[Chimera-users] Chimera-users Digest, Vol 61, Issue 29
Ibrahim Moustafa
I.moustafa at psu.edu
Mon Jun 2 15:42:09 PDT 2008
Dear Chimera developers,
Many many thanks for your great help. The script provided by Eric Peterson
did the job very easily.
Many thanks,
Ibrahim
On 5/31/08 12:54 PM, "chimera-users-request at cgl.ucsf.edu"
<chimera-users-request at cgl.ucsf.edu> wrote:
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> Today's Topics:
>
> 1. Re: Plotting modes from PCA onto the structure (Eric Pettersen)
> 2. Re: add atom type in MMTK (Elaine Meng)
> 3. Import error with chimera-1.2509-osx_x11.dmg, May 01, 2008
> (Bruce D. Ray)
> 4. Re: Import error with chimera-1.2509-osx_x11.dmg, May 01,
> 2008 (Randy Heiland)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Fri, 30 May 2008 15:15:02 -0700
> From: Eric Pettersen <pett 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-users at cgl.ucsf.edu" <chimera-users at cgl.ucsf.edu>
> Message-ID: <476E9F7A-2FDD-4558-8053-5345D9995A02 at cgl.ucsf.edu>
> Content-Type: text/plain; charset="utf-8"
>
> Hi Ibrahim,
> As Bala pointed out, IED in VMD may well be the way to go for now.
> Also, the "porcupine needles" can be accomplished with BILD, as
> Elaine mentioned. I've attached a script that reads a file of
> displacements and applies them to the CAs of a structure. Obviously,
> there should be as many lines in the file as there are CAs in the
> structure. Each line should consist of 3 numbers, the X, Y, and Z
> displacements. Since the script only modifies the CAs, you should
> probably only be displaying the CAs -- the rest of the structure will
> be out of position. You may need to edit the script to put in the
> name of the file with the displacements, otherwise it will use a file
> named "displacements" in the same directory as the script. You run
> the script by simply opening it with File...Open or the "open" command.
> We are working on closer coordination between Amber and Chimera,
> with the help of Wei Zhang. He has already contributed one tool,
> Solvate, which uses sleap to solvate a system. Solvate is available
> in daily builds. In the short term he hopes to write tools to add
> ions and write parmtop files. Longer term goals are to include the
> minimization and MD functionality of NAB, and ptraj trajectory analysis.
>
> --Eric
>
> Eric Pettersen
> UCSF Computer Graphics Lab
> http://www.cgl.ucsf.edu
>
> ?
> 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
>> _______________________________________________
>> Chimera-users mailing list
>> Chimera-users at cgl.ucsf.edu
>> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
>
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> ------------------------------
>
> Message: 2
> Date: Fri, 30 May 2008 17:34:49 -0700
> From: Elaine Meng <meng at cgl.ucsf.edu>
> Subject: Re: [Chimera-users] add atom type in MMTK
> To: Lionel Nauton <lionel.nauton at univ-bpclermont.fr>
> Cc: chimera-users at cgl.ucsf.edu
> Message-ID: <7F83CFB3-19E1-4C36-9C28-5BE5B55DB005 at cgl.ucsf.edu>
> Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed
>
> Hello Lionel,
> Are you trying to run "addcharge" or "minimize"?
>
> If "addcharge" to calculate partial charges on some Pt complex (e.g.
> cisplatin or carboplatin):
>
> Nonstandard residues are sent to Antechamber, but that program is
> only meant to be used on organic molecules (C,H,O,N,S,P,F,Cl,Br,I),
> not metal complexes or inorganic species. See the antechamber site:
> http://amber.scripps.edu/antechamber/tips.html
> I think you have to use some other program that can handle metal
> complexes to derive partial charges. I don't think it is possible to
> simply edit some antechamber data files to get it to work on such
> compounds.
>
> If "minimize" and you just wanted to treat the Pt as a monatomic ion
> with integer charge:
>
> I had thought it possible to add a metal ion type by editing a
> parameter file. However, I have not been successful at minimizing a
> structure with the "new" type even when the file appears to include
> the necessary parameters. Maybe there is an additional step that I
> don't know about. So currently my best answer is that it is not
> possible, but if we find a way, we will send another message. (I may
> be wrong given my lack of success, but I think the relevant parameter
> file within the Chimera installation is lib/python2.5/site-packages/
> MMTK/ForceFields/amber/amber_parm99 )
>
> Sorry about that,
> 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 30, 2008, at 5:52 AM, Lionel Nauton wrote:
>
>> hello everybody
>> this is my first question since I use chimera, more than 3 years ago,
>> and I would like to know
>> if is it possible to add atom type in the MMTK basis set ?
>> I actually work on a molecule containing platinium, and I can't run
>> mopac
>> because there is no description.
>> I'm looking for some description files , and I found this :
>> /antechamber/dat/antechamber/*****.DAT
>> which is the good one and which is the way to modify it ?
>> thank's for your answer and excuse me for my english.....
>> best regards
>>
>
>
> ------------------------------
>
> Message: 3
> Date: Sat, 31 May 2008 08:50:53 -0700 (PDT)
> From: "Bruce D. Ray" <brucedray at yahoo.com>
> Subject: [Chimera-users] Import error with
> chimera-1.2509-osx_x11.dmg, May 01, 2008
> To: chimera-users at cgl.ucsf.edu
> Message-ID: <640107.47762.qm at web35804.mail.mud.yahoo.com>
> Content-Type: text/plain; charset=iso-8859-1
>
> I have a Mac G4 PPC running OS X 10.3.9 on which
> previous versions of chimera have run without
> incident.
> I installed chimera-1.2509 of May 01, 2008 after
> removing the chimera-1.2492 of Feb 11, 2008 I had been
> using. However, when I attempted to run
> chimera-1.2509
> it did not start and the following error messages were
> written to the console.log file accessible by
> console.app rather than to the X-terminal:
>
> Traceback (most recent call last):
>
> File
> "/Applications/Chimera.app/Contents/Resources/share/__main__.py",
> line 65, in <module>
>
> value = chimeraInit.init(sys.argv)
>
> File
> "/Applications/Chimera.app/Contents/Resources/share/chimeraInit.py",
> line 279, in init
>
> import chimera
>
> File
> "/Applications/Chimera.app/Contents/Resources/share/chimera/__init__.py",
> line 15, in <module>
>
> from _chimera import *
>
> ImportError: dynamic module does not define init
> function (init_chimera)
>
>
>
> This appears to be specific to the Mac OS X version
> as the Windows version of chimera-1.2509 works.
> Obviously, I removed chimera-1.2509 from the Mac and
> reinstalled chimera-1.2492 of Feb 11, 2008 which does
> work on this Mac.
>
>
> Sincerely,
>
>
>
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