[Chimera-users] morph interpolation

[Souroprobho Chowdhury]

Hello, 

I am trying to use morph interpolate on two (for this post) PDBs (I2.pdb and I3.pdb, attached) but something peculiar is happening. The Hydrogen on the HIS 1082 (N1) does a ‘cork-screw’ like movement. Essentially, instead of interpolating directly from position A to B, it is taking a more round-about angle. A similar movement is observed for the O3 in the T1 O ligand. 

This problem has come up recurrently in my work and I am yet to find a solution. I have used most of the options that apply on morph interpolate that are mentioned on the chimera website without much improvement. 

I am using Maestro by Schrodinger to model my structures. 

Please find attached I2.pdb , I3.pdb and mov_all.pdb. mov_all.pdb is the trajectory file, works on Pymol (I am attaching a pymol script called auto-script.pml as well for selection of the correct residues, and a reasonable representation). The chimera interpolation script is also attached. 

Thanks! 

Souro 

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20170711/0db86c8b/attachment.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: I2.pdb
Type: application/octet-stream
Size: 542068 bytes
Desc: not available
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20170711/0db86c8b/attachment.obj>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20170711/0db86c8b/attachment-0001.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: I3.pdb
Type: application/octet-stream
Size: 542078 bytes
Desc: not available
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20170711/0db86c8b/attachment-0001.obj>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20170711/0db86c8b/attachment-0002.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: interpolate.com
Type: application/octet-stream
Size: 131 bytes
Desc: not available
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20170711/0db86c8b/attachment-0002.obj>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20170711/0db86c8b/attachment-0003.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: mov_all.pdb
Type: application/octet-stream
Size: 11050520 bytes
Desc: not available
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20170711/0db86c8b/attachment-0003.obj>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20170711/0db86c8b/attachment-0004.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: auto-script.pml
Type: application/octet-stream
Size: 266 bytes
Desc: not available
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20170711/0db86c8b/attachment-0004.obj>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20170711/0db86c8b/attachment-0005.html>