[chimera-dev] Measure dimer symmetry axis

[Tom Goddard]

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
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