Re: [ccp4bb] SUMMARY [ccp4bb] List of conserved waters

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From: vijay srivastava vijaytechno {- at -} YAHOO {- dot -} CO {- dot -} IN
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Date: 2008-09-01

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

I forgot to mention K. Sekar who suggested 3dss at
http://cluster.physics.iisc.ernet.in/3dss/

I am sorry about this.

Tim

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

GPG Key ID = A46BEE1A

On Mon, 1 Sep 2008, Tim Gruene wrote:

> 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 unpublished program written particularly for this purpose.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
>>
>

CCP4bb navigation

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

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

Next message:
Subject: Re: List of conserved waters
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2008-09-01