Re: [ccp4bb] map display in pymol

- Protein crystallography

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

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Subject: Re: Offtopic - In vitro protein interaction analysis using Diazirine crosslinkers.
From: Artem Evdokimov artem {- at -} XTALS {- dot -} ORG
Date: 2009-11-04

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From: Ajit Datta adatta4 {- at -} JHMI {- dot -} EDU
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Subject: Re: map display in pymol
From: James Stroud xtald00d {- at -} GMAIL {- dot -} COM
Date: 2009-11-05

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.

CCP4bb navigation

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

Previous message:
Subject: Re: Offtopic - In vitro protein interaction analysis using Diazirine crosslinkers.
From: Artem Evdokimov artem {- at -} XTALS {- dot -} ORG
Date: 2009-11-04

Next message:
Subject: Re: Zalman monitor on Linux and Coot
From: Ajit Datta adatta4 {- at -} JHMI {- dot -} EDU
Date: 2009-11-05