If you create a file (e.g. "resb.dat") where each line has
(space-separated) the chain, residue number and value:
A 1 7.5
A 2 5.4
B 1 11.9
B 2 0.4
/and/ you use PDB format:
awk -v f=resb.dat 'BEGIN{
while(getline<f) b[$1,$2]=$3-0.0
}
/^ATOM|^HETATM/{
c=substr($0,22,1)
r=substr($0,23,4)-0
if(b[c,r]!=""){
printf("%s%6.2f%s\n",substr($0,1,60),b[c,r],substr($0,67))
next
}
}
{print}' your.pdb > new.pdb
(could be a "one-liner", but easier to read this way)
Cheers
Clemens
On Mon, Jan 13, 2025 at 03:51:11PM +0000, Hui YAN 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 <[email protected]> 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 <[email protected]>
> > *To: *CCP4BB <[email protected]>
> > *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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> >
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--
*--------------------------------------------------------------
* Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com
* Global Phasing Ltd., Sheraton House, Castle Park
* Cambridge CB3 0AX, UK www.globalphasing.com
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