Re: [PyMOL] Caver 3.0 pugin

2013-11-18 Thread Stephen P. Molnar 


On 11/17/2013 03:02 PM, James Starlight wrote:

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 >


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 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
www.FoundationForChemistry.com  
(614)312-7528 (c)
Skype:  smolnar1



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Got it!

Many thanks.

--
Stephen P. Molnar, Ph.D.   Life is a fuzzy set
Foundation for Chemistry   Stochastic and multivariate
www.FoundationForChemistry.com
(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 

>  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 
>
>>   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=63469471&iu=/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
> 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=63469471&iu=/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
>
--
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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 >


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
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--
Stephen P. Molnar, Ph.D.   Life is a fuzzy set
Foundation for Chemistry   Stochastic and multivariate
www.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
Free app hosting. Or install the open source package on any LAMP server.
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Re: [PyMOL] Caver 3.0 pugin

2013-11-15 Thread James Starlight 
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 

> 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.
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[PyMOL] Caver 3.0 pugin

2013-11-15 Thread James Starlight 
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.
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