Re: [ccp4bb] Replacement for arp waters?

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

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Subject: Re: Replacement for arp waters?
From: Donnie Berkholz dberkholz {- at -} GENTOO {- dot -} ORG
Date: 2009-01-20

Subject: Re: Replacement for arp waters?
From: "Soisson, Stephen M" stephen_soisson {- at -} MERCK {- dot -} COM
Date: 2009-01-20

Might I add yet another call for the reinstatement of arp_waters - a
very useful program indeed.

Steve

________________________________

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
Bernhard Rupp
Sent: Tuesday, January 20, 2009 2:50 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Replacement for arp_waters?

arp_waters is very useful for a variety of purposes.

I would like to see it supported in future releases.

Best, BR

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
Roger Rowlett
Sent: Tuesday, January 20, 2009 11:40 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Replacement for arp_waters?

I will second noting the loss of arp_waters in CCP4 6.1. I know there is
a "find waters" option in Coot 0.5.2 under "Calculate...Other modeling
tools", and perhaps this is adequate, but it doesn't seem to have as
many options for fine-tuning as arp_waters did. Coot allows for finding
waters above a certain sigma value; arp_waters allowed this option plus
setting minimum and maximum hydrogen bonding distances between heavy
atoms.

At any rate, it was very handy to have this option for refmac for both
Windows and Linux platforms, especially for teaching new users or
undergraduates working in the CCP4i environment. I suppose I can always
add ARP/WARP to CCP4i in the Linux environment, but that leave Windows
users out in the cold.

Just my 2 cents.

Cheers,

--

________________________________

Roger S. Rowlett
Professor
Colgate University Presidential Scholar
Department of Chemistry
Colgate University
13 Oak Drive
Hamilton, NY 13346

tel: (315)-228-7245
ofc: (315)-228-7395
fax: (315)-228-7935
email: rrowlett@mail.colgate.edu

David J. Schuller wrote:

I note that in CCP4 6.1.0, arp_waters has been deprecated. Is there a
program in the suite which fills the role formerly filled by arp_waters,
of automatically adding waters?

Cheers,
-
=======================================================================
You can't possibly be a scientist if you mind people
thinking that you're a fool. - Wonko the Sane
=======================================================================
David J. Schuller
modern man in a post-modern world
MacCHESS, Cornell University
schuller@cornell.edu

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CCP4bb navigation

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

Previous message:
Subject: 3D 120hz LCD setups available
From: Francis E Reyes Francis {- dot -} Reyes {- at -} COLORADO {- dot -} EDU
Date: 2009-01-20

Next message:
Subject: Re: Replacement for arp waters?
From: Donnie Berkholz dberkholz {- at -} GENTOO {- dot -} ORG
Date: 2009-01-20