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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
Subject: [Chimera-users] transposing a pdb structure ("copy & paste")
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
------------------------------
Message: 2
Date: Fri, 10 Aug 2007 16:04:20 -0700
Subject: Re: [Chimera-users] transposing a pdb structure ("copy &
paste")
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
Subject: Re: [Chimera-users] transposing a pdb structure ("copy &
paste")
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
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Message: 4
Date: Sat, 11 Aug 2007 09:30:29 +0530
Subject: Re: [Chimera-users] chimera on AMD workstation
Message-ID:
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
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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