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
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
Hi Kavya, (1) this is exactly the same problem you had before when trying to follow my example, and we had already solved it by figuring out you had to use the newer Chimera!! The emails are shown below. Please do not keep asking the same question. (2) If you want to ask questions you should put some useful information in the email subject line. “no subject” is not useful. Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
From: Kavya Shankar <kavshank@umail.iu.edu> Subject: Re: Chimera comparing homodimer with flipped homodimer Date: March 31, 2017 at 7:47:52 AM PDT To: Elaine Meng <meng@cgl.ucsf.edu>
Hi,
Ya I was testing it on 1.7. It works on 1.11. Thank you so much, you have been a great help!
Thank you.
Regards, Kavya Shankar
On Fri, Mar 31, 2017 at 10:39 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote: Hi Kavya, Your “mm” command matched A to A and B to B, so there was no rotation between the two copies. It was hard to see if you entered exactly the same “mm” command as in my example (needs to be exactly the same, with colon : dot . and no extra spaces), but it you did, maybe you are using an old version of Chimera that interpreted the command differently. I only started Chimera and entered those 5 exact commands to get the result I showed. Tested in Chimera version 1.11.2 and recent 1.12 daily build. Elaine
On Apr 5, 2017, at 11:31 AM, Kavya Shankar <kavshank@umail.iu.edu> 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
participants (3)
-
Elaine Meng -
Kavya Shankar -
Tom Goddard