I suggest you do not use Chimera 1.7 as it is from 2013. You may be hitting a bug where the specified chain order was not used. If you still have the problem, try running the commands on the specific file by hand and see what happens. Tom
On Apr 5, 2017, at 11:31 AM, Kavya Shankar wrote:
Hi,
I am trying to open the same pdb file twice and apply mm command on the chains.
The following script loops through the files in the folder so i open the same pdb twice:
#!/bin/bash
for file in `ls tmp_d2` do
chimera --nogui --silent tmp_d2/$file tmp_d2/$file tmp_d2/$file tmp_d2/$file chim.cmd > test_A.pdb mv test_A.pdb temper/$file echo "$file"
done
File "chim.cmd" has the following: mm #0:.A:.B #1:.B:.A pair ss measure rotation #0 #1
I get the following error: 1c9o_1.pdb Error while sourcing chim.cmd, line 1:
"measure rotation #0 #1"
Rotation angle is near zero (0 degrees)
I should be getting an angle of 180 degrees because they are all dimers. I have two versions of chimera on my system 1.7 and 1.11.2, does that make a difference?
Thank you.
Regards, Kavya Shankar _______________________________________________ Chimera-dev mailing list Chimera-dev@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev