Could someone please help with this. . Using Chimera, I am trying to calculate rmsd between an observed ligand versus GOLD docked ligand, however the problem is the ligands load into different reading frames. The format for both ligands is .mol2. How can I correct this problem, in other words load both ligands into the same reading frame so that I can then calculate their rmsd. Thanks. Mark
Dear Mark, The structures should automatically be in the same coordinate system (i.e. all the transformations applied by rotating and scaling interactively will apply to all open models, or if you haven't manipulated anything, they will both be in shown in their untransformed coordinates). The only thing I can think of is that during preparation for GOLD docking, some transformation was applied to the system, resulting in its differing from the original coordinates of the system. You could try comparing the original receptor coordinates with the receptor in its prepared state to check for that. If you don't think anything like that happened, it would be great if you could supply two example files and tell us why/how you can tell that they are not in a consistent coordinate system when displayed in Chimera. You could send the info just to me (and I'd share it only with the Chimera development team) if you'd like. When/if the structures are in the same frame of reference, you would then use the command "rmsd" to calculate the RMSD without performing fitting. Manual page for rmsd: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/rmsd.html Best, Elaine On Jun 9, 2006, at 4:26 PM, markcunningham wrote:
Could someone please help with this. .
Using Chimera, I am trying to calculate rmsd between an observed ligand versus GOLD docked ligand, however the problem is the ligands load into different reading frames. The format for both ligands is .mol2. How can I correct this problem, in other words load both ligands into the same reading frame so that I can then calculate their rmsd.
Thanks. Mark _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html
To supplement Elaine's reply a little, if the problem is that the receptors' coordinates differ, you can use the "match" command to superimpose them. So for example if the receptor is composed of residues 1-200 and the two copies are open in models 0 and 1, then "match #0:1-200 #1:1-200" should superimpose them. --Eric On Jun 10, 2006, at 11:26 AM, Elaine Meng wrote:
Dear Mark, The structures should automatically be in the same coordinate system (i.e. all the transformations applied by rotating and scaling interactively will apply to all open models, or if you haven't manipulated anything, they will both be in shown in their untransformed coordinates).
The only thing I can think of is that during preparation for GOLD docking, some transformation was applied to the system, resulting in its differing from the original coordinates of the system. You could try comparing the original receptor coordinates with the receptor in its prepared state to check for that.
If you don't think anything like that happened, it would be great if you could supply two example files and tell us why/how you can tell that they are not in a consistent coordinate system when displayed in Chimera. You could send the info just to me (and I'd share it only with the Chimera development team) if you'd like.
When/if the structures are in the same frame of reference, you would then use the command "rmsd" to calculate the RMSD without performing fitting. Manual page for rmsd: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/rmsd.html
Best, Elaine
On Jun 9, 2006, at 4:26 PM, markcunningham wrote:
Could someone please help with this. .
Using Chimera, I am trying to calculate rmsd between an observed ligand versus GOLD docked ligand, however the problem is the ligands load into different reading frames. The format for both ligands is .mol2. How can I correct this problem, in other words load both ligands into the same reading frame so that I can then calculate their rmsd.
Thanks. Mark _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (3)
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Elaine Meng -
Eric Pettersen -
markcunningham