[Chimera-users] mmaker usage with md-movie perframe

Elaine Meng meng at cgl.ucsf.edu
Thu Nov 27 17:03:51 PST 2014

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


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 Nov 27, 2014, at 7:02 AM, Bala subramanian <bala.biophysics at 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

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