[phenixbb] Grid size in max_entropy maps

Schubert, Carsten [JRDUS] CSCHUBER at its.jnj.com
Fri May 17 08:34:45 PDT 2013

Hi Pavel,

Thanks for the background info and implementing the utility. Looks like the map option would be best way to go.  These big maps just represent a usability problem; on a large unit cell coot slows down considerably even on a powerful workstation.



-----Original Message-----
From: phenixbb-bounces at phenix-online.org [mailto:phenixbb-bounces at phenix-online.org] On Behalf Of Pavel Afonine
Sent: Thursday, May 16, 2013 6:29 PM
To: phenixbb at phenix-online.org
Subject: Re: [phenixbb] Grid size in max_entropy maps

Hi Carsten,

Fourier map coefficients calculated from MEM map typically extend to high resolutions (d_min) ~0.2-0.7A or so:

Since map gridding is d_min/4 that in turn means you get very fine sampling. Cutting back resolution essentially means invalidating MEM results. phenix.maximum_entropy_map outputs MTZ file with two sets of map coefficients, original and MEM, so if you load them into Coot you will get both maps sampled at the same grid so at least visually they are comparable, and therefore sampling should not be a problem.

Alternatively, I can add an option to phenix.maximum_entropy_map so it outputs actual MEM map (in CCP4 binary format or in X-plor format). Then it will have d_min/4 sampling, where d_min is the resolution on input data set.


On 5/16/13 11:09 AM, Schubert, Carsten [JRDUS] wrote:
> Is there a way to control the grid size in the maximum entropy maps? The current grid size is quite small, resulting in a very fine mesh.
> Thanks
> 	Carsten

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