Dear Chimera team, I am trying to use sym command to generate symmetry related copy of a protein. I followed this link: http://www.cgl.ucsf.edu/chimera/experimental/symmetrycopies/ symcopies.html The version I am using is 1.2422. When I write sym, I get this error: "unrecognized command: "sym" Then I found this link http://www.cgl.ucsf.edu/pipermail/chimera- users/2005-September/000464.html and put necessary files to Chimera.app/Contents/Resources/share folder. Then I restart Chimera, I get same error. Is there another way to use sym command in Chimera? Thanks for your help, Z. Nevin Gerek, Ph.D. Postdoctoral Fellow ----------------------------------------------------- The Center for Biological Physics Arizona State University PO Box 871504 Tempe, AZ 85287-1504 Phone: (480) 727-8897 nevin.gerek@asu.edu On Aug 11, 2007, at 12:00 PM, chimera-users-request@cgl.ucsf.edu wrote:
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Today's Topics:
1. transposing a pdb structure ("copy & paste") (Ben Keshet) 2. Re: transposing a pdb structure ("copy & paste") (Elaine Meng) 3. Re: transposing a pdb structure ("copy & paste") (Eric Pettersen) 4. Re: chimera on AMD workstation (Vinay Kumar)
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Message: 1 Date: Fri, 10 Aug 2007 15:53:33 -0400 From: "Ben Keshet" <keshet1@umbc.edu> Subject: [Chimera-users] transposing a pdb structure ("copy & paste") To: <chimera-users@cgl.ucsf.edu> Message-ID: <000001c7db88$238da8b0$29ad5582@umbc80a173302c> Content-Type: text/plain; charset="us-ascii"
Dear Chimera fans and team,
I have a pdb file of a fragment of an amyloid fibril constructed of 8 layers (8 parallel strands of beta sheet). I would like to overcome the end effects when modeling it, so I would like extend the existing structure by duplicating it at its end.
Does Chimera has a tool do the following: duplicate existing pdb molecule coordinates, position the duplicated molecule at a desired location, and then align it reasonably with respect to the original molecule?
Thank you very much for your time and help.
Ben
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Message: 2 Date: Fri, 10 Aug 2007 16:04:20 -0700 From: Elaine Meng <meng@cgl.ucsf.edu> Subject: Re: [Chimera-users] transposing a pdb structure ("copy & paste") To: "Ben Keshet" <keshet1@umbc.edu> Cc: chimera-users@cgl.ucsf.edu Message-ID: <8f3e5fad823ed51cc9da3fa7677864cc@cgl.ucsf.edu> Content-Type: text/plain; charset=US-ASCII; format=flowed
Dear Ben, Chimera doesn't have the ability to figure out for you the proper position of one copy relative to another. You could open multiple copies, perform manual positioning, and then write out all the coordinates, but I imagine it might be difficult to get the right position of one copy relative to another, even manually/interactively.
To manually position a structure relative to another, you could interactively rotate/translate and/or use the "move" (translation) and "turn" (rotation) commands. You can freeze/unfreeze a copy using the Active checkbox in the Model Panel (in the Favorites menu by default), the command "select," or the little checkboxes under the Command Line (also under Favorites).
If you did manage to position copy 2 relative to copy 1 to your liking, you could write the transformation matrices out (see "matrixget" command). From those you could calculate the transformation of 2 relative to 1 and also generate appropriate matrices that would then position 3, 4, ... correctly (see "matrixset" command). I admit I don't know how to do those calculations. Anyone?
Yet another snag depends on how you will be using these coordinates. Does it require all the PDB files to be merged into one? If so, can they be in a multi-MODEL form, or in a single model? Chimera can output separate PDB files or a single multi-MODEL PDB file. If you need all the coordinates to be in one model, however, you would have to edit the PDB output from Chimera so there are not atoms with duplicate atom numbers and chain IDs. However, it all depends on what the *next* program you will be using requires and expects. If you will just be using Chimera, however, no further editing would be required (in fact, you could just save a session rather than writing out coordinates).
Maybe someone else will have a smarter and less discouraging set of suggestions! Best, Elaine
On Aug 10, 2007, at 12:53 PM, Ben Keshet wrote:
Dear Chimera fans and team,
I have a pdb file of a fragment of an amyloid fibril constructed of 8 layers (8 parallel strands of beta sheet). I would like to overcome the end effects when modeling it, so I would like extend the existing structure by duplicating it at its end.
Does Chimera has a tool do the following: duplicate existing pdb molecule coordinates, position the duplicated molecule at a desired location, and then align it reasonably with respect to the original molecule?
Thank you very much for your time and help.
Ben
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Message: 3 Date: Fri, 10 Aug 2007 16:53:36 -0700 From: Eric Pettersen <pett@cgl.ucsf.edu> Subject: Re: [Chimera-users] transposing a pdb structure ("copy & paste") To: Ben Keshet <keshet1@umbc.edu> Cc: Chimera BB <chimera-users@cgl.ucsf.edu> Message-ID: <E5C1411A-58C1-49A8-8899-24816E53E043@cgl.ucsf.edu> Content-Type: text/plain; charset="us-ascii"
On Aug 10, 2007, at 4:04 PM, Elaine Meng wrote:
To manually position a structure relative to another, you could interactively rotate/translate and/or use the "move" (translation) and "turn" (rotation) commands. You can freeze/unfreeze a copy using the Active checkbox in the Model Panel (in the Favorites menu by default), the command "select," or the little checkboxes under the Command Line (also under Favorites).
If you did manage to position copy 2 relative to copy 1 to your liking, you could write the transformation matrices out (see "matrixget" command). From those you could calculate the transformation of 2 relative to 1 and also generate appropriate matrices that would then position 3, 4, ... correctly (see "matrixset" command). I admit I don't know how to do those calculations. Anyone?
It's a little tricky. Basically, you want to get copy 1's matrix to be the identity matrix while keeping copy 2 in the same relative position. Here's one way to do it (and maybe someone can suggest something better):
1) open yet another copy (copy 3) as a reference 2) use "matrixset" to set copy 3's matrix to be the identity matrix 3) use the "match" command with the 'active' keyword to match copy 1 onto the reference (copy 3) while also moving copy 2 appropriately 4) use "matrixget" to get copy 2's new transformation matrix
I would imagine that copy 2's matrix is essentially all translation components (i.e. the upper 3x3 is all zeroes or near-zeroes) so all you need to do to place additional copies to multiply the translation components by 2, 3, etc.
--Eric
Eric Pettersen UCSF Computer Graphics Lab pett@cgl.ucsf.edu http://www.cgl.ucsf.edu