[buster-discuss] buster maps in pymol

[Marlene Grünwald]

Hi Donald and Clemens,

On Sep 28, 2011, at 8:51 AM, Clemens Vonrhein wrote:
> On Tue, Sep 27, 2011 at 04:22:16PM -0400, Donald Damian Raymond wrote:
>> I am having the same issue opening an MTZ generated by buster in the
>> latest version of PyMOL.
> 
> Can pymol now open reflection files directly? I thought it could only
> open maps ... but haven't used it for a while now.

the latest incentive PyMOL versions can, yes. But not yet the open source version.

>> It appears that the MTZ generated by buster only draws the map in
>> the unit cell when loaded in PyMOL.
> 
> ...
>> However, in many cases some of the modeled atoms are not in the unit
>> cell. See attached image.
>> 
>> It may be both a buster and PyMOL issue.
> 
> Yes, it's a map preparation issue triggered by a lack of a PyMOL
> feature.


PyMOL can show density around selections outside the unit cell as mesh representation! It has also a new "volume" representation that (as far as I know) does not yet expand outside the unit cell, but that's work in progress. If you do "Open MTZ with Defaults..." from the file menu you will get a volume representation!

So to show density around your molecule, delete or disable the "volume" object and create a "mesh" with the isomesh command.

See: http://pymolwiki.org/index.php/Isomesh

Hope that helps,

Cheers,
  Marlene

***********************************************************
Marlene Grünwald
PhD Student

Max Planck Institute for Developmental Biology
AG Bono
Spemannstrasse 35
D-72076 Tübingen
Germany

phone: +49-(0)7071-601 1449
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