Dear All, Thank you very much to everyone who replied, both on and off the mailing list (Andy Karplus and Ensemblator from his team; Joseph Ellaway and his scripts available at https://github.com/Joseph-Ellaway/per-residue-distance).
As I was analysing conformations of the same protein from the MD simulation and had corresponding trajectories from GROMACS/OpenMM, I transitioned away from PyMOL and used the GROMACS 'gmx rmsf' command. Best wishes, Tomas On Fri, Jan 5, 2024 at 10:49 AM Tomas Malinauskas <[email protected]> wrote: > > Dear All, > > I apologize for asking a somewhat off-topic question. > > I have multiple aligned PDB files loaded in PyMOL, each representing > different conformations of the same protein. I'm interested in > creating a graph displaying RMSD per residue, similar to those shown > at > https://www.ks.uiuc.edu/Training/Tutorials/science/aars/aars_html.bak/node22.html > or > https://www.compchems.com/how-to-compute-the-rmsf-using-gromacs/#the-gmx-rmsf-command. > > I'm wondering if anyone has a script available that can calculate RMSD > per residue and write the data to a text file for graph generation. If > so, would they be able to share it with everyone? > > Thank you for your help. > > Best wishes, > Tomas ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
