was in prmtop format while my coordinate file was in dcd format. So, I opened both files in chimera and then saved the trajectory as a pdb. I am now using a combination of the pdb file and the dcd coordinate file in chimeraX.}

This is what I got from the Python Shell of ChimeraX:

run(session, 'open '+ r'C:\Users\Shubham\Desktop\SK_Lab\myfile.pdb')

Out[3]: [<chimerax.atomic.structure.AtomicStructure at 0x2ef81670040>]

run(session, 'open ' + r'C:\Users\Shubham\Desktop\mycoord.dcd' + ' structureModel #1')

Out[4]: []

s = session.models

s

Out[6]: <chimerax.core.models.Models at 0x2efc7fece50>

s.coordset_ids

---------------------------------------------------------------------------

AttributeError                            Traceback (most recent call last)

~\AppData\Local\Temp/ipykernel_9612/1923568490.py in <module>

----> 1 s.coordset_ids

AttributeError: 'Models' object has no attribute 'coordset_ids'

My goal with this is to get a way to obtain the total number of frames available for the trajectory.

My chimeraX version 1.5.dev202205200152 (2022-05-20).

Regards,

Shubham

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From: Eric Pettersen<mailto:pett at cgl.ucsf.edu>
Sent: Tuesday, May 24, 2022 22:15
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] Coordset command not working in nogui mode

Hi Shubham,

Since the "coordset" command sets up playback of coordinate frames, it doesn't actually do anything until a frame is drawn, which is why in nogui mode nothing changes, and why you have to "create a delay" in GUI mode.  You can force a frame to get drawn with the "wait 1" command, which will get your script working in both modes.

Alternatively, if you have the structure model in a variable (i.e. from the list of models returned by the 'open' command, or culled from session.models), you can change the coordset directly, e.g.:

# if the structure model is in the 's' variable

for cid in s.coordset_ids:

s.active_coordset_id = cid

# do whatever you need to do with this coordset

--Eric

Eric Pettersen

UCSF Computer Graphics Lab

On May 24, 2022, at 1:22 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 have a python script for measuring the distance between aromatic rings of specific residues for different frames of a trajectory.

To measure the distance, I am first defining centroids at the center of aromatic rings and then use the command distance. This process is repeated for each frame to be analyzed.

To navigate between frames, I am using the command ‘coordset #1 {desired frame}’.

When executing the script in no gui mode, the centroids are always defined with respect to the residue’s location in frame 1 even though the command coordset has changed the frame.

In gui mode, the script only works if a delay is created between changing the frame and defining the new centroids.

I introduced that delay by asking for a dummy user input (I ran the script from python Shell):

run(session, 'coordset #1 ' + {new_frame})

y = input('dummy')

run (session, 'define centroid /A:8 & aromatic-ring radius 0.3 color yellow mass false name d1’)

My chimeraX version: 1.4rc202205060510 (2022-05-06)

Should I be using a different command for changing frames of trajectories when in nogui mode?

Regards,

Shubham

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