Hello,
Just thought I would add one actionable suggestion to Robbie’s good advice.
At least one program is well equipped to do this type of operations without
doing PDB file surgery: ChimeraX. See relevant documentation:
- the setattr command can set named "attributes" to atom selections, and c
Can we please start thinking a bit more in mmCIF please? Instead of hacking columns in PDB formatted files, perhaps we should look at molecular graphics programs' capabilities of colouring atoms or residues by a some column with label _somecategory.someitem. That way we are not hacking together cor
> (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
On 13/01/2025 16:43, Marcin Wojdyr wrote:
Dear Yahui,
I am looking for a PDB editing tool to replace the B-factors numbers with
another column of numbers
It depends where you get that new column of numbers from.
Yes, this is most of the problem.
Presuming, as did Clemens, that your input
AC.UK
Subject: [EXTERNAL] [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 individua
Dear Yahui,
>
> I am looking for a PDB editing tool to replace the B-factors numbers with
> another column of numbers
It depends where you get that new column of numbers from. There are
tools in CCP4 that set all B-factors to a given value, or clamp the
values to a certain range. Recently, it lo
---Ursprüngliche Nachricht-
>> Von: CCP4 bulletin board 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
>&
: 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
.
Hope this is of help,
Andy Purkiss
From: CCP4 bulletin board on behalf of Hughes, Jonathan
Sent: 13 January 2025 16:11
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] AW: [ccp4bb] replacing B-factor column and color accordingly
External Sender: Use caution.
hi
hey presto! thanks doriano (it does run on windows, right?)...
best
jon
-Ursprüngliche Nachricht-
Von: CCP4 bulletin board 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
en
&
Guest Scientist
Department of Physics
Free University of Berlin
Germany
Von: CCP4 bulletin board 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 ther
> European XFEL
> >
> >
> > --
> > *From: *Hui
> > *To: *CCP4BB
> > *Date: *Monday, 13 January 2025 16:02 CET
> > *Subject: *[ccp4bb] replacing B-factor column and color accordingly
> >
> > Happy New Year, everyo
Hi Yahui, using a text editor like Mac TextEdit you can also click the option
key (cursor will change to cross shape), click and drag to select column, copy
and paste.
All the best,John
On Monday, January 13, 2025 at 09:02:49 AM CST, Hui YAN
wrote:
Happy New Year, everyone!
I am look
changes
using command line text editing of the PDB files.
Cheers,
Peter Smyth
Postdoc scientist, SEC Group
European XFEL
-
From: Hui
To: CCP4BB
Date: Monday, 13 January 2025 16:02 CET
Subject: [ccp4bb] replacing B-factor column and color accordingly
Happy New Year, ev
European XFEL
>>
>>
>> ------
>> *From: *Hui
>> *To: *CCP4BB
>> *Date: *Monday, 13 January 2025 16:02 CET
>> *Subject: *[ccp4bb] replacing B-factor column and color accordingly
>>
>> Happy New Year, everyone!
>>
>
mmand line text editing of the PDB files.
>
> Cheers,
>
> Peter Smyth
> Postdoc scientist, SEC Group
> European XFEL
>
>
> --
> *From: *Hui
> *To: *CCP4BB
> *Date: *Monday, 13 January 2025 16:02 CET
> *Subject: *[ccp4bb] replacing B-fac
files.
>
> Cheers,
>
> Peter Smyth
> Postdoc scientist, SEC Group
> European XFEL
>
>
> --
> *From: *Hui
> *To: *CCP4BB
> *Date: *Monday, 13 January 2025 16:02 CET
> *Subject: *[ccp4bb] replacing B-factor column and color accordingl
g 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
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
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