Fitting pdb model into difference map
I generated an Fo-Fc difference map using CCP4i and was able to superimpose the PDB model structure onto the map in Coot but I am unable to do so with Chimera. The model and map are offset/rotated away from each other and I have not been able to fit the model into the map with Volume Viewer --> Tools --> Fit in Map. Please let me know how I can get around this issue. Thank you. CE
When you open your Fo-Fc map and the PDB model in Coot they automatically align right? They should also automatically align in Chimera provided you read the map in with the right file type (CCP4, file suffix .ccp4 or .map). If you read the map in as MRC format then you might get misalignment because that will use a different header value in the map file for the origin used for electron microscopy data. The Chimera Fit in Map tool isn’t going to correctly fit a molecule in an Fo-Fc difference map since that map shows the errors (amplitudes observed in x-ray experiment minus amplitudes calculated for the current best guess at the atomic model). Chimera has no tools for fitting using a difference map that represents the errors in a fit. Tom
On Apr 6, 2015, at 1:48 PM, Chinaza Egbuta wrote:
I generated an Fo-Fc difference map using CCP4i and was able to superimpose the PDB model structure onto the map in Coot but I am unable to do so with Chimera. The model and map are offset/rotated away from each other and I have not been able to fit the model into the map with Volume Viewer --> Tools --> Fit in Map. Please let me know how I can get around this issue.
Thank you.
CE
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Hello CE, It may be the problem discussed earlier of differences between the two programs in handling the map origin, see: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2015-February/010736.html> So it may be a matter of changing the origin index in Chimera as described in that post. However, if you are starting from scratch to do the fitting in Chimera, note that the "Fit in Map" GUI does only a local optimization and you would have to place the structure in a reasonable starting location. If it is very far away, nothing will happen. So you could try either manually moving the structure to a reasonable starting position... <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/mouse.html#activedef> … and/or using the "fitmap" command, which has some global search options. <http://www.rbvi.ucsf.edu/home/meng/docs/UsersGuide/midas/fitmap.html> <http://www.rbvi.ucsf.edu/home/meng/docs/UsersGuide/midas/fitmap.html#global> I'd probably try the manual way first. I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Apr 6, 2015, at 1:48 PM, Chinaza Egbuta <egbutac@upstate.edu> wrote:
I generated an Fo-Fc difference map using CCP4i and was able to superimpose the PDB model structure onto the map in Coot but I am unable to do so with Chimera. The model and map are offset/rotated away from each other and I have not been able to fit the model into the map with Volume Viewer --> Tools --> Fit in Map. Please let me know how I can get around this issue.
Thank you.
CE
Hi CE, Thanks for sending me your map and PDB model — they are correctly aligned. The problem is that the map doesn’t cover the atomic model because the map contains only 1/6 of the full unit cell, and there are 6 crystallographic symmetry operators to extend the map to the full unit cell. Coot knows how to extend the map using the crystallographic symmetry operators but Chimera does not. To make the map overlap with the atomic model in Chimera you will need to compute a full unit cell map using other software. Tom
On Apr 6, 2015, at 1:48 PM, Chinaza Egbuta wrote:
I generated an Fo-Fc difference map using CCP4i and was able to superimpose the PDB model structure onto the map in Coot but I am unable to do so with Chimera. The model and map are offset/rotated away from each other and I have not been able to fit the model into the map with Volume Viewer --> Tools --> Fit in Map. Please let me know how I can get around this issue.
Thank you.
CE
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Actually Chimera can extend your difference map to cover the unit cell with this Chimera command vop cover #0 ibox 0,0,0,156,156,132 where #0 is your difference map. The “vop cover” command extends a map by symmetry and the 0,0,0,156,156,132 argument is the grid indices to cover extending your map which is of size 156,156,23 to cover a full unit cell. I didn’t think this would work, but in fact Chimera read the crystal symmetry operators from the CCP4 map file and it worked on the map you sent me. http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/vop.html#cover Tom
On Apr 13, 2015, at 4:45 PM, Tom Goddard wrote:
Hi CE,
Thanks for sending me your map and PDB model — they are correctly aligned. The problem is that the map doesn’t cover the atomic model because the map contains only 1/6 of the full unit cell, and there are 6 crystallographic symmetry operators to extend the map to the full unit cell. Coot knows how to extend the map using the crystallographic symmetry operators but Chimera does not. To make the map overlap with the atomic model in Chimera you will need to compute a full unit cell map using other software.
Tom
On Apr 6, 2015, at 1:48 PM, Chinaza Egbuta wrote:
I generated an Fo-Fc difference map using CCP4i and was able to superimpose the PDB model structure onto the map in Coot but I am unable to do so with Chimera. The model and map are offset/rotated away from each other and I have not been able to fit the model into the map with Volume Viewer --> Tools --> Fit in Map. Please let me know how I can get around this issue.
Thank you.
CE
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participants (3)
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Chinaza Egbuta -
Elaine Meng -
Tom Goddard