Hi Saif,

I checked the same file in PyMOL and Coot.  You're right, there are
some differences at the boundaries, but they still look insignificant.
 Maybe you can point out a residue with a large deviation.  For this
map, Coot shows large blocks of red/green mesh indicating differences
in the observed and calculated densities.  The resolution of that map
is 3.0 Ang.  So, I'm not surprised to see slight variations in the
mesh due to algorithmic differences, especially at that resolution
near boundaries.

Cheers,

-- Jason

On Wed, Oct 27, 2010 at 2:29 PM, S. Saif Hasan <ssha...@purdue.edu> wrote:
> Hello,
>
> The structure is PDB2E74 and I downloaded the 2Fo-Fc and Fo-Fc maps in the 
> CCP4
> format from the EDS website (http://eds.bmc.uu.se/eds/) and named the former 
> map
> 2e74a.
>
> Once I open the 2e74.pdb file (downloaded from the PDB) and the 2Fo-Fc map in
> PyMol, I selected the lipid (OPC, part of chain H) and used this command in
> PyMol-  "isomesh msh1, 2e74a, 2.0, sele, carve=2"
>
> Thanks.
>
> --
> S. Saif Hasan
>
> Graduate Student
> Department of Biological Sciences
> Hockmeyer Hall of Structural Biology
> Purdue University
> 240 S. Martin Jischke Drive
> West Lafayette, IN 47907
>
>
>
> Quoting Jason Vertrees <jason.vertr...@schrodinger.com>:
>
>> Hi Saif,
>>
>> Can you please show us the commands you used in PyMOL to load the data
>> and generate the map?  (Also, can you send me a copy of the map and
>> structure?)  Has anyone else seen this problem?
>>
>> I've looked over a few CCP4 maps in PyMOL, Maestro, and Coot
>> side-by-side, and at various contours, they all look virtually
>> identical.  There are slight differences, probably due to algorithmic
>> deviations, but they look good to me.
>>
>> In PyMOL:
>> # mimic Coot
>> set orthoscopic
>> set line_width, 5
>>
>> # get the data
>> fetch 1cll, async=0
>> fetch 1cll, type=2fofc, async=0
>>
>> # create the map; carve 2.5 Ang from the polymer
>> isomesh 1cll_map,1cll_2fofc, 1.06, poly, carve=2.5
>>
>> # find example residue
>> orient i. 78
>>
>> # color
>> color magenta, e. N
>> color tv_yellow, e. C
>>
>>
>> In Coot:
>>   * Fetch 1CLL and its map from EDS
>>   * zoom to residue 78
>>   * scroll to 1.06 sigma
>>
>> What do you see here?
>>
>> Cheers,
>>
>> -- Jason
>>
>>
>> On Tue, Oct 26, 2010 at 9:50 AM, S. Saif Hasan <ssha...@purdue.edu> wrote:
>> > Hello,
>> >
>> > I am trying to carve a 2Fo-Fc map around a lipid molecule. The electron
>> density
>> > at 2 sigma is much smaller in PyMol than in Coot (the map at 1 sigma in
>> PyMol
>> > is similar to the 2 sigma level map in Coot). I used the "unset
>> > normalize_ccp4_maps" command but that stops the carved map from being
>> > generated. What should I do to solve this problem ?
>> >
>> > Thank you.
>> > --
>> > Saif Hasan
>> >
>> >
>> >
>> >
>> ------------------------------------------------------------------------------
>> > Nokia and AT&T present the 2010 Calling All Innovators-North America
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>> > _______________________________________________
>> > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
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>>
>>
>>
>> --
>> Jason Vertrees, PhD
>> PyMOL Product Manager
>> Schrodinger, LLC
>>
>> (e) jason.vertr...@schrodinger.com
>> (o) +1 (603) 374-7120
>>
>



-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

(e) jason.vertr...@schrodinger.com
(o) +1 (603) 374-7120

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