Re: [ccp4bb] RMSD per residue graph for multiple aligned PDB files

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 M

Re: [ccp4bb] RMSD per residue graph for multiple aligned PDB files

AFAIK the CCP4 tools “superpose” and “gesamt” both give tables of per-residue RMSD Harry > On 5 Jan 2024, at 10:49, Tomas Malinauskas > wrote: > > Dear All, > > I apologize for asking a somewhat off-topic question. > > I have multiple aligned PDB files loaded in PyMOL, each representing > d

Re: [ccp4bb] RMSD per residue graph for multiple aligned PDB files

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 variat

[ccp4bb] RMSD per residue graph for multiple aligned PDB files

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/Trai