Re: [PyMOL] PyMOL updates

Hi Jason,

1. I am wondering if I have the latest version of pymol. I got it via 
ubuntu package. How do I update the pymol version?

2. I was trying to do some procedures from the Warren's letter:

Builder use:

(1) activate the builder by clicking on the "Builder" button on the
upper window
 
(2) click the "Bumps" checkbox
 
(3) click the "Sculpt" button


When I click on the "Builder" button on the upper window, I do not have 
the "Bumps" checkbox and the "Sculpt" button.
I have the autopick, the autozoom and the valence checkboxes.

That is why I am wondering if I have the same version of pymol.

Could you also give me some explanation what are  polymer or organic,  byres (organic expand 4), and flag fix, not organic


Maia


Jason Vertrees wrote:
> Maia,
>
>   
>> 1. How can I undo a plugin. By mistake I tried to plugin a program using a
>> wrong file and now I get an error message every time I open pymol.
>>     
>
> Newer versions of PyMOL have a menu option to remove plugins: Plugin >
> Manage Plugins > Remove.  You can also remove a plugin by simply
> removing the plugin file.  PyMOL stores plugins in the Python
> distribution's "site-packages/pmg_tk/startup" directory.  My Mac OS X
> Fink build has them here:
>    /sw/lib/python2.5/site-packages/pmg_tk/startup/
> for example.
>
> If you're on Mac or Linux you can try
>   locate pmg_tk/startup
> or
>   find / -name yourPlugin.py
> for hints as to the plugin's installed location.
>
>
>   
>> 2. Which