From: Lenin Domínguez (acheron24_at_gmail.com)
Date: Sun Jan 05 2014 - 18:20:50 CST
Dear Nicholas,
I have installed grcarma and it is working fine for me. However, I would
like to know hot to configure it to find the helper programs I have
installed (VMD, weblogo, etc).
I have look at the documentation but couldn't find any pointers.
Best regards
On Wednesday, April 17, 2013 9:33:24 AM UTC-5, Nicholas M. Glykos wrote:
>
>
>
> Dear All,
>
> Panagiotis Koukos wrote (after a great deal of suffering ;-)
> a graphical user interface for carma, called 'grcarma'. The
> interface follows the paradigm of automated pipelines. For
> example, doing dPCA or cPCA will run carma several times in
> order to extract the clusters, prepare PDB files with the
> average and representative structures for each cluster, plus a
> superposition of 500 structures from the cluster. Or for
> another example, running the 'secondary structure' task will
> not only run stride, but will also prepare a graphical
> representation of the results plus a weblogo representation.
>
> We believe that the interface is lean, minimal and functional
> while allowing complicated analyses to be performed easily
> (but do note that we are probably biased on this matter).
> A screenshot of the main grcarma window (plus some of the
> supported analyses) is available via
>
> http://tinyurl.com/grcarma
>
>
> The program is written in Perl/Tk, but to save you from
> installing all sorts of modules, we have prepared ready-to-go
> executables for GNU/Linux, MacOSX and windoze. For things to
> go smoothly you'll also need the carma executables distributed
> together with grcarma. These grcarma+carma executables,
> together with instructions for installing them are available
> via
>
> https://github.com/pkoukos/grcarma
>
> or -if you feel confident that you can guess what you need to do
> in order to install them- you can get them directly from
>
> http://utopia.duth.gr/~glykos/progs/grcarma/
>
>
>
> We would be grateful if you would decide to test grcarma.
> Please forward all correspondence concerning the program to
> the carma mailing list at
>
> http://groups.google.com/group/carma-molecular-dynamics
>
>
>
> All the best,
> Nicholas
>
>
>
> --
>
>
> Nicholas M. Glykos, Department of Molecular Biology
> and Genetics, Democritus University of Thrace, University Campus,
> Dragana, 68100 Alexandroupolis, Greece, Tel/Fax (office) +302551030620,
> Ext.77620, Tel (lab) +302551030615, http://utopia.duth.gr/~glykos/
>
>
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