[ccp4bb] SUMMARY [ccp4bb] List of conserved waters

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Date: 2008-09-01

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Subject: SUMMARY List of conserved waters
From: Tim Gruene tg {- at -} SHELX {- dot -} UNI-AC {- dot -} GWDG {- dot -} DE
Date: 2008-09-01

This is the summary for my question from Fri, 29 Aug 2008, when I wanted
to learn about programs that produce a list of overlapping (conserved)
waters after superpositioning of two structures.

- Somebody who did not want to answer in public offered to send a small
unpublished program written particularly for this purpose.
- Jens T. Kaiser menstioned that Rasmol, CNS, MAIN and similar programs
have such featured and listed the lines for Rasmol
select (water and *:W) and within(0.7,(water and *:X))
write pdb conserved.pdb
to select waters that are closer than .7A. I found this code very
interesting for I like rasmol
- G. Kleywegt mentioned the WAters command in lsqman
http://xray.bmc.uu.se/usf/lsqman_man.html#S71
which was handy since I was using lsqman to superpose the two structures.
- G. Sheldrick mentioned (during coffee break) that the envi command in xp
(that's NOT a product by Microsoft) would also do the job.

Thank you to everyone who considered my question.

Tim

--
Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

GPG Key ID = A46BEE1A

On Fri, 29 Aug 2008, Tim Gruene wrote:

> Hello,
>
> I am (lazily ;-)) looking for a program that list all conserved waters
> between to structures (after superposition), i.e. all waters between both
> structures within a certain distance cut-off.
>
> Could anyone please point me to a program that does this?
>
> Thanks a lot, Tim
>
> --
> Tim Gruene
> Institut fuer anorganische Chemie
> Tammannstr. 4
> D-37077 Goettingen
>
> GPG Key ID = A46BEE1A
>

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Nikos Oikonomakos
From: "Demetres D {- dot -} Leonidas" ddl {- at -} EIE {- dot -} GR
Date: 2008-09-01

Next message:
Subject: regarding cloning
From: vijay srivastava vijaytechno {- at -} YAHOO {- dot -} CO {- dot -} IN
Date: 2008-09-01