hey presto! thanks doriano (it does run on windows, right?)...
best
jon

-----Ursprüngliche Nachricht-----
Von: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> Im Auftrag von Doriano Lamba
Gesendet: Montag, 13. Januar 2025 17:01
An: CCP4BB@JISCMAIL.AC.UK
Betreff: Re: [ccp4bb] replacing B-factor column and color accordingly
Priorität: Hoch

Dear Yahui,

you may wish to use:

PDB Editor: a user-friendly Java-based Protein Data Bank file editor with a GUI 
Acta Cryst. (2009). D65, 399-402 https://doi.org/10.1107/S090744490900451X

PDB Editor can be downloaded from
http://sourceforge.net/projects/pdbeditorjl/

Good luck

Doriano

Il 2025-01-13 16:52 Daniel M. Himmel, Ph. D. ha scritto:
> I don't know how many people still use it, but doesn't CNS give you 
> that capability?  In the bgroup.inp script, I think you can easily 
> specify which atoms or residues to include in each overall B-factor.
> 
> Daniel
> 
> ________
> 
> Daniel M. Himmel, Ph. D.
> 
> Principal, Himmel Sci Med Com, LLC
> 
> E-mail:  danielmhim...@gmail.com
> 
> URL   :  https://himmelscimedcom.com [2]
> 
> Member, American Medical Writers Association
> 
> You can also find me at https://www.talusfreelance.com [3]
> 
> On Mon, Jan 13, 2025 at 10:26 AM 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
>>> 
>>> -------------------------
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> Links:
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> [2] https://himmelscimedcom.com/
> [3] https://www.talusfreelance.com/

--
Dr. Doriano Lamba
Retired Senior Research Associate
Istituto di Cristallografia - C.N.R.
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____________________________________________________________________________________________
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