Emacs has a pdb mode add-on which is still available (https://github.com/mmagnus/emacs-pdb-mode) and works in current versions of both Emacs and Xemacs including under Windows.
However, with the move to mmcif as the standard coordinate format, there may need to be other tools made available. Hope this is of help, Andy Purkiss ________________________________ From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Hughes, Jonathan <jon.hug...@bot3.bio.uni-giessen.de> Sent: 13 January 2025 16:11 To: CCP4BB@JISCMAIL.AC.UK <CCP4BB@JISCMAIL.AC.UK> Subject: [ccp4bb] AW: [ccp4bb] replacing B-factor column and color accordingly External Sender: Use caution. hi everyone, i know you're all busy doing experiments, writing papers, teaching and running the whole joint while being underpaid on fixed-period contracts, but wouldn't it be nice if someone were to put together a dedicated PDB screen editor? my pals in HH tell me to edit PDB files from the command line too, but the last time i edited anything that way was in 1980 using a PDP11-44 – and even then people thought i was mad! i think computers have got better in the meantime too.... cheers jon -- Prof. Dr. Jon Hughes Institute for Plant Physiology Justus Liebig University Giessen & Guest Scientist Department of Physics Free University of Berlin Germany Von: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> Im Auftrag von Hui YAN Gesendet: Montag, 13. Januar 2025 16:51 An: CCP4BB@JISCMAIL.AC.UK Betreff: Re: [ccp4bb] replacing B-factor column and color accordingly 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<mailto: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<mailto:butterflycam...@gmail.com>> To: CCP4BB <CCP4BB@JISCMAIL.AC.UK<mailto: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 The Francis Crick Institute Limited is a registered charity in England and Wales no. 1140062 and a company registered in England and Wales no. 06885462, with its registered office at 1 Midland Road London NW1 1AT ######################################################################## 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/
