[chimera-dev] Question regarding MMTK

Wed Feb 11 07:11:56 PST 2009

Hi everyone,

I have a question regarding the MMTK interfase.  How complicate it is to get the hand on a the  MMTK script and input files generated by chimera to perform the minimization ? Is it located in some subfolder? Is there a way to write it down so that I can perform further calculations outside the chimera environment? 
All the best,
JD

Dr. Jean-Didier Maréchal
Lecturer
Computational Bioorganic and Bioionorganic 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, Febrer 4, 2009 9:00 pm
Assumpte: Chimera-dev Digest, Vol 61, Issue 1

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> Today's Topics:
> 
>   1. alias menu (Richmond  Timothy J.)
>   2. Re: alias menu (Elaine Meng)
>   3. Re: alias menu (Eric Pettersen)
> 
> 
> --------------------------------------------------------------------
> --
> 
> Message: 1
> Date: Wed, 4 Feb 2009 14:09:53 +0100
> From: "Richmond  Timothy J." <richmond at mol.biol.ethz.ch>
> Subject: [chimera-dev] alias menu
> To: <chimera-dev at cgl.ucsf.edu>
> Message-ID: <874055BA140585479966DE1694AB0421F058B5 at EX6.d.ethz.ch>
> Content-Type: text/plain; charset="iso-8859-1"
> 
> Dear Chimera Developers,
> 
> 
> 
> Perhaps I have missed it, but I would find a menu for selected 
> aliases very useful. Having returned to Chimera from PyMol 
> recently, it would be great to have an option for the alias command 
> that allowed the particular alias to be listed in a separate window 
> and ran the alias by clicking on the alias name listed there.
> 
> 
> 
> Best regards,
> 
> 
> 
> Tim
> 
> 
> 
> -------------------------
> 
> 
> 
> ETH Zurich
> 
> Prof. Timothy J. Richmond
> 
> Institute of Molecular Biology and Biophysics
> 
> HPK F 18
> 
> Schafmattstr. 20
> 
> 8093 Z?rich
> 
> SWITZERLAND
> 
> 
> 
> richmond at mol.biol.ethz.ch
> 
> http://www.mol.biol.ethz.ch/groups/richmond
> 
> 
> 
> +41 44 633 24 70 phone
> 
> +41 44 633 11 50 fax
> 
> 
> 
> 
> 
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> ------------------------------
> 
> Message: 2
> Date: Wed, 4 Feb 2009 10:10:20 -0800
> From: Elaine Meng <meng at cgl.ucsf.edu>
> Subject: Re: [chimera-dev] alias menu
> To: "Richmond Timothy J." <richmond at mol.biol.ethz.ch>
> Cc: chimera-dev at cgl.ucsf.edu
> Message-ID: <BFF540B7-7F60-442D-95EA-25B19CF86441 at cgl.ucsf.edu>
> Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes
> 
> Dear Tim,
> I see where you are coming from, but aliases are not necessarily  
> commands.  I use them all the time, but mainly to refer to some set 
> of  
> residues, e.g.
> 
> alias refats #1:57.a,230.a,301.a
> alias matchats #0:10.a,218.a,287.a
> alias residues #0:8.a,10.a,164.a,218.a,287.a
> alias showchain :.a
>   [...]
> match matchats refats
> ~modeldisp #1
> ~disp
> ribbon showchain
> ribrepr smooth
> disp residues
> repr stick residues
> 
> (taken from real command files I used a couple of days ago)  One  
> purpose of aliases is to make a hard-to-type thing into an easy-to- 
> type thing, so perhaps it would help to make shorter aliases.  If 
> it  
> is a matter of remembering what they are, the command "alias" 
> without  
> any arguments will show all the aliases and their definitions in 
> the  
> Reply Log.
> Best,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>                      http://www.cgl.ucsf.edu/home/meng/index.html
> 
> 
> 
> On Feb 4, 2009, at 5:09 AM, Richmond Timothy J. wrote:
> 
> > Dear Chimera Developers,
> >
> > Perhaps I have missed it, but I would find a menu for selected  
> > aliases very useful. Having returned to Chimera from PyMol 
> recently,  
> > it would be great to have an option for the alias command that  
> > allowed the particular alias to be listed in a separate window 
> and  
> > ran the alias by clicking on the alias name listed there.
> >
> > Best regards,
> >
> > Tim
> >
> 
> 
> ------------------------------
> 
> Message: 3
> Date: Wed, 4 Feb 2009 11:05:53 -0800
> From: Eric Pettersen <pett at cgl.ucsf.edu>
> Subject: Re: [chimera-dev] alias menu
> To: "Richmond  Timothy J." <richmond at mol.biol.ethz.ch>
> Cc: chimera-dev at cgl.ucsf.edu,	"chimera-users at cgl.ucsf.edu BB"
> 	<chimera-users at cgl.ucsf.edu>
> Message-ID: <EAFCFBD1-0A2F-47F7-B39B-A7E6E3A22CA1 at cgl.ucsf.edu>
> Content-Type: text/plain; charset="us-ascii"
> 
> On Feb 4, 2009, at 5:09 AM, Richmond Timothy J. wrote:
> 
> > Dear Chimera Developers,
> >
> > Perhaps I have missed it, but I would find a menu for selected  
> > aliases very useful. Having returned to Chimera from PyMol 
> recently,  
> > it would be great to have an option for the alias command that  
> > allowed the particular alias to be listed in a separate window 
> and  
> > ran the alias by clicking on the alias name listed there.
> >
> > Best regards,
> >
> > Tim
> 
> Hi Tim,
> 	As Elaine pointed out in her reply, aliases are frequently used as 
> 
> shorthands for long atom specs rather than as replacements for  
> complete commands.  However, the form of the alias command that 
> uses  
> '^' (so that matching only occurs at the start of the line) 
> typically  
> is used to define full command aliases.
> 
> 	So my thinking is this: aliases defined with the '^' character 
> would  
> be placed in an 'Aliases' top-level menu (created on the fly as  
> needed).  Such aliases would automatically be remembered across  
> Chimera invocations (and populate an Aliases menu).  The menu could 
> be  
> torn-off (except on Aqua) to make a stand-alone window.  Those 
> aliases  
> could be deleted as normal with the ~alias command (which would 
> remove  
> them from the menu and no longer remember then in subsequent 
> Chimeras).
> 	Would this be good enough?
> 
> --Eric
> 
>                         Eric Pettersen
>                         UCSF Computer Graphics Lab
>                         http://www.cgl.ucsf.edu
> 
> 
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