Similar to distang, one can also do it with the gemmi contact program
and some
simple filtering with awk (or other tool). It will also look for
symmetry related
contacts and can read mmcif or pdb format. (One can adjust distance
thresholds etc with
parameters to gemmi
https://gemmi.readt
Modification of Eleanor's suggestion-
It is fairly trivial to write a program (e.g.
https://www.cytbc1.com/berry/for/pdbdist3w.for) which;
reads coordinates from one pdb file into memory
reads a second pdb file, and for each atom/hetatm
checks whether it is within threshold distance of th
Ugly, but could you rename them to something else ;-?
Best wishes, Jon Cooper.
jon.b.coo...@protonmail.com
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Original Message
On 07/11/2024 11:09, Kajander, Tommi A wrote:
> it doesnt seem to include waters in the analysis unfortunatelly no, at lea
Hi Tommi,
This can be done in cns with the following script I wrote. You will need to
make the cns-formatted molecular topology and coordinate files with the
generate_easy.inp script, which can be found in the input files section of
http://cns-online.org/v1.3/.
Best Regards,
Jack Tanner
Hi Tommi,
This should be possible with watFinder in prody. It can’t currently focus on
water molecules between chains but we can add a filter for that.
Best wishes
James
> On 6 Nov 2024, at 15:44, Kajander, Tommi A wrote:
>
> Is there a something available to automatically analyse/identifiy
A very old fashioned hands on way to do it..
Run distang
Find those H2O which contact two protein molecules..
5od5.pdb has 3 chains..
distang xyzin CCP4_DOWNLOADED_FILES/5od5.pdb > d
You get a list like this
Atom I Atom J DijSym TX TY TZ occ(i)*occ(j) av_bi+bj
M 23 SD A
Dear Tommi,
You can try HBPLUS or contacts(in CCP4). They are something you
might like, for what you want to do. They are not specifically for water
at interface but you can filter the results with basic unix commands eg.
grep. NACCESS is another program that you may want to conside
Is it possible to extract this info from pdbepisa?
Best wishes, Jon Cooper.
Emeritus at UCL.
jon.b.coo...@protonmail.com
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Original Message
On 07/11/2024 09:31, Italo Carugo Oliviero wrote:
> Dear Tommi,
> you could write a program (perhaps with Ch
Dear Tommi,
you could write a program (perhaps with ChatGPT) that (i) stores water
molecules, (ii) stores protein atoms, and (iii) searches, among the water
molecules, for those that are close to two protein atoms that belong to
different chains.
Oliviero
Il giorno mer 6 nov 2024 alle ore 16:43 Ka
