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





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