Coordset command not working in nogui mode
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 Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows
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@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
Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for Windows
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Hi Shubham, This coordset command behavior is confusing so I changed it in tomorrow's ChimeraX daily build (not in 1.4) so that "coordset #1 5" will act immediately without waiting for a frame to be drawn. If you specify a range of frames "coordset #1 5,15" then they are still only drawn one at a time when the graphics is drawn -- that is for recording movies. Tom
On May 24, 2022, at 11:15 AM, Eric Pettersen via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
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@cgl.ucsf.edu <mailto:chimerax-users@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
Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for Windows
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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 Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows From: Eric Pettersen<mailto:pett@cgl.ucsf.edu> Sent: Tuesday, May 24, 2022 22:15 To: Shubham Devesh Ramgoolam<mailto:sdramgoolam@uwaterloo.ca> Cc: chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@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@cgl.ucsf.edu<mailto:chimerax-users@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 Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu<mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
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@cgl.ucsf.edu> on behalf of Shubham Devesh Ramgoolam via ChimeraX-users <chimerax-users@cgl.ucsf.edu> Sent: Thursday, May 26, 2022 11:17 AM To: ChimeraX Users Help <chimerax-users@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 Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows From: Eric Pettersen<mailto:pett@cgl.ucsf.edu> Sent: Tuesday, May 24, 2022 22:15 To: Shubham Devesh Ramgoolam<mailto:sdramgoolam@uwaterloo.ca> Cc: chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@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@cgl.ucsf.edu<mailto:chimerax-users@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 Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu<mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Hi Anthony, I understand it now. Thank you so much for the help, Shubham Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows From: Anthony James Schaefer<mailto:tony.schaefer@uga.edu> Sent: Thursday, May 26, 2022 19:48 To: Shubham Devesh Ramgoolam<mailto:sdramgoolam@uwaterloo.ca> Cc: ChimeraX Users Help<mailto:chimerax-users@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@cgl.ucsf.edu> on behalf of Shubham Devesh Ramgoolam via ChimeraX-users <chimerax-users@cgl.ucsf.edu> Sent: Thursday, May 26, 2022 11:17 AM To: ChimeraX Users Help <chimerax-users@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 Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows From: Eric Pettersen<mailto:pett@cgl.ucsf.edu> Sent: Tuesday, May 24, 2022 22:15 To: Shubham Devesh Ramgoolam<mailto:sdramgoolam@uwaterloo.ca> Cc: chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@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@cgl.ucsf.edu<mailto:chimerax-users@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 Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu<mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
participants (4)
-
Anthony James Schaefer -
Eric Pettersen -
Shubham Devesh Ramgoolam -
Tom Goddard