Part of the reasoning was that arp_waters corresponded to a very old version
of arp/warp It was felt that up-to-date arp/warp and/or findwaters covered
the functionality.
Of course, every implementation does things in a slightly different way, and
each has their fans. Which means it is hard to deprecate anything. Which means
the suite bloats ...
Cheers
Martyn
-----Original Message-----
From: CCP4 bulletin board on behalf of Roger Rowlett
Sent: Tue 1/20/2009 7:39 PM
To: [log in to unmask]
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: [log in to unmask]
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,
-
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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
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