[Chimera-users] chimera/coot coordinates way off

Greg Pintilie gregdp at gmail.com
Wed Apr 29 09:10:21 PDT 2020

Hi Jesse,

In my experience this discrepancy has to do with Coot not using the same ‘origin’ of the map the same way that Chimera does. 

In Chimera, Volume Viewer, if you open the ‘Coordinates’ panel from the Features, take a look at the ‘Origin index’. If this is not 0, then it’s likely that when you open the same map and model in Coot, they won’t align the way they do in Chimera. 

One way to make the alignment the same is to set the origin to 0 in Chimera. Then fit the model again to this map, save it, and open the new model and map in Coot; they should now align.

If you are working with multiple maps and sub-maps, the above may not always be convenient. In this case, what I usually do is to subtract the origin of the map from each atom coordinate in the model, and save this as a new model. Then open the map and newly saved model in Coot, they should again align. 

I have a script to do this quickly which is a bit cumbersome to run but does the job - maybe the Chimera team may have advice here, I get the feeling this could be a quick command on the command line; otherwise I’m happy to send it out. The problem is then if you open the model after saving it in coot, it won’t align to the map in Chimera (unless you’ve saved this map with 0 origin and are now using this map). To make them align I usually use Matchmaker to do it quickly, i.e. match the new Coot model to the model with the original coordinates.

While the above is a bit ad-hoc, I would myself love to know exactly which origin Coot uses, if at all, and which one Chimera uses in different cases. The MRC file format allows for two ways to specify an ‘origin’:
https://www.ccpem.ac.uk/mrc_format/mrc2014.php <https://www.ccpem.ac.uk/mrc_format/mrc2014.php>

There are NX/Y/ZSTART and ORIGIN fields. Perhaps it may be possible to convert between one and the other so that we can still use some type of origin that translates between the two, though given that one is integer and one is float I’m not sure if that would be possible.


> On Apr 28, 2020, at 8:04 PM, Jesse M. Hansen <jhansen6 at uw.edu> wrote:
> Hi all
> I am building a model in coot after aligning that model to my map in chimera.  However when I open the PDB and map in coot I notice the two are not at all aligned. 
> I have tried:
> Open the map and pdb in chimera.  Fit the pdb into map. Save PDB.      
> Open map/pdb in chimera (pdb fits map on load).  Center map in box ("center" button in vol viewer").  Save map w/ new name.  Fit PDB into map.  Save PDB.  Re-open and confirm that pdb fits map on load and that map is centered in box.
> Opening PDB first in coot then MRC.   Then vice versa.
> Opening a "good" similar map and pdb in chimera that DO open together correctly in coot.   Open my "bad" map which does not align.  Fit the "bad" map into the "good" map and do vop resample.   Save the map.  Open it to confirm pdb fits map on load.  
> Open map/pdb in chimera (pdb fits map on load).  Use "vop cover ..." and save the output (reduced) map.  
> I really feel like I've tried a lot and am baffled as to why I can't get the pdb and mrc to load on the same coordinate system, despite having tens of other similar maps and PDBs that work just fine.
> Thanks in advance
> Jesse
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