Re: [ccp4bb] quick question...

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CCP4bb <-- 2007 <-- May 2007 <-- 11 May 2007

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Subject: quick question... thanks
From: James Pauff pauffjm {- at -} YAHOO {- dot -} COM
Date: 2007-05-11

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Subject: Re: quick question.... .
From: "Kerr, Iain" Iain {- dot -} Kerr {- at -} STJUDE {- dot -} ORG
Date: 2007-05-11

Subject: Re: quick question...
From: Roger Rowlett RRowlett {- at -} MAIL {- dot -} COLGATE {- dot -} EDU
Date: 2007-05-11

Here are the quick directions to reading CCP4 maps into pymol and
creating nice diagrams:

1. Use fft to create a map in CCP4. (This task can be run from the Run
FFT-Create Map option undere Map & Mask Utilities) You can create a
simple map or a nFo-mFc map as you wish. Select the option to cover 'all
atoms in PDB file'. For pymol to read the map later, you will need to
add the file extension .ccp4 to the generated map. You may find this map
too coarse to make for a pretty diagram. You can generate a nicer
(albeit much larger) map by re-running fft with a tighter grid spacing.
I usually take the default values generated by FFT and double them. You
can change grid spacing under 'Infrequently Used Options'.

2. Open pymol and read in your PDB file. Create a selection about
whatever you want to see the map around. I usually display the selection
as sticks.

3. Open your map in pymol, e.g. mymap.map.ccp4 (you need the ccp4
extension)

4. To display the map around your selection (e.g., named 'site') issue a
command similar to this:
isomesh map, mymap.map.ccp4, 2.0, site, carve=1.6

This command will create a mesh object map from mymap.map.ccp4,
countoured at 2.0 sigma, around the
selection 'site', only within 1.6A of selected atoms. You can
change the contour level and carve
parameter to suit.

5. For a publication quality figure than can be labeled in GIMP or
Photoshop, I would further suggest:
* select the map object and change the color to 30% gray
* change the background to white with the command 'bg_color
white'

You should be able to generate a really nice diagram that look something
like the attached image. The operation of CCP4 or pymol is
platform-independent.

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
James Pauff
Sent: Friday, May 11, 2007 12:06 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] quick question...

Good day all,

First off, thank you all so much for your help a
couple days ago! I just have a quick question
regarding the use of CCP4 to generate density maps.
Is there a way to generate a map(s) that can be read
into PyMol? I understand that PyMol can only read CNS
or XPLOR maps, is this correct? Is there a means by
which I can output maps (on a Windows platform) in a
format that can be read by PyMol?

My only option in CCP4 is to create my FFT map in CCP4
format.

Thank you,
Jim

________________________________________________________________________
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CCP4bb <-- 2007 <-- May 2007 <-- 11 May 2007

Previous message:
Subject: quick question... thanks
From: James Pauff pauffjm {- at -} YAHOO {- dot -} COM
Date: 2007-05-11

Next message:
Subject: Re: quick question.... .
From: "Kerr, Iain" Iain {- dot -} Kerr {- at -} STJUDE {- dot -} ORG
Date: 2007-05-11