Re: [ccp4bb] carving up maps (was re: pymol help)

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

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Subject: Re: carving up maps (was re: pymol help)
From: Anastassis Perrakis a {- dot -} perrakis {- at -} NKI {- dot -} NL
Date: 2007-10-29

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From: Iain Kerr ikerr {- at -} CMP {- dot -} UCSF {- dot -} EDU
Date: 2007-10-29

Subject: Re: carving up maps (was re: pymol help)
From: Bart Hazes bart {- dot -} hazes {- at -} UALBERTA {- dot -} CA
Date: 2007-10-29

Anastassis Perrakis wrote:
> Dear Andrew,
>
> Thank you for that posting; I would like to simply agree with the
> Bobscript manual and your suggested practice.
>
> I think the 'carve' commands should not be there; if you wonder why,
> take a ligand, put it wherever you want in space,
> set the map sigma to -0.5, display a map with carve=1.2 and think if
> this picture is informative, especially in the context
> of your favorite competitor publishing it in Nature.
>
> A.
>

The fact that a tool can be misused does not necessarily mean that there
is something wrong with the tool, just with some users. I agree that
with current ray-traced images there is less need for this tool than in
the old black&white line diagrams where a lack of 3D perception easily
led to cluttered images. However, if showing the density of interest
really benefits from this trick then it's fine with me as long as you
indicate in the legend what map and carve settings were used.

Bart

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==============================================================================

Bart Hazes (Assistant Professor)
Dept. of Medical Microbiology & Immunology
University of Alberta
1-15 Medical Sciences Building
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Canada, T6G 2H7
phone: 1-780-492-0042
fax: 1-780-492-7521

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CCP4bb navigation

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

Previous message:
Subject: Re: carving up maps (was re: pymol help)
From: Anastassis Perrakis a {- dot -} perrakis {- at -} NKI {- dot -} NL
Date: 2007-10-29

Next message:
Subject: Re: Pseudo-merohedral twinning and Molecular replacement
From: Iain Kerr ikerr {- at -} CMP {- dot -} UCSF {- dot -} EDU
Date: 2007-10-29