Warren,
Thanks for the note. The version I had been using was version 1.0r2
(on the lab computers). My personal laptop is running 1.2b2. I'll try
there (and also upgrade to the latest-and-greatest).
Thanks for your help,
-Andy
On 9/17/2009 3:06 PM, Warren DeLano wrote:
> To Everyone:
>
> When posting such questions, please always indicate what specific vesion
> of PyMOL you are using, since the program continues to evolve with every
> release (to reflect numerous end-user suggestions, as enabled by
> contributions from our sponsors.)
>
> To Andy:
>
> PyMOL version 1.2r1 should symmetry-expand the map assuming that density
> values have been provided somewhere within the ASU. PyMOL cannot yet
> render a map straight from a reflection file.
>
> Cheers,
> Warren
>
>> -----Original Message-----
>> From: Andy Torelli [mailto:at...@cornell.edu]
>> Sent: Thursday, September 17, 2009 11:54 AM
>> To: pymol-users@lists.sourceforge.net
>> Subject: [PyMOL] Displaying electron density from maps output by Coot.
>>
>> Hi everyone,
>>
>> I have a simple problem that has come up before (4/2/2009 post),
> but
>> I
>> haven't found a solution yet.
>> Maps written out from Coot and display in Pymol seem to be
> situated
>> on
>> a different origin compared to the PDB coordinates. E.g., if I:
>> load my-structure.pdb
>> load my-map.map, map1, 1, ccp4
>> isomesh msh1,map1,1.0
>> A nice electron density map is rendered (no errors), but offset
> from
>> the my-structure.pdb coordinates (both map and coords were output from
>> Coot where they were overlaid correctly). It sometimes works to
>> explicitly indicate the residues around which to render the map:
>> isomesh msh1,map1,1.0,(chain a and resi 10),carve=3.0
>> In my current case however, an NCS-averaged map output from Coot
> is
>> not
>> displaying at the desired location. To be clear, the map can be
>> displayed elsewhere in space, but it does not overlap with my
>> coordinates (these are not symmetry-generated molecules, they're part
> of
>> the ASU). As Robert Campbell indicated in response to the earlier
> post,
>> Pymol expects maps to be calculated to cover the whole molecule of
>> interest. My question is why does this map/model pair display
> correctly
>> in Coot while Pymol shows the map offset from the model? Is there a
> way
>> to tell Pymol to place the map at a different origin (i.e. so that it
>> overlays with the coordinates)?
>>
>> I realize this may also be a Coot question, but I'm not sure of
> the
>> source of the problem yet so I'm posting here. I'll try the other bb
> if
>> necessary.
>>
>> Thanks for your help,
>> -Andy Torelli
>>
>> ===========================================
>> Andrew T. Torelli Ph.D.
>> Postdoctoral Associate
>> Department of Chemistry & Chemical Biology
>> Baker Laboratory, Cornell University
>> Ithaca, NY 14853
>> ===========================================
>>
>>
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