[PyMOL] Plugin menu options and measuring protein cavity volumes in PyMol

[Thomas Pochapsky]

I am trying to load a plugin (CAVER) onto my MacPyMOL v 1.7, and 
according to the Wiki, any version later than 1.5 should have a menu 
option to manage plugins, but I do not see this anywhere.  Was something 
incorrectly set at installation?  Can I correct this?
Alternatively (or additionally), if anybody has any info on how to 
measure cavity volumes in a protein structure by PyMOL with standard 
commands, I would appreciate it.
Thanks,
Tom Pochapsky


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Re: [PyMOL] pymol alignment help

[Thomas Holder]

Hi Clarisa,

Please rephrase your question and describe what your goal is. Please give some 
details about what you already tried, and at what step you got stuck or need 
help. "Download an aligment" is not common terminology, so it's likely that 
nobody on the list understood your question.

You might be looking for this:
http://pymolwiki.org/index.php/Align

Cheers,
  Thomas

On 24 Aug 2016, at 09:10, Clarisa Alvarez  wrote:

> Hello!
> could someone help me to download a pymol alignment? and know with which 
> score it makes the alignment.
> Thanks in advance.
> 
> Clarisa.

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.


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Re: [PyMOL] Plugin menu options and measuring protein cavity volumes in PyMol

[Thomas Holder]

Hi Tom,

To get the Plugin menu with MacPyMOL, see the "X11 Hybrid" section on the 
PyMOLWiki:

http://pymolwiki.org/index.php/MAC_Install#X11_Hybrid

Cheers,
  Thomas

On 25 Aug 2016, at 13:52, Thomas Pochapsky  wrote:

> I am trying to load a plugin (CAVER) onto my MacPyMOL v 1.7, and 
> according to the Wiki, any version later than 1.5 should have a menu 
> option to manage plugins, but I do not see this anywhere.  Was something 
> incorrectly set at installation?  Can I correct this?
> Alternatively (or additionally), if anybody has any info on how to 
> measure cavity volumes in a protein structure by PyMOL with standard 
> commands, I would appreciate it.
> Thanks,
> Tom Pochapsky

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.


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