Re: [ccp4bb] Manipulating electron density

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

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Subject: System virtual machine recommendation for crystallography?
From: Andy Torelli att29 {- at -} CORNELL {- dot -} EDU
Date: 2009-05-11

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Subject: Re: phasing with se-met at low resolution
From: Clemens Vonrhein vonrhein {- at -} GLOBALPHASING {- dot -} COM
Date: 2009-05-11

Subject: Re: Manipulating electron density
From: Phoebe Rice price {- at -} UCHICAGO {- dot -} EDU
Date: 2009-05-11

You're right; my apologies to the original question-poster.

I think a better way to do it would be with a mask that covers
the entire molecule of interest, rather than an atom-by-atom
carving job.

Phoebe

---- Original message ----
>Date: Sun, 10 May 2009 20:29:00 -0700
>From: James Stroud
>Subject: Re: [ccp4bb] Manipulating electron density
>To: CCP4BB@JISCMAIL.AC.UK
>
>On May 10, 2009, at 12:21 PM, Phoebe Rice wrote:
>> Of COURSE the map will look lovely if you carve it off at 1.5A
>> from your atoms. And your gels will look lovely too if you
>> just touch them up with with some white-out and a sharpie.
>> Do the honest thing and show the whole truth, using the
>> z-clipping to get a comprehensible slab.
>
>Maybe we should give Jason the benefit of the doubt that he
wants to
>present an honest representation of his density. Clipping off
symmetry
>related molecules is not the same as "carving" density from
amorphous
>blobs. The former is more akin to showing only part of a lane
of a
>gel, which is common practice even in prestigious journals.
In fact,
>my other monitor presently displays such a "carved" gel
picture from a
>recent Cell paper.
>
>James
Phoebe A. Rice
Assoc. Prof., Dept. of Biochemistry & Molecular Biology
The University of Chicago
phone 773 834 1723
http://bmb.bsd.uchicago.edu/Faculty_and_Research/01_Faculty/01_Faculty_Alphabetically.php?faculty_id=123

RNA is really nifty
DNA is over fifty
We have put them
both in one book
Please do take a
really good look
http://www.rsc.org/shop/books/2008/9780854042722.asp

CCP4bb navigation

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

Previous message:
Subject: System virtual machine recommendation for crystallography?
From: Andy Torelli att29 {- at -} CORNELL {- dot -} EDU
Date: 2009-05-11

Next message:
Subject: Re: phasing with se-met at low resolution
From: Clemens Vonrhein vonrhein {- at -} GLOBALPHASING {- dot -} COM
Date: 2009-05-11