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

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CCP4bb <-- 2007 <-- November 2007 <-- 01 November 2007
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Subject: Postdoc position at The University of Chicago
From: Enrico Malito emalito {- at -} HUGGINS {- dot -} BSD {- dot -} UCHICAGO {- dot -} EDU
Date: 2007-11-01 		Next message:
Subject: Two post doc positions in Tromsų?
From: Elin Moe elin {- dot -} moe {- at -} CHEM {- dot -} UIT {- dot -} NO
Date: 2007-11-02


Subject: Re: carving up maps (was re: pymol help)
From: Warren DeLano warren {- at -} DELSCI {- dot -} COM
Date: 2007-11-01
Along those lines, one of the things you can do with PyMOL is color map
density based on the color of the nearest atom (if any):

Example image at: http://delsci.com/img/map_color.jpg

Example script:

load ref.pdb
load map.xplor
isomesh mesh, ref, 1.0
ramp_new ramp, ref, [0,1.5,2], [-1, -1, grey70]
color ramp, mesh


Cheers,
Warren

-----Original Message-----
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
Robert Esnouf
Sent: Thursday, November 01, 2007 5:06 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] carving up maps (was re: pymol help)

Having put the "make my density look publishable" (mapcover) command in
BobScript, my conscience wouldn't ever let me use it as it gives a false
impression of experimental maps!

It is useful, though, in a couple of cases: where the map is not
representing electron density but calculated from the structure (e.g.
binding pockets...) and - artistic tip for the day - to draw a map in
two colours which I have used in presentations to help show ligand
density. You draw the map in one colour, then increase the map line
width ever so slightly and draw it again with map cover and in a
different colour. The ligand density is then highlighted but the rest of
the structure and noise are still visible.

However, the original question seemed to be targeted at obscuring
information (the ligand structure) rather than showing it. I assume this
is not for academic purposes! My suggestion there would be to use a low
resolution map (say calculated to 3.5A) covering where the ligand is and
the full resolution map for the rest of the molecule. (Effectively
rendering the ligand density as a blob).

Otherwise Tassos is spot on... use Illustrator...
Cheers,
Robert

CCP4bb navigation

CCP4bb <-- 2007 <-- November 2007 <-- 01 November 2007
Previous message:
Subject: Postdoc position at The University of Chicago
From: Enrico Malito emalito {- at -} HUGGINS {- dot -} BSD {- dot -} UCHICAGO {- dot -} EDU
Date: 2007-11-01 		Next message:
Subject: Two post doc positions in Tromsų?
From: Elin Moe elin {- dot -} moe {- at -} CHEM {- dot -} UIT {- dot -} NO
Date: 2007-11-02


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