Re: [Chimera-users] Generate the tranfromation or bio matrix from the docking complex using Chimera
On Jun 14, 2017, at 9:35 AM, Elumalai Pavadai <epavadai@fiu.edu> wrote:
Dear Meng,
I have a cylindrical symmetry protein complex modeled with the protein-protein docking. Since the docking complex is very big in terms of size and number of atoms, I would like to generate the transformation matrix from it. Using the matrix , I can be able to generate the complex with Chimera. So, my question is that how to generate the transformation matrix from the protein complex with Chimera?
Thank you, and I look forward to hearing from you.
Kind regards, Elumalai
Dear Elumalai, I’m CC-ing chimera-users@cgl.ucsf.edu … it is the recommended address for Chimera questions, to ensure you get a response and allowing others to make suggestions. I’m guessing that you mean your large complex is several copies of the same protein, arranged in some symmetrical way, and instead you would like to have a file with only one copy but also the matrices describing the whole thing. If you had such a file, you could open it in Chimera and then generate the whole thing from the matrices. However, Chimera does not have the tools to go in the opposite direction, to figure out all the matrices from the whole complex. So if I understood your problem correctly, you would need to find some other program to do this. I haven’t done it myself, so I don’t know what you could use. If your protein-protein docking program created this symmetrical structure, maybe it can output the needed matrices. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
Hi Elumalai, You can get the symmetry operations out of Chimera. Open your complex twice, models #0 and #1. Suppose chains A and B are the same protein and you want the transformation to get from A to B. First align the first copy chain A to the second copy chain B: matchmaker #2:.B #1:.A Then measure the motion measure rotation #1 #2 The 3 by 4 matrix (rotation in first 3 columns, translation in 4th column) is output to the reply log. Also a rotation axis and angle is output. You can use the matrix and add in a text editor REMARK 350 BIOMT matrices to the PDB file containing just chain A to place it using the matrix. Take a look at an example PDB file to see the format (e.g. 2bbv). Or you can use the Chimera sym command with the rotation axis and angle to create copies of chain A in Chimera. Tom
On Jun 14, 2017, at 10:32 AM, Elaine Meng wrote:
On Jun 14, 2017, at 9:35 AM, Elumalai Pavadai <epavadai@fiu.edu> wrote:
Dear Meng,
I have a cylindrical symmetry protein complex modeled with the protein-protein docking. Since the docking complex is very big in terms of size and number of atoms, I would like to generate the transformation matrix from it. Using the matrix , I can be able to generate the complex with Chimera. So, my question is that how to generate the transformation matrix from the protein complex with Chimera?
Thank you, and I look forward to hearing from you.
Kind regards, Elumalai
Dear Elumalai,
I’m CC-ing chimera-users@cgl.ucsf.edu … it is the recommended address for Chimera questions, to ensure you get a response and allowing others to make suggestions.
I’m guessing that you mean your large complex is several copies of the same protein, arranged in some symmetrical way, and instead you would like to have a file with only one copy but also the matrices describing the whole thing. If you had such a file, you could open it in Chimera and then generate the whole thing from the matrices.
However, Chimera does not have the tools to go in the opposite direction, to figure out all the matrices from the whole complex. So if I understood your problem correctly, you would need to find some other program to do this. I haven’t done it myself, so I don’t know what you could use. If your protein-protein docking program created this symmetrical structure, maybe it can output the needed matrices.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
One more trick to help get BIOMT matrices into a PDB file to place multiple copies of a chain. If you figure out the symmetry parameters, e.g. symmetry axis direction, axis point for say C6 symmetry, then use the Chimera “sym” command to create the copies from a single chain, you can use the “biomtSet true” option with the sym command and it will include the BIOMT matrices in a PDB file written from Chimera (menu File / Save PDB…). https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/sym.html <https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/sym.html> Tom
On Jun 14, 2017, at 12:26 PM, Tom Goddard <goddard@sonic.net> wrote:
Hi Elumalai,
You can get the symmetry operations out of Chimera. Open your complex twice, models #0 and #1. Suppose chains A and B are the same protein and you want the transformation to get from A to B. First align the first copy chain A to the second copy chain B:
matchmaker #2:.B #1:.A
Then measure the motion
measure rotation #1 #2
The 3 by 4 matrix (rotation in first 3 columns, translation in 4th column) is output to the reply log. Also a rotation axis and angle is output. You can use the matrix and add in a text editor REMARK 350 BIOMT matrices to the PDB file containing just chain A to place it using the matrix. Take a look at an example PDB file to see the format (e.g. 2bbv). Or you can use the Chimera sym command with the rotation axis and angle to create copies of chain A in Chimera.
Tom
On Jun 14, 2017, at 10:32 AM, Elaine Meng wrote:
On Jun 14, 2017, at 9:35 AM, Elumalai Pavadai <epavadai@fiu.edu> wrote:
Dear Meng,
I have a cylindrical symmetry protein complex modeled with the protein-protein docking. Since the docking complex is very big in terms of size and number of atoms, I would like to generate the transformation matrix from it. Using the matrix , I can be able to generate the complex with Chimera. So, my question is that how to generate the transformation matrix from the protein complex with Chimera?
Thank you, and I look forward to hearing from you.
Kind regards, Elumalai
Dear Elumalai,
I’m CC-ing chimera-users@cgl.ucsf.edu … it is the recommended address for Chimera questions, to ensure you get a response and allowing others to make suggestions.
I’m guessing that you mean your large complex is several copies of the same protein, arranged in some symmetrical way, and instead you would like to have a file with only one copy but also the matrices describing the whole thing. If you had such a file, you could open it in Chimera and then generate the whole thing from the matrices.
However, Chimera does not have the tools to go in the opposite direction, to figure out all the matrices from the whole complex. So if I understood your problem correctly, you would need to find some other program to do this. I haven’t done it myself, so I don’t know what you could use. If your protein-protein docking program created this symmetrical structure, maybe it can output the needed matrices.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (2)
-
Elaine Meng -
Tom Goddard