[Chimera-users] coot/chimera model-map misalignment

[Elaine Meng]

Hi Gabriel,
Map formats don’t include rotation information, at least not in a standardized way (maybe Coot writes information that it can read but Chimera doesn’t?)  but other possibilities are that just the origin is “off”  or that the map is just not covering the atoms due to the repeating nature of the unit cell.

The last one can be remedied by “vop cover”
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#cover>

Map origin can be changed in the Volume Viewer dialog or with the “volume” command
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html#dimensions>

Then there is (re)fitting the PDB to the map and then saving the PDB in that fit position, although I can understand it’s not ideal.  However, there is no way to save the map to a file in a different orientation without resampling it as described here under “saving maps after fitting”
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#afterfitting>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On May 22, 2018, at 10:38 AM, Gabriel Brandt <gbrandt at fandm.edu> wrote:
> 
> 
> Hi. I've always been able to work around this problem, but I do often have to work around it, so I was wondering whether there's an easier way.
> 
> Let's say I open a PDB file in Coot and export the map that it generates from the mtz file.
> 
> If I attempt to open this ccp4-formatted map in Chimera, the coordinates appear to transformed so that the model and map are wildly misaligned in space.
> 
> Normally, I work around this problem by using the map-generating feature in Phenix, which generates a model and map that align in Chimera. 
> 
> However, in this case, I'm trying to compare the maps that Coot generates on the fly to the those produced by Phenix, so it would be nice to be able to export a map from Coot and open it in Chimera.
> 
> Thanks very much.
> 
> gsb
> 
>  
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