Dear Thomas,
Just have a look at this paper where we have made three-dimensional
sketches of both backbone and side chain RMSDs:
https://pubmed.ncbi.nlm.nih.gov/34988429
The illustrations were done with Chimera, but "B-factor" plots with
PyMOL can be generated,at least for the backbone variation,following the
same procedure.
Cheers, Arne
Am 05.01.24 um 11:49 schrieb Tomas Malinauskas:
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
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--
Prof. Dr. Arne Skerra
Lehrstuhl f. Biologische Chemie | Technische Universitaet Muenchen
Emil-Erlenmeyer-Forum 5 | 85354 Freising (Weihenstephan) | Germany
Phone: +49 8161 71 4351 | Fax: 4352
eMail: [email protected] | http://biologische-chemie.userweb.mwn.de
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