Friends, I have a crystal structure of a protein (370aa). I have a trajectory of a similar protein (not same) with (210aa). I opened the crystal structure and the trajectory via md-movie tool. In the perframe analysis, i gave the following command (#1 my traj, #0 crystal.pdb) *mmaker #1 #0 computeSS false* mmaker uses different number of atom pairs for rmsd calculation. If there are say 150aa that match between my target and crystal, then mmaker should make the rmsd firt for 150 atom pairs in every frame. Why does it use different no. of atom pairs. Do i need to give some extra options ? Thanks, Bala -- C. Balasubramanian
Hi Bala, By default there is iteration of the fit so that you get a well-matched core structure. Probably in different trajectory frames, the loops are moving around so different amounts of the protein get pruned from the final fit. However, you can use the “iterate false” option of the “mmaker” command so that it won’t do that pruning, and instead always use the whole alignment, e.g. something like: mmaker #1 #0 computeSS false iterate false <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/mmaker.html> 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 Nov 27, 2014, at 7:02 AM, Bala subramanian <bala.biophysics@gmail.com> wrote:
Friends, I have a crystal structure of a protein (370aa). I have a trajectory of a similar protein (not same) with (210aa). I opened the crystal structure and the trajectory via md-movie tool. In the perframe analysis, i gave the following command
(#1 my traj, #0 crystal.pdb) mmaker #1 #0 computeSS false
mmaker uses different number of atom pairs for rmsd calculation. If there are say 150aa that match between my target and crystal, then mmaker should make the rmsd firt for 150 atom pairs in every frame. Why does it use different no. of atom pairs. Do i need to give some extra options ? Thanks, Bala
Hi Elain, Happy new year! I would like to rotate a single mrc density map to a specific orientation and then save it with the new orientation, how can I do it in Chimera? Thanks! Zongli
Hi Zongli, Happy new year! The main issue is that the map file format doesn’t include rotation information. If you rotated your map to go with some atomic structure (PDB file), it is better to save a new PDB relative to the map instead. If you rotated your map (“map1”) to go with some other map (“map2”), you could create a new map (“map3”) by resampling map1 on the grid of map2 with the “vop resample” command. Please see “Saving Maps After Fitting” here for the details and links: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#afterfitting> I hope this helps, ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Jan 2, 2015, at 1:49 PM, Li, Zongli <Zongli_Li@hms.harvard.edu> wrote:
Hi Elain, Happy new year!
I would like to rotate a single mrc density map to a specific orientation and then save it with the new orientation, how can I do it in Chimera?
Thanks! Zongli
Thank you, Elaine! Best, Zongli ________________________________________ From: Elaine Meng [meng@cgl.ucsf.edu] Sent: Friday, January 02, 2015 5:05 PM To: Li, Zongli Cc: Mailing List Subject: saving a map after rotation Hi Zongli, Happy new year! The main issue is that the map file format doesn’t include rotation information. If you rotated your map to go with some atomic structure (PDB file), it is better to save a new PDB relative to the map instead. If you rotated your map (“map1”) to go with some other map (“map2”), you could create a new map (“map3”) by resampling map1 on the grid of map2 with the “vop resample” command. Please see “Saving Maps After Fitting” here for the details and links: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#afterfitting> I hope this helps, ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Jan 2, 2015, at 1:49 PM, Li, Zongli <Zongli_Li@hms.harvard.edu> wrote:
Hi Elain, Happy new year!
I would like to rotate a single mrc density map to a specific orientation and then save it with the new orientation, how can I do it in Chimera?
Thanks! Zongli
participants (3)
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Bala subramanian -
Elaine Meng -
Li, Zongli