Hi Yahui, There are definitely some old python scripts floating around online to help with this sort of thing. pdb-tools · PyPI <https://pypi.org/project/pdb-tools/> GitHub - harmslab/pdbtools: A set of tools for manipulating and doing calculations on wwPDB macromolecule structure files <https://github.com/harmslab/pdbtools>
Best, Mike On Mon, Jan 13, 2025 at 10:51 AM Hui YAN <butterflycam...@gmail.com> wrote: > Thanks Peter. Given there are only 150 residues in my PDB file, it is > doable (if I can't work out a script)! > > Kind regards, > Yahui > > > > > On Mon, Jan 13, 2025 at 3:16 PM Peter Smyth <peter.sm...@xfel.eu> wrote: > >> Dear Yahui, >> >> It is possible to set the B-factor (temperature factor) for all atoms in >> a residue at once using the residue info dialogue in Coot (Measures>Residue >> Info... in Coot 0.9). You would still have to go through residue by >> residue, though. >> >> For something more automated, you could look into scripting changes using >> command line text editing of the PDB files. >> >> Cheers, >> >> Peter Smyth >> Postdoc scientist, SEC Group >> European XFEL >> >> >> ------------------------------ >> *From: *Hui <butterflycam...@gmail.com> >> *To: *CCP4BB <CCP4BB@JISCMAIL.AC.UK> >> *Date: *Monday, 13 January 2025 16:02 CET >> *Subject: *[ccp4bb] replacing B-factor column and color accordingly >> >> Happy New Year, everyone! >> >> I am looking for a PDB editing tool to replace the B-factors numbers with >> another column of numbers, then color the structure by pseudo-B-factors in >> ChimeraX. All the atoms of one individual residue will have the same number >> at the B-factor column. I can possibly edit the coordinate manually atom by >> atom, which is not very fun to do. Does anybody know of any programme doing >> this process? >> >> Thanks a lot! >> >> Kind regards, >> Yahui >> >> >> ------------------------------ >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >> >> > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > ######################################################################## 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/
