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Re: [ccp4bb] Refmac and B factors
 

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CCP4bb <-- 2007 <-- May 2007 <-- 10 May 2007
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Subject: Re: CCP4 GUI
From: Dima Klenchin klenchin {- at -} FACSTAFF {- dot -} WISC {- dot -} EDU
Date: 2007-05-10 		Next message:
Subject: Re: CCP4 GUI
From: Juergen Bosch jbosch {- at -} U {- dot -} WASHINGTON {- dot -} EDU
Date: 2007-05-10


Subject: Re: Refmac and B factors
From: Roger Rowlett RRowlett {- at -} MAIL {- dot -} COLGATE {- dot -} EDU
Date: 2007-05-10
IMO, the GUI is a lifesaver for getting undergraduates involved in
crystallography in an efficient way. While it is possible to teach my
undergraduates to write scripts for CNS, CCP4, and O, it is much, much
easier for them to learn the CCP4 GUI. Sooner or later, real problems
require you to look under the hood to some degree or other, so it is not
so much a black box as one would think, but to the extent that it is, it
has made crystallography accessible to many more investigators and
students than otherwise. (If you had asked me a decade ago if my
undergraduates would be solving protein X-ray structures I may have
laughed.) Personally, I would like to see as many options as possible
included in the GUI, just for consistency and ease of use, although I
realize that this requires a lot more work on the developers' part. But
when all else fails, there is always RTFM...or CCP4BB.

Cheers,
___________________________________________
Roger S. Rowlett
Professor
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

-----Original Message-----
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On
Behalf Of Kolstoe S.E.
Sent: Thursday, May 10, 2007 5:09 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Refmac and B factors


Thanks very much for the replies, and especially for the link to
the previous thread on this topic (Eva).

Just a comment about the ccp4i GUI in general - pretty much all
the students in my department are slowly becoming dependant on the GUI
because it is so much easier to use for those brought up using MS
windows. However, is it really fair to be distributing the GUI as a
"finished" product when it has so many limitations, and in this
particular case is just plain misleading? Although I applaud the idea of
making crystallography more user friendly, is it not just asking for
trouble (and bad science) when software is written that gives the
illusion that things are more straight forward than they actually are?

Simon



________________________________

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On
Behalf Of Eva Kirchner
Sent: 09 May 2007 17:37
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Refmac and B factors


Hi Simon,

you can't stop it - I asked the same question (with some more
questions) some weeks ago.

You can find the original email and the tips I got for
not-so-good resolution B-factor refinement here:
http://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg01224.html

Good luck,
Eva



2007/5/9, Kolstoe S.E. :


Dear all,

I have a structure at fairly low resolution that I am
trying to refine
with Refmac. I do not want to refine B factors so have
arbitrarily set
them all to 20 and then run refmac in the ccp4i GUI
after deselecting
the "refine temperature factors" box. However, when I
look at the
resulting pdb file my B factors vary from 2 to 90.

Is Refmac just calculating my B factors or is it still
refining them,
and if the latter how can I stop it?

Thanks,

Simon
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