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 ………………………………... Gabriel Brandt Assistant Professor Department of Chemistry Franklin & Marshall College PO Box 3003 Lancaster, PA 17604 ph: 717.358.4846 shipping address: 415 Harrisburg Ave Lancaster, PA 17603 ………………………………...
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@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
………………………………... Gabriel Brandt Assistant Professor Department of Chemistry Franklin & Marshall College PO Box 3003 Lancaster, PA 17604 ph: 717.358.4846
shipping address: 415 Harrisburg Ave Lancaster, PA 17603 ………………………………...
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Elaine & Tom - Thanks so much for your help. The vop cover command worked perfectly, which is a bit embarrassing because I know you've posted on that before. I thought there was a rotation involved, which I guess reflects rather badly on my ability to compare electron density maps to models. I was also thinking that it was a more complicated transformation, because I could see that the Coot map headers include some symmetry operators that were different from the working Phenix maps. (symop=x,y,z versus symop= ). ChimeraX opens the map but returns this error: Unable to parse symmetry operators of coot-map.ccp4 b'x, y, z Either way, vop cover solves the problem. gsb ………………………………... Gabriel Brandt Assistant Professor Department of Chemistry Franklin & Marshall College PO Box 3003 Lancaster, PA 17604 ph: 717.358.4846 shipping address: 415 Harrisburg Ave Lancaster, PA 17603 ………………………………...
Hi Gabriel, If you send me the Coot ccp4 map where Chimera cannot parse symmetry operators I will see what the problem is and if I can put in a fix. Tom
On May 22, 2018, at 6:51 PM, Gabriel Brandt <gbrandt@fandm.edu> wrote:
Elaine & Tom -
Thanks so much for your help. The vop cover command worked perfectly, which is a bit embarrassing because I know you've posted on that before.
I thought there was a rotation involved, which I guess reflects rather badly on my ability to compare electron density maps to models.
I was also thinking that it was a more complicated transformation, because I could see that the Coot map headers include some symmetry operators that were different from the working Phenix maps. (symop=x,y,z versus symop= ). ChimeraX opens the map but returns this error:
Unable to parse symmetry operators of coot-map.ccp4 b'x, y, z
Either way, vop cover solves the problem.
gsb
………………………………... Gabriel Brandt Assistant Professor Department of Chemistry Franklin & Marshall College PO Box 3003 Lancaster, PA 17604 ph: 717.358.4846
shipping address: 415 Harrisburg Ave Lancaster, PA 17603 ………………………………...
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
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@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
………………………………... Gabriel Brandt Assistant Professor Department of Chemistry Franklin & Marshall College PO Box 3003 Lancaster, PA 17604 ph: 717.358.4846
shipping address: 415 Harrisburg Ave Lancaster, PA 17603 ………………………………...
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (3)
-
Elaine Meng -
Gabriel Brandt -
Tom Goddard