Hi all, I'm a new Chimera user. I'm performing some molecular dynamics with a more or less simple system with Amber,and now that I have them done, I would like to analyze some specific data,like changes in a dihedral angle during the dynamic process, or distances between pairs of atoms. If I select several dihedral angles in Chimera and I play the dynamic movie, I can see these changes, but is it possible to get a table of results that shows the value of this angle for each step of the dynamic process? Thank you every body! Eduardo
On Apr 12, 2010, at 9:12 AM, eduardo.troche@uvigo.es wrote:
Hi all,
I'm a new Chimera user. I'm performing some molecular dynamics with a more or less simple system with Amber,and now that I have them done, I would like to analyze some specific data,like changes in a dihedral angle during the dynamic process, or distances between pairs of atoms. If I select several dihedral angles in Chimera and I play the dynamic movie, I can see these changes, but is it possible to get a table of results that shows the value of this angle for each step of the dynamic process?
Hi Eduardo, You can get this information by defining some actions to perform at each frame. To do this use MD Movie's Per Frame->Define Script... menu item. This will bring up a dialog that allows you to define Chimera commands or Python code to execute at each frame (controlled with the "Interpret script as..." menu at the top of the per-frame dialog). The Chimera command "angle" can be used to report dihedrals to the reply log, so something like: angle #0:5@o4',c1',n9,c4 would report the specified dihedral angle to the reply log. Something similar can be done with the "distance" command but it's a little trickier since the distance command sets up a distance monitor and it won't let you set up a duplicate monitor, so you need to clear existing distance monitors first (with "~dist"). So something like this: ~dist all dist #0:6@o4',h8 would report the given distance to the reply log. If you are reporting many distances/angles you might consider using the "echo" command to insert additional text into the reply log to help you keep track of things. Also, you can use the "help" command (e.g. "help echo") to get more info on any command. I hope this helps. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
Hi all,
my reply is not really related but similar.
I work with NMR data and often we need list of distances or dihedral
angles for the whole molecule, like distances between a NH protons and
the rest of the molecule, or list of the chi1 dihedral angles. It
seems that at present there is no way to get this. Scripts are possible?
Thanks,
Marco
Def. Quota "Eric Pettersen"
On Apr 12, 2010, at 9:12 AM, eduardo.troche@uvigo.es wrote:
Hi all,
I'm a new Chimera user. I'm performing some molecular dynamics with a more or less simple system with Amber,and now that I have them done, I would like to analyze some specific data,like changes in a dihedral angle during the dynamic process, or distances between pairs of atoms. If I select several dihedral angles in Chimera and I play the dynamic movie, I can see these changes, but is it possible to get a table of results that shows the value of this angle for each step of the dynamic process?
Hi Eduardo, You can get this information by defining some actions to perform at each frame. To do this use MD Movie's Per Frame->Define Script... menu item. This will bring up a dialog that allows you to define Chimera commands or Python code to execute at each frame (controlled with the "Interpret script as..." menu at the top of the per-frame dialog). The Chimera command "angle" can be used to report dihedrals to the reply log, so something like:
angle #0:5@o4',c1',n9,c4
would report the specified dihedral angle to the reply log. Something similar can be done with the "distance" command but it's a little trickier since the distance command sets up a distance monitor and it won't let you set up a duplicate monitor, so you need to clear existing distance monitors first (with "~dist"). So something like this:
~dist all dist #0:6@o4',h8
would report the given distance to the reply log. If you are reporting many distances/angles you might consider using the "echo" command to insert additional text into the reply log to help you keep track of things. Also, you can use the "help" command (e.g. "help echo") to get more info on any command. I hope this helps.
--Eric
Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
Dr.Marco Sette, Ph.D. Department of Chemical Sciences and Technology University of Rome, "Tor Vergata" via della Ricerca Scientifica, 00133, Rome, Italy e-mail: sette@uniroma2.it e-mail: m77it@yahoo.it Tel.: +39-0672594424 Fax: +39-0672594328 ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program.
Hi Marco, (a) distances. If you have Chimera 1.5 (daily build) you can use the findclash command to find all distances between two sets of atoms. The two sets can contain the same or different atoms. For example, you could find all distances among NH protons or between NH protons and other protons. See these previous replies: <http://www.cgl.ucsf.edu/pipermail/chimera-users/2010-February/004826.html
http://www.cgl.ucsf.edu/pipermail/chimera-users/2010-March/004887.html (except note that the mail program has expanded "@" to " at "!) (b) peptide dihedrals. The phi,psi,chiN values for amino acid residues are automatically assigned as attributes. You can save an attribute (list of values) to a file from the Render by Attribute tool. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html#...
Currently there is no Chimera command to save attributes, however. 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 Apr 13, 2010, at 2:24 AM, sette@uniroma2.it wrote:
Hi all, my reply is not really related but similar. I work with NMR data and often we need list of distances or dihedral angles for the whole molecule, like distances between a NH protons and the rest of the molecule, or list of the chi1 dihedral angles. It seems that at present there is no way to get this. Scripts are possible? Thanks, Marco
On Apr 13, 2010, at 8:58 AM, Elaine Meng wrote:
(b) peptide dihedrals. The phi,psi,chiN values for amino acid residues are automatically assigned as attributes. You can save an attribute (list of values) to a file from the Render by Attribute tool. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html#...
Also, a short Python script could be used for this: from chimera import openModels, Molecule for m in openModels.list(modelTypes=[Molecule]): for r in m.residues: print r, r.chi1 If you save the above in a file ending in .py and open it in Chimera (e.g. File...Open, or the "open" command) then the chi1 angles of all residues will be printed to the reply log. --Eric
Hi,
I used suggestion a) of Elaine for distances and the script of Eric
for the angles.
both work fine :))
Thanks a lot!!!!
Marco
Quoting "Eric Pettersen"
On Apr 13, 2010, at 8:58 AM, Elaine Meng wrote:
(b) peptide dihedrals. The phi,psi,chiN values for amino acid residues are automatically assigned as attributes. You can save an attribute (list of values) to a file from the Render by Attribute tool. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html#...
Also, a short Python script could be used for this:
from chimera import openModels, Molecule for m in openModels.list(modelTypes=[Molecule]): for r in m.residues: print r, r.chi1
If you save the above in a file ending in .py and open it in Chimera (e.g. File...Open, or the "open" command) then the chi1 angles of all residues will be printed to the reply log.
--Eric
Dr.Marco Sette, Ph.D. Department of Chemical Sciences and Technology University of Rome, "Tor Vergata" via della Ricerca Scientifica, 00133, Rome, Italy e-mail: sette@uniroma2.it e-mail: m77it@yahoo.it Tel.: +39-0672594424 Fax: +39-0672594328 ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program.
participants (4)
-
eduardo.troche＠uvigo.es -
Elaine Meng -
Eric Pettersen -
sette＠uniroma2.it