On Apr 13, 2016, at 9:27 AM, F.Xavier Gomis-Rüth <fxgr@ibmb.csic.es> wrote:
Dear Elaine, I am encountering problems while trying to display a fragment of a structure from a PDB file superimposed with its Fourier map. When I load the latter, it is presented displaced from the model and I cannot get it centered onto it. All other features (contouring, mesh/solid style, etc.) work fine, it's just that atoms and density do not superimpose. I've tried it with different space groups, just for the case it was a problem in a particular library, but without success. I am working on a Mac, I don´t know if there is a problem, and I am using CCP4 maps. Any suggestions would be very welcomed! Best wishes, Xavier -- <fxgr_signanew.jpg>
Dear Xavier, I don’t know where or from what program these files came frome, so it is hard to say why the coordinates don’t match up. In some cases the map file does not include information that aligns its coordinates with the corresponding atomic structure, or maybe the map file header does have this information but it is not in a format understood by Chimera. You can change the offset of the map in Chimera, if you know what it should be. After opening the map, in the Volume Viewer dialog choose Features… Coordinates, and in the resulting options you can change origin index, spacing, etc. However, I don’t know how to figure out what values are needed, if you don’t already have that information. The options are explained here: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/frame...> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volum...> It is generally recommended to send Chimera questions to chimera-users@cgl.ucsf.edu (CC’d here), especially in certain areas where others know more than I do. 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
Dear Elaine, thanks a lot for your prompt answer and sorry for not using the . The coordinates are regular PDB coordinates coming from a crystallographic refinement program such as PHENIX, BUSTER/TNT, REFMAC5, and the map file was likewise generated by these programs. It's the regular pair of coordinates and map one uses to perform subsequent model building with COOT and, in this program, everything is fine as to the matching of coordinates and map. In this case, should I really change the origin of the map? Best wishes, Xavier -------- Forwarded Message -------- Subject: Re: Density display with CHIMERA Date: Wed, 13 Apr 2016 09:52:07 -0700 From: Elaine Meng <meng@cgl.ucsf.edu> Reply-To: Chimera User Forum <chimera-users@cgl.ucsf.edu> To: fxgr@ibmb.csic.es CC: Chimera User Forum <chimera-users@cgl.ucsf.edu> On Apr 13, 2016, at 9:27 AM, F.Xavier Gomis-Rüth <fxgr@ibmb.csic.es> wrote:
Dear Elaine, I am encountering problems while trying to display a fragment of a structure from a PDB file superimposed with its Fourier map. When I load the latter, it is presented displaced from the model and I cannot get it centered onto it. All other features (contouring, mesh/solid style, etc.) work fine, it's just that atoms and density do not superimpose. I've tried it with different space groups, just for the case it was a problem in a particular library, but without success. I am working on a Mac, I don´t know if there is a problem, and I am using CCP4 maps. Any suggestions would be very welcomed! Best wishes, Xavier -- <fxgr_signanew.jpg>
Dear Xavier, I don’t know where or from what program these files came frome, so it is hard to say why the coordinates don’t match up. In some cases the map file does not include information that aligns its coordinates with the corresponding atomic structure, or maybe the map file header does have this information but it is not in a format understood by Chimera. You can change the offset of the map in Chimera, if you know what it should be. After opening the map, in the Volume Viewer dialog choose Features… Coordinates, and in the resulting options you can change origin index, spacing, etc. However, I don’t know how to figure out what values are needed, if you don’t already have that information. The options are explained here: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/frame...> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volum...> It is generally recommended to send Chimera questions to chimera-users@cgl.ucsf.edu (CC’d here), especially in certain areas where others know more than I do. 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
Hi Xavier, Chimera positions the map according to the header values in the CCP4 file. Perhaps the alignment is correct but the map does not cover the PDB model. Coot will use the crystal unit cell size to replicate the map to cover the atomic model but Chimera does not do that. You can make a new map that covers the atomic coordinates in Chimera using the “vop cover” command, for example, "vop cover #0 atombox #1” where #0 is the original map and #1 is the atomic model. If this isn’t the problem and really the atomic model does not match the density then you might try Chimera command “volume #0 dumpheader true” to get the CCP4 header values. The nrstart, ncstart, nzstart values control the map alignment and other values give the unit cell size and cell angles. Send me all those header values and maybe I’ll have an idea why Chimera and Coot give different alignment. Tom
On Apr 13, 2016, at 9:58 AM, F.Xavier Gomis-Rüth <fxgr@ibmb.csic.es> wrote:
Dear Elaine, thanks a lot for your prompt answer and sorry for not using the . The coordinates are regular PDB coordinates coming from a crystallographic refinement program such as PHENIX, BUSTER/TNT, REFMAC5, and the map file was likewise generated by these programs. It's the regular pair of coordinates and map one uses to perform subsequent model building with COOT and, in this program, everything is fine as to the matching of coordinates and map. In this case, should I really change the origin of the map? Best wishes, Xavier
-------- Forwarded Message -------- Subject: Re: Density display with CHIMERA Date: Wed, 13 Apr 2016 09:52:07 -0700 From: Elaine Meng Reply-To: Chimera User Forum <chimera-users@cgl.ucsf.edu> <mailto:chimera-users@cgl.ucsf.edu>
CC: Chimera User Forum <chimera-users@cgl.ucsf.edu> <mailto:chimera-users@cgl.ucsf.edu>
On Apr 13, 2016, at 9:27 AM, F.Xavier Gomis-Rüth wrote:
Dear Elaine, I am encountering problems while trying to display a fragment of a structure from a PDB file superimposed with its Fourier map. When I load the latter, it is presented displaced from the model and I cannot get it centered onto it. All other features (contouring, mesh/solid style, etc.) work fine, it's just that atoms and density do not superimpose. I've tried it with different space groups, just for the case it was a problem in a particular library, but without success. I am working on a Mac, I don´t know if there is a problem, and I am using CCP4 maps. Any suggestions would be very welcomed! Best wishes, Xavier -- <fxgr_signanew.jpg>
Dear Xavier, I don’t know where or from what program these files came frome, so it is hard to say why the coordinates don’t match up. In some cases the map file does not include information that aligns its coordinates with the corresponding atomic structure, or maybe the map file header does have this information but it is not in a format understood by Chimera.
