Supoort for automating superimposition process of multiple pairs of structures using command line
Hello Chimera team, I am seeking your assistance in automating the process of superimposing multiple pairs of structures using the command line. I've performed the MD simulation of the UBA domain (PDB ID - 1OQY), and for analyzing the structural changes, I've extracted the 11 structures from the trajectory at 500ns to 1000ns with steps of 50ns. In total, I've 12 structures [1 reference structure (em.gro - energy minimized structure) and 11 extracted structures]. Now I want to superimpose each extracted structure w.r.t. em.gro and save the image of superimposition with the image name to be (time + rmsd_value). For the RMSD value, I'll have to save the reply log file (or the last 10-15 lines of the reply log) and then copy the rmsd value and save my image file with it. Could you please give me an outline or references on how I can do this task? Thank you for your attention Regards, Vaibhav
Hi Vaibhav, It is not simple to automate that process because it requires getting the RMSD value from the log, and there is no command to do that. There are commands to do the superposition and to save the image ("copy" command in Chimera), but not to automatically figure out time+RMSD and embed it in the filename when saving. "copy" command help: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/copy.html> I personally would NOT try to automate (code) it -- instead I would just do all the steps manually (repeating the superposition and image-saving commands 11 times, and noting the time and RMSD for each structure to get the filename to save). I don't know python myself, but even for a programmer it would probably take much more time trying to write code than just to do it manually. As for automation, the following link describes how to embed Chimera commands into a python script and how to save the reply log to a file. However, that process is only recommended when you have already figured out commands to do all the necessary steps. <https://www.rbvi.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry
On Jun 26, 2023, at 5:26 AM, Vaibhav Anand via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hello Chimera team, I am seeking your assistance in automating the process of superimposing multiple pairs of structures using the command line. I've performed the MD simulation of the UBA domain (PDB ID - 1OQY), and for analyzing the structural changes, I've extracted the 11 structures from the trajectory at 500ns to 1000ns with steps of 50ns.
In total, I've 12 structures [1 reference structure (em.gro - energy minimized structure) and 11 extracted structures]. Now I want to superimpose each extracted structure w.r.t. em.gro and save the image of superimposition with the image name to be (time + rmsd_value). For the RMSD value, I'll have to save the reply log file (or the last 10-15 lines of the reply log) and then copy the rmsd value and save my image file with it.
Could you please give me an outline or references on how I can do this task? Thank you for your attention Regards, Vaibhav
Hi Elaine, Regarding the process, I was trying to automate. I've finally been able to make Python scripts with some help from my lab mates. I first generated all the images and then manually saved the reply log and used this saved log file to rename image files. I've attached the script files with the email. Thank you for all your help Regards, Vaibhav On 26-06-2023 23:04, Elaine Meng wrote:
Hi Vaibhav, It is not simple to automate that process because it requires getting the RMSD value from the log, and there is no command to do that. There are commands to do the superposition and to save the image ("copy" command in Chimera), but not to automatically figure out time+RMSD and embed it in the filename when saving.
"copy" command help: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/copy.html>
I personally would NOT try to automate (code) it -- instead I would just do all the steps manually (repeating the superposition and image-saving commands 11 times, and noting the time and RMSD for each structure to get the filename to save). I don't know python myself, but even for a programmer it would probably take much more time trying to write code than just to do it manually.
As for automation, the following link describes how to embed Chimera commands into a python script and how to save the reply log to a file. However, that process is only recommended when you have already figured out commands to do all the necessary steps. <https://www.rbvi.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry
On Jun 26, 2023, at 5:26 AM, Vaibhav Anand via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hello Chimera team, I am seeking your assistance in automating the process of superimposing multiple pairs of structures using the command line. I've performed the MD simulation of the UBA domain (PDB ID - 1OQY), and for analyzing the structural changes, I've extracted the 11 structures from the trajectory at 500ns to 1000ns with steps of 50ns.
In total, I've 12 structures [1 reference structure (em.gro - energy minimized structure) and 11 extracted structures]. Now I want to superimpose each extracted structure w.r.t. em.gro and save the image of superimposition with the image name to be (time + rmsd_value). For the RMSD value, I'll have to save the reply log file (or the last 10-15 lines of the reply log) and then copy the rmsd value and save my image file with it.
Could you please give me an outline or references on how I can do this task? Thank you for your attention Regards, Vaibhav
participants (2)
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Elaine Meng -
Vaibhav Anand