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From: Lisa Perez (mouse_at_mail.chem.tamu.edu)
Date: Tue Dec 21 2010 - 13:30:33 CST

I am trying to rmsd a small molecule against a small protein using a subset of 4 atoms and am getting odd results. If I remove all of the 4 atoms of interest from the pdb files and proceed with the rmsd fit, I get expected results but, if the other atoms are present, I get poor results. Here is the small script that I am using to rmsd my 2 molecules (molid 0 is my small molecule and molid 1 is my small protein):

 set ref_frame [ atomselect 1 "serial 163 164 141 142" ]
 set other_frame [ atomselect 0 "serial 13 29 6 16" ]
 set trans_matrix [measure fit $other_frame $ref_frame]
 set move_sel [atomselect 0 "all"]
 $move_sel move $trans_matrix
 set rmsdval [measure rmsd $other_frame $ref_frame]
 puts $rmsdval
 
I have also tried using index instead of serial number. 1 atom overlays perfectly... more than 1 does not.

Any comments and/or help would be greatly appreciated.

Sincerely,

Lisa M. Pérez, Ph.D.

Texas A&M University
Laboratory for Molecular Simulation, Manager
Graduate Faculty
http://lms.chem.tamu.edu/

Department of Chemistry
580 Ross Street
College Station, TX 77842

Chemistry Bldg. RM. 2109
Ofc: (979) 845-9384
Fax: (979) 845-2971