[Chimera-users] sym command in Chimera
Z. Nevin Gerek
Nevin.Gerek at asu.edu
Tue Aug 14 17:55:26 PDT 2007
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 at asu.edu
On Aug 11, 2007, at 12:00 PM, chimera-users-request at 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)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Fri, 10 Aug 2007 15:53:33 -0400
> From: "Ben Keshet" <keshet1 at umbc.edu>
> Subject: [Chimera-users] transposing a pdb structure ("copy & paste")
> To: <chimera-users at cgl.ucsf.edu>
> Message-ID: <000001c7db88$238da8b0$29ad5582 at 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
>
>
>
>
> ------------------------------
>
> Message: 2
> Date: Fri, 10 Aug 2007 16:04:20 -0700
> From: Elaine Meng <meng at cgl.ucsf.edu>
> Subject: Re: [Chimera-users] transposing a pdb structure ("copy &
> paste")
> To: "Ben Keshet" <keshet1 at umbc.edu>
> Cc: chimera-users at cgl.ucsf.edu
> Message-ID: <8f3e5fad823ed51cc9da3fa7677864cc at 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
>
>
>
> ------------------------------
>
> Message: 3
> Date: Fri, 10 Aug 2007 16:53:36 -0700
> From: Eric Pettersen <pett at cgl.ucsf.edu>
> Subject: Re: [Chimera-users] transposing a pdb structure ("copy &
> paste")
> To: Ben Keshet <keshet1 at umbc.edu>
> Cc: Chimera BB <chimera-users at cgl.ucsf.edu>
> Message-ID: <E5C1411A-58C1-49A8-8899-24816E53E043 at 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 at cgl.ucsf.edu
> http://www.cgl.ucsf.edu
>
>
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> ------------------------------
>
> Message: 4
> Date: Sat, 11 Aug 2007 09:30:29 +0530
> From: "Vinay Kumar" <ksvinaykumar at gmail.com>
> Subject: Re: [Chimera-users] chimera on AMD workstation
> To: "Chimera BB" <chimera-users at cgl.ucsf.edu>
> Message-ID:
> <ef4e9c1a0708102100jfb52ed0m66e0f5dc3cf30dd0 at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hello Tom,
> Thank you. I shall check with my system person and get back with you.
> But when i tried installing the last time, the error message was
> somewhat
> like the following-
> "cannot execute ./chimera*.exe"
> this was after i had done "chmod +x"
>
> anyways, will post the correct error message.
>
> Vinay
>
> On 8/10/07, Thomas Goddard <goddard at cgl.ucsf.edu> wrote:
>>
>> Hi Vinay,
>>
>> The chimera-1.2422-linux_x86_64.exe distribution is for 64-bit
>> versions of Linux. If you are using a 32-bit linux (even with a
>> 64-bit
>> processor) then you need chimera-1.2422-linux.exe instead.
>>
>> If that is not the problem, could you be more specific about what
>> goes wrong when you try to install? What is the error message?
>>
>> Tom
>>
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