May 2010 - Chimera-users - RBVI Mailing Lists

Adjust torsion and bump checking
by Kim, Sunghoon 04 May '10

04 May '10

Hi all, I would like to do the bump checking for the various rotameric states of a specific side chain generated by the rotation about dihedral angles. Bumps were detected by chimera command 'rotation' and 'findclash' and at first the script seemed working OK, but I'm not sure if the chi angles were correctly defined. When we look at the 'clashes/contacts' panel in Chimera, there are atom options for "Near" and "Far" positions in the rotating bonds. How can I specifying the 'Near' and 'Far' atoms in my 'rotation' command line in my python script to define my chi angles ? Thanks in advance for any info that you can provide. Thanks, Sunghoon Kim

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place fragment (again)
by Elisabeth Ortega 04 May '10

04 May '10

Dear all, We are trying to place a fragment in an exact position. We created a fragment with tetrahedral symmetry and we are trying to link an atom of other molecule at 2.00 A of the central atom of the new fragment and making a certain angle (120 degrees for example) with one of the substituents to get the correct orientation of the new fragment. Has anybody an idea that how can we do that? Thanks.

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about centroid
by Francesco Pietra 03 May '10

03 May '10

On running movie with centroid - as I was instructed by Eric; sorry I lost the email - I noticed that on long runs a shift is introduced between the protein and the centroid thread. To restore the relative positions between protein and centroid thread, I had to bring back (through the movie) the centroid to its initial position. francesco pietra

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rmsd between two ligands
by Miriam Gochin 01 May '10

01 May '10

Is there a way in chimera to obtain an RMSD between two structures without matching them, ie. just to know the difference between them? Miriam Gochin Touro University - CA miriam.gochin(a)tu.edu 707-638-5463

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Chimera-users May 2010