You can change the offset of the map in Chimera, if you know what it should be. After opening the map, in the Volume Viewer dialog choose Features… Coordinates, and in the resulting options you can change origin index, spacing, etc. However, I don’t know how to figure out what values are needed, if you don’t already have that information. The options are explained here:
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/frame...> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/frame...> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volum...> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volum...>
It is generally recommended to send Chimera questions to chimera-users@cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu> (CC’d here), especially in certain areas where others know more than I do. 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
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Fantastic, Tom, it worked right away with the vop cover command! Thanks a lot! Best, Xavier On 13/4/16 11:12 PM, Tom Goddard wrote:
Hi Xavier,
Chimera positions the map according to the header values in the CCP4 file. Perhaps the alignment is correct but the map does not cover the PDB model. Coot will use the crystal unit cell size to replicate the map to cover the atomic model but Chimera does not do that. You can make a new map that covers the atomic coordinates in Chimera using the “vop cover” command, for example, "vop cover #0 atombox #1” where #0 is the original map and #1 is the atomic model.
If this isn’t the problem and really the atomic model does not match the density then you might try Chimera command “volume #0 dumpheader true” to get the CCP4 header values. The nrstart, ncstart, nzstart values control the map alignment and other values give the unit cell size and cell angles. Send me all those header values and maybe I’ll have an idea why Chimera and Coot give different alignment.
Tom
On Apr 13, 2016, at 9:58 AM, F.Xavier Gomis-Rüth <fxgr@ibmb.csic.es <mailto:fxgr@ibmb.csic.es>> wrote:
Dear Elaine, thanks a lot for your prompt answer and sorry for not using the . The coordinates are regular PDB coordinates coming from a crystallographic refinement program such as PHENIX, BUSTER/TNT, REFMAC5, and the map file was likewise generated by these programs. It's the regular pair of coordinates and map one uses to perform subsequent model building with COOT and, in this program, everything is fine as to the matching of coordinates and map. In this case, should I really change the origin of the map? Best wishes, Xavier
-------- Forwarded Message -------- Subject: Re: Density display with CHIMERA Date: Wed, 13 Apr 2016 09:52:07 -0700 From: Elaine Meng Reply-To: Chimera User Forum <chimera-users@cgl.ucsf.edu>
CC: Chimera User Forum <chimera-users@cgl.ucsf.edu>
On Apr 13, 2016, at 9:27 AM, F.Xavier Gomis-Rüth wrote:
Dear Elaine, I am encountering problems while trying to display a fragment of a structure from a PDB file superimposed with its Fourier map. When I load the latter, it is presented displaced from the model and I cannot get it centered onto it. All other features (contouring, mesh/solid style, etc.) work fine, it's just that atoms and density do not superimpose. I've tried it with different space groups, just for the case it was a problem in a particular library, but without success. I am working on a Mac, I don´t know if there is a problem, and I am using CCP4 maps. Any suggestions would be very welcomed! Best wishes, Xavier -- <fxgr_signanew.jpg>
Dear Xavier, I don’t know where or from what program these files came frome, so it is hard to say why the coordinates don’t match up. In some cases the map file does not include information that aligns its coordinates with the corresponding atomic structure, or maybe the map file header does have this information but it is not in a format understood by Chimera.
You can change the offset of the map in Chimera, if you know what it should be. After opening the map, in the Volume Viewer dialog choose Features… Coordinates, and in the resulting options you can change origin index, spacing, etc. However, I don’t know how to figure out what values are needed, if you don’t already have that information. The options are explained here:
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/frame...> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volum...>
It is generally recommended to send Chimera questions tochimera-users@cgl.ucsf.edu (CC’d here), especially in certain areas where others know more than I do. 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
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
--
participants (3)
-
Elaine Meng -
F.Xavier Gomis-Rüth -
Tom Goddard