[Chimera-users] Chimera-users Digest, Vol 61, Issue 27
bala
bala at igib.res.in
Fri May 30 05:31:16 PDT 2008
Dear Ibrahim,
Try to use IED Plugin in VMD to analyze your PCA output. In fact there is a server that can produce the arrows (you want) that can show the direction and magnitude of the displacement along a Eigen vector. But i guess the server works on gromacs output only.
A month ago, i posted the same query to Chimera (Analyzing PCA with chimera). I thank Elaine for his support. I would surely send some samples files of PCA analysis done with PTRAJ. I think addition of this analysis facility in Chimera is surely going to help all chimeran's a lot.
Bala
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Subject: Chimera-users Digest, Vol 61, Issue 27
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Today's Topics:
1. Plotting modes from PCA onto the structure (Ibrahim Moustafa)
2. Re: Plotting modes from PCA onto the structure (Elaine Meng)
----------------------------------------------------------------------
Message: 1
Date: Thu, 29 May 2008 13:08:01 -0400
From: Ibrahim Moustafa <I.moustafa at psu.edu>
Subject: [Chimera-users] Plotting modes from PCA onto the structure
To: "chimera-users at cgl.ucsf.edu" <chimera-users at cgl.ucsf.edu>
Message-ID: <C4645B32.132A%I.moustafa at psu.edu>
Content-Type: text/plain; charset="us-ascii"
Dear Chimera support,
I hope Chimera (with supporting scripts) can be used to make the figures
described below:
I want to make a figure to display the different modes obtained from
PCA analysis (on MD trajectory obtained from AMBER) as different snapshots
of the structure under study.
To explain it more, I have a file containing the displacement in X, Y, Z
for each C-alpha in a column format. Is there a simple script that can add
the displacement vectors to the x, y, z coordinates of the original
structure? So the new structure with modified C-alpha can be plotted
representing a particular mode in Chimera.
Also, related to the same point, is it possible to represent the vectors
at each C-alpha as arrows/porcupine needle in Chimera?
P.S. It would be great if Chimera can add features to represent these kind
of figures from PTRAJ output or similar analysis programs used in MD
simulation. Especially, Chimera support analysis of AMBER trajectory.
Thanks in advance for your great support,
Ibrahim
--
Ibrahim M. Moustafa, Ph.D.
Biochemistry and Molecular Biology Dept.
201 Althouse Lab., University Park,
Pennsylvania State University
PA 16802
Tel. (814) 863-8703
Fax (814) 865-7927
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Message: 2
Date: Thu, 29 May 2008 10:44:34 -0700
From: Elaine Meng <meng at cgl.ucsf.edu>
Subject: Re: [Chimera-users] Plotting modes from PCA onto the
structure
To: Ibrahim Moustafa <I.moustafa at psu.edu>
Cc: Chimera BB <chimera-users at cgl.ucsf.edu>
Message-ID: <BACB5EBE-BA74-44EA-B798-38A27406E8F5 at cgl.ucsf.edu>
Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed
Hi Ibrahim,
I don't write code myself and cannot promise (given time constraints)
that others will work on this, but it would help if you could send us
some example files: perhaps a PCA file and the structure snapshot
that is the basis for the displacements, and any other files that you
think are relevant (are the trajectory and prmtop also needed to show
the results?). You could send them just to me and I would share them
as needed.
Are your PCA results from PTRAJ? I know that several programs and
web servers do similar PCA or NM calculations, and probably each
produces a different output format.
You may want to take a look at converting your PCA results file into
lines and arrows in the BILD format. Simply opening the file in
Chimera displays the objects. This format is extremely simple and is
documented here, including an example file:
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/bild.html
Best,
Elaine
-----
Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
http://www.cgl.ucsf.edu/home/meng/index.html
On May 29, 2008, at 10:08 AM, Ibrahim Moustafa wrote:
> Dear Chimera support,
>
> I hope Chimera (with supporting scripts) can be used to make the
> figures described below:
>
> I want to make a figure to display the different modes
> obtained from PCA analysis (on MD trajectory obtained from AMBER)
> as different snapshots of the structure under study.
>
> To explain it more, I have a file containing the displacement in
> X, Y, Z for each C-alpha in a column format. Is there a simple
> script that can add the displacement vectors to the x, y, z
> coordinates of the original structure? So the new structure with
> modified C-alpha can be plotted representing a particular mode in
> Chimera.
>
> Also, related to the same point, is it possible to represent the
> vectors at each C-alpha as arrows/porcupine needle in Chimera?
>
> P.S. It would be great if Chimera can add features to represent
> these kind of figures from PTRAJ output or similar analysis
> programs used in MD simulation. Especially, Chimera support
> analysis of AMBER trajectory.
>
> Thanks in advance for your great support,
> Ibrahim
> --
> Ibrahim M. Moustafa, Ph.D.
> Biochemistry and Molecular Biology Dept.
> 201 Althouse Lab., University Park,
> Pennsylvania State University
> PA 16802
>
> Tel. (814) 863-8703
> Fax (814) 865-7927
>
------------------------------
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