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

[Tom Goddard]

Hi Gabriel,

 Coot automatically extends a map by crystal symmetry to cover the atomic model.  Chimera does not do that.  When you say the Coot exported map is misaligned and far from the PDB model, I’d guess the map position is correct only it has to be extended by crystal symmetry to cover the PDB model.  This can be done with the Chimera “vop cover” command, for instance,

	vop cover #1 atom #0

where #1 is the map and #0 is the PDB model.  Here are the vop cover docs

	https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#cover <https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#cover>

You can then save the map using Volume Viewer menu File / Save Map As… so you have a copy that covers the PDB without needing to use crystal symmetry, or the command

	volume #2 save mymap.mrc

  Tom


> 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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