Dear Chimera people, I'm trying to create a series of pdb files showing a single structure rotated around a given axis. Using the GUI I can turn the molecule and save the pdb after unclicking the "Use untransformed coordinates" box. However, when I run a script using the write command I don't know how to invoke this option. The docs on the "relative" option suggest that the default is to write transformed coordinates. I've tried the following: for i in xrange(0,90,10): rc("rock " + "y " + str(i) + " 1") fn = basefn + str(i) + '.pdb' rc("write format pdb 0 " + fn) and the files end up identical although the rotation around y does appear on the screen. I had the problem in version 1.10.2 and it remains after upgrading to 1.11. thanks for your help, Michael
Hi Michael, I was unable to reproduce this problem… I tried “turn y 90” and then "write #0 ~/Desktop/test.pdb” and it did write the transformed coordinates, and should behave the same way if run via python with rc. I guess you can doublecheck by actually typing commands (let us know if still problematic) and then make sure the same commands are used in your script. A separate issue: I see your script uses “rock” whereas you probably wanted “roll” or “turn” … note that “rock y 10 1” will not rotate 10 degrees, but perform 1 frame of a rocking oscillation that would have covered a 10 X 20 = 200-degree angle had it been allowed to perform a full cycle of 136 frames. Instead use “turn y 10” or “roll y 10 1” if you want to rotate 10 degrees around Y. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/rock.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/turn.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Dec 1, 2016, at 10:23 AM, Michael Elbaum <michael.elbaum@weizmann.ac.il> wrote:
Dear Chimera people,
I'm trying to create a series of pdb files showing a single structure rotated around a given axis. Using the GUI I can turn the molecule and save the pdb after unclicking the "Use untransformed coordinates" box. However, when I run a script using the write command I don't know how to invoke this option. The docs on the "relative" option suggest that the default is to write transformed coordinates.
I've tried the following: for i in xrange(0,90,10): rc("rock " + "y " + str(i) + " 1") fn = basefn + str(i) + '.pdb' rc("write format pdb 0 " + fn) and the files end up identical although the rotation around y does appear on the screen. I had the problem in version 1.10.2 and it remains after upgrading to 1.11.
thanks for your help, Michael
Elaine’s response caused me to realize the other problem with your script — you are going to need to add “; wait” to the end of any rock/roll/turn command you use. Otherwise the script will keep going without any frames being drawn, which also means that no motion from the rock/roll/turn will have occurred, and therefore the coordinates will be unchanged when the script reaches your “write” command. —Eric Eric Pettersen UCSF Computer Graphics Lab
On Dec 1, 2016, at 1:04 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Michael, I was unable to reproduce this problem… I tried “turn y 90” and then "write #0 ~/Desktop/test.pdb” and it did write the transformed coordinates, and should behave the same way if run via python with rc. I guess you can doublecheck by actually typing commands (let us know if still problematic) and then make sure the same commands are used in your script.
A separate issue: I see your script uses “rock” whereas you probably wanted “roll” or “turn” … note that “rock y 10 1” will not rotate 10 degrees, but perform 1 frame of a rocking oscillation that would have covered a 10 X 20 = 200-degree angle had it been allowed to perform a full cycle of 136 frames. Instead use “turn y 10” or “roll y 10 1” if you want to rotate 10 degrees around Y.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/rock.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/turn.html>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Dec 1, 2016, at 10:23 AM, Michael Elbaum <michael.elbaum@weizmann.ac.il> wrote:
Dear Chimera people,
I'm trying to create a series of pdb files showing a single structure rotated around a given axis. Using the GUI I can turn the molecule and save the pdb after unclicking the "Use untransformed coordinates" box. However, when I run a script using the write command I don't know how to invoke this option. The docs on the "relative" option suggest that the default is to write transformed coordinates.
I've tried the following: for i in xrange(0,90,10): rc("rock " + "y " + str(i) + " 1") fn = basefn + str(i) + '.pdb' rc("write format pdb 0 " + fn) and the files end up identical although the rotation around y does appear on the screen. I had the problem in version 1.10.2 and it remains after upgrading to 1.11.
thanks for your help, Michael
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Thanks Elaine and Erik! I changed to turn but the wait step was the key. It seems the writing got out of sync with the transform otherwise. working now :-) regards, Michael ________________________________ From: Eric Pettersen [pett@cgl.ucsf.edu] Sent: Thursday, December 01, 2016 23:12 To: chimera-users@cgl.ucsf.edu BB Cc: Michael Elbaum Subject: Re: [Chimera-users] saving pdb with transformed coordinates Elaine’s response caused me to realize the other problem with your script — you are going to need to add “; wait” to the end of any rock/roll/turn command you use. Otherwise the script will keep going without any frames being drawn, which also means that no motion from the rock/roll/turn will have occurred, and therefore the coordinates will be unchanged when the script reaches your “write” command. —Eric Eric Pettersen UCSF Computer Graphics Lab On Dec 1, 2016, at 1:04 PM, Elaine Meng <meng@cgl.ucsf.edu<mailto:meng@cgl.ucsf.edu>> wrote: Hi Michael, I was unable to reproduce this problem… I tried “turn y 90” and then "write #0 ~/Desktop/test.pdb” and it did write the transformed coordinates, and should behave the same way if run via python with rc. I guess you can doublecheck by actually typing commands (let us know if still problematic) and then make sure the same commands are used in your script. A separate issue: I see your script uses “rock” whereas you probably wanted “roll” or “turn” … note that “rock y 10 1” will not rotate 10 degrees, but perform 1 frame of a rocking oscillation that would have covered a 10 X 20 = 200-degree angle had it been allowed to perform a full cycle of 136 frames. Instead use “turn y 10” or “roll y 10 1” if you want to rotate 10 degrees around Y. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/rock.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/turn.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Dec 1, 2016, at 10:23 AM, Michael Elbaum <michael.elbaum@weizmann.ac.il<mailto:michael.elbaum@weizmann.ac.il>> wrote: Dear Chimera people, I'm trying to create a series of pdb files showing a single structure rotated around a given axis. Using the GUI I can turn the molecule and save the pdb after unclicking the "Use untransformed coordinates" box. However, when I run a script using the write command I don't know how to invoke this option. The docs on the "relative" option suggest that the default is to write transformed coordinates. I've tried the following: for i in xrange(0,90,10): rc("rock " + "y " + str(i) + " 1") fn = basefn + str(i) + '.pdb' rc("write format pdb 0 " + fn) and the files end up identical although the rotation around y does appear on the screen. I had the problem in version 1.10.2 and it remains after upgrading to 1.11. thanks for your help, Michael _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu<mailto:Chimera-users@cgl.ucsf.edu> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (3)
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Elaine Meng -
Eric Pettersen -
Michael Elbaum