Re: [PyMOL] Caver 3.0 pugin

2013-11-17 Thread Stephen P. Molnar

I would be interested in just how the problem has been solved!

I just installed caver v-2.1.2 in the 64 bit Debian Testing with PyMOL 
v-1.6.0.0 compiled from the latest svn and functioning perfectly on my 
system.


Carver installed from the PyMOL wicki via the PyMOL Plugin Manager 
without any complaints.  Yet when I try to use the plugin I get:


ERROR: Directory incorrectly specified -plugin.jar not found, check 
directory/where/jar/with/plugin/is/locate/Carver2_1.jar


Both Carver2_1_2.py and Carver2_1_2.pyc are in the startup 
subdirectory.  Also other plugins are working without complaint.


This is exactly the way the plug was working the last time that I 
attempted its installation and use.


On 11/15/2013 03:14 PM, James Starlight wrote:
This issue have been solved. Caver works fine. Does anyone tried to 
include path information obtained by caver to the NAMD steered md 
simulation? I'm looking for the protocol for guiding namd forces along 
the direction obtaned from CAVER.



James


2013/11/15 James Starlight jmsstarli...@gmail.com 
mailto:jmsstarli...@gmail.com


Dear Pymol Users!


In the latest 3.0 releases of the CAVER plugin lack the source
path for the caver.jar launch file. Could you tell me how I could
define this path manually from pymol shell? I've try to make
calculations with thus plugin having Caver 3.0 dir in the work
folder but obtained error that /where/caver3 not found


Thanks for help

James




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Stephen P. Molnar, Ph.D.   Life is a fuzzy set
Foundation for Chemistry   Stochastic and multivariate
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(614)312-7528 (c)
Skype:  smolnar1

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Re: [PyMOL] Caver 3.0 pugin

2013-11-17 Thread James Starlight
Hi Stephen,

you should try lattest CAVER which could be downloaded from
http://www.caver.cz

before installing it via Pymol plugin menu, you should to open
caver-3.0-1.py and find here
CAVER3_LOCATION = directory/where/caver3/is/located

and modify this on your path providing it to the jar file directly ( in
this version there is no jar path in pymol plugin itself).

Does anyone use it for the analysis of the ligand sites? I've test it with
the GPCR and found 3 possible pathways. I'n not sure how It have been
clustered but now I'n looking for the method for the steered MD along
caver-predicted pathes

James


2013/11/17 Stephen P. Molnar s.mol...@sbcglobal.net

  I would be interested in just how the problem has been solved!

 I just installed caver v-2.1.2 in the 64 bit Debian Testing with PyMOL
 v-1.6.0.0 compiled from the latest svn and functioning perfectly on my
 system.

 Carver installed from the PyMOL wicki via the PyMOL Plugin Manager without
 any complaints.  Yet when I try to use the plugin I get:

 ERROR: Directory incorrectly specified -plugin.jar not found, check
 directory/where/jar/with/plugin/is/locate/Carver2_1.jar

 Both Carver2_1_2.py and Carver2_1_2.pyc are in the startup subdirectory.
 Also other plugins are working without complaint.

 This is exactly the way the plug was working the last time that I
 attempted its installation and use.


 On 11/15/2013 03:14 PM, James Starlight wrote:

  This issue have been solved. Caver works fine. Does anyone tried to
 include path information obtained by caver to the NAMD steered md
 simulation? I'm looking for the protocol for guiding namd forces along the
 direction obtaned from CAVER.


  James


 2013/11/15 James Starlight jmsstarli...@gmail.com

   Dear Pymol Users!


  In the latest 3.0 releases of the CAVER plugin lack the source path for
 the caver.jar launch file. Could you tell me how I could define this path
 manually from pymol shell? I've try to make calculations with thus plugin
 having Caver 3.0 dir in the work folder but obtained error that
 /where/caver3 not found


  Thanks for help

  James




 --
 DreamFactory - Open Source REST  JSON Services for HTML5  Native Apps
 OAuth, Users, Roles, SQL, NoSQL, BLOB Storage and External API Access
 Free app hosting. Or install the open source package on any LAMP server.
 Sign up and see examples for AngularJS, jQuery, Sencha Touch and 
 Native!http://pubads.g.doubleclick.net/gampad/clk?id=63469471iu=/4140/ostg.clktrk



 ___
 PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
 Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
 Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net


 --
 Stephen P. Molnar, Ph.D.   Life is a fuzzy set
 Foundation for Chemistry   Stochastic and 
 multivariatewww.FoundationForChemistry.com
 (614)312-7528 (c)
 Skype:  smolnar1



 --
 DreamFactory - Open Source REST  JSON Services for HTML5  Native Apps
 OAuth, Users, Roles, SQL, NoSQL, BLOB Storage and External API Access
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 Sign up and see examples for AngularJS, jQuery, Sencha Touch and Native!
 http://pubads.g.doubleclick.net/gampad/clk?id=63469471iu=/4140/ostg.clktrk
 ___
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 Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net

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