[chimera-dev] a request again...adjust torsion for pseudo bonds

[Jean Didier Pie Marechal]

Dear all,
sorry to bother you again. 
I want to perform a conformational search rotating residues around their chelation bond with a metal. With the adjust torsion tool, I can't rotate around  pseudo bond, and I actually need to transform the different pseudo bonds in bonds.

Could you authorize pseudo bonds to be rotated around? (in the contrary I'll continue with transforming pseudo bonds in bonds, but I thought that remaining with pseudo bonds is better especially when you do "add hydrogens" or other stuffs afterwards )

All the best,
JD


Dr. Jean-Didier Maréchal
Lecturer
Computational Biotechnological Chemistry @ Transmet
Unitat de Química Física
Departament de Química
Universitat Autònoma de Barcelona
Edifici C.n.
08193 Cerdanyola (Barcelona)
Tel: +34.935814936
e-mail: JeanDidier.Marechal at uab.es

----- Missatge original -----
De: chimera-dev-request at cgl.ucsf.edu
Data: Dimecres, Maig 13, 2009 9:00 pm
Assumpte: Chimera-dev Digest, Vol 64, Issue 5

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>   1. [Chimera-dev] Compiling chimera from source code (christopher 
> lau)   2. Re: [Chimera-dev] Compiling chimera from source code 
> (Greg Couch)
> 
> 
> --------------------------------------------------------------------
> --
> 
> Message: 1
> Date: Tue, 12 May 2009 21:15:56 -0700
> From: christopher lau <chris.d.lau at gmail.com>
> Subject: [chimera-dev] [Chimera-dev] Compiling chimera from source
> 	code
> To: chimera-dev at cgl.ucsf.edu
> Message-ID:
> 	<f2026a300905122115w3cd5df71mdc8090670593ad94 at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
> 
> Dear Madam/Sir,
> 
> I am currently involved in a project which requires compiling the 
> Chimerasource code from scratch. I have been using:
> 
> http://www.cgl.ucsf.edu/chimera/sourcecode.html
> 
> for reference, and I understand that surfacing library is not 
> availabledue to licensing issues.  Because I am not interested in 
> using this
> feature, I wanted to know if it was still possible to compile the 
> Chimerasource code.  I know that it will be difficult but any 
> knowledge or past
> experience that may help me would be greatly appreciated.
> 
> Thanks in advance,
> 
> Chris
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> ------------------------------
> 
> Message: 2
> Date: Tue, 12 May 2009 23:55:49 -0700
> From: Greg Couch <gregc at cgl.ucsf.edu>
> Subject: Re: [chimera-dev] [Chimera-dev] Compiling chimera from source
> 	code
> To: christopher lau <chris.d.lau at gmail.com>
> Cc: chimera-dev at cgl.ucsf.edu
> Message-ID: <Pine.CYG.4.58.0905122245160.4512 at retief>
> Content-Type: TEXT/PLAIN; charset=US-ASCII
> 
> On Tue, 12 May 2009, christopher lau wrote:
> 
> > Dear Madam/Sir,
> >
> > I am currently involved in a project which requires compiling the 
> Chimera> source code from scratch. I have been using:
> >
> > http://www.cgl.ucsf.edu/chimera/sourcecode.html
> >
> > for reference, and I understand that surfacing library is not 
> available> due to licensing issues.  Because I am not interested in 
> using this
> > feature, I wanted to know if it was still possible to compile the 
> Chimera> source code.  I know that it will be difficult but any 
> knowledge or past
> > experience that may help me would be greatly appreciated.
> >
> > Thanks in advance,
> >
> > Chris
> 
> You are very brave.  But, if you have experience porting software, it
> should be fairly easy.
> 
> The prerequisites vary by platform.  For instance, on Windows you need
> both Microsoft Visual Studio 2003 .NET and the cygwin 1.5 development
> environment.  On Linux and Mac OS X, you need gcc, g++, 
> g77/gfortran 3.4.4
> or later, but if you're compiling on Red Hat/Fedora and want it to 
> run on
> other versions of Linux, you'll need to install a stock binutils 
> packageto get cross-platform symbol tables.  And you'll need gnu 
> make 3.81, flex,
> bison, and a bunch of other tools.  You'll discover what else you 
> need as
> the compiles fail :-).  If you have specific problems, please ask.
> 
> The platform dependent make rules are in mk/os.make.
> 
> Total compilation time is about 3 hours.  If you don't need some of 
> thethird-party software, e.g., ffmpeg, povray, amber tools, cmake, 
> and boost,
> you can take those of out of the foreign make file and speed things up
> considerably.
> 
> 	Good luck and please tell us more about your project,
> 
> 	Greg
> 
> 
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> End of Chimera-dev Digest, Vol 64, Issue 5
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