Re: [ccp4bb] map display in pymol

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

Previous message:
Subject: Programmer for NE-CAT/APS
From: Leslie Kinsland lk65 {- at -} CORNELL {- dot -} EDU
Date: 2009-11-05

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From: Axel Brunger brunger {- at -} STANFORD {- dot -} EDU
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Subject: Re: map display in pymol
From: Raja Dey deyraja1 {- at -} YAHOO {- dot -} CO {- dot -} IN
Date: 2009-11-05

No, this is not a symmetry related part. This residue is within the AU and the map ctreated using the pdb (AU) not containing that residue. I have no idea what could be the reason when I can create the mesh at that residue using 2Fo-Fc map, but not with Fo-Fc map using PYMOL. Both maps are created using phenix. This is not an issue with that particular residue, but about to display Fo-Fc map in PYMOL. In COOT I used _map_coeffs.mtz file to display Fo-Fc map, wheres in PYMOL I used mFo-DFc.map (.xplor needs to append to display the map in PYMOL). I checked the density can also be seen using mFo-DFc.map file in COOT.

Raja

________________________________
From: James Stroud
To: CCP4BB@JISCMAIL.AC.UK
Sent: Wed, 4 November, 2009 10:17:26 PM
Subject: Re: [ccp4bb] map display in pymol

Are you sure that your model does not extend into a region related by symmetry but not covered by the map. Perhaps someone else knows better, but my recollection is that pymol does not automatically apply symmetry. The attached file is a perl script I wrote that makes sure your map covers your pdb file, etc.

You need to have mapman, perl, and ccp4 all in your path. Get a unix guru to help you if it isn't immediately obvious.

perl mapreg -h

will get help info included below. Please read the help if you decide to use the program.

James

**************************************************
*** mapreg version 0.02
*** output a region of a cns map
*** copyright James C. Stroud, 2008
*** distributed under the GNU Public License
**************************************************
Usage: mapreg [-h] [-c weight] [-b border] [-s symm] [-t type]
[-x 'a b c alpha beta gamma'] mapfile
[x1 y1 z1 x2 y2 z2
ASU
CELL
pdbfile ]

Flags: -h print this help
-b border define a border if using a pdb file to define region
default is 5 (5 Angstroms)
-c weight culls according to a weighting factor between 0 and 1
-x cell the sides and angles *must* be in single quotes
-s symm usually symmetry number is needed (ispcgr number)
-t type type of input map - default is cns
-o outfile name of output file (name generated if not supplied)

Description: Mapreg takes a cns map as input and outputs a new
region of the map as specified at the command line.

The possible region specifiers are:
x1 y1 z1 x2 y2 z2 : the region defined by the two grid unit or
fractional coordinate points (x1,y1,z1) and (x2,y2,z2)
'ASU' : the CCP4 default asymmetric unit
'CELL' : the whole unit cell
pdbfile : a pdb file defining the limits of the region
if border is defined, then this will be the border
in Angstroms around pdbfile to define the region
If the region specifier is left out, then mapreg will
output the whole unit cell.

CULLING
=======
If a culling factor is supplied and a pdb file is used
for trimming, then culling will be attempted.

Culling trims the map to the the atoms of the pdb file
if supplied. Without the pdb file, the program terminates
with an error if a culling factor is supplied.

The culling weighting factor is, for all practical purposes,
arbitrary. Play with it to get the desired results.
Start with 0.1 and go up (tighter) or down (less tight).
Make sure you are aware of the caveats of culling
before you use this to make figures for publication.

On Nov 4, 2009, at 3:20 PM, Raja Dey wrote:

> Dear Friends,
> I can create a mesh in pymol as follows:
> isomesh 2ffmesh, nov42_001_2mFo-DFc.map, 2.5, sele, carve=1.6, where the 'sele' is a particular residue and the map is created ommiting that residue from the pdb.
> But, I can't create the mesh in pymol when I am using Fo-Fc map as follows:
> isomesh ffmesh, nov42_001_mFo-DFc.map, 2.5, sele, carve=1.6
>
> I can see both 2ff and ff maps at that residue in coot.
>
> I shall be grateful if someone can help me to solve this problem.
> Thanks...
>
> Raja
>
>
> Yahoo! India has a new look. Take a sneak peek.

Yahoo! India has a new look. Take a sneak peek http://in.yahoo.com/trynew

CCP4bb navigation

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

Previous message:
Subject: Programmer for NE-CAT/APS
From: Leslie Kinsland lk65 {- at -} CORNELL {- dot -} EDU
Date: 2009-11-05

Next message:
Subject: Warren DeLano
From: Axel Brunger brunger {- at -} STANFORD {- dot -} EDU
Date: 2009-11-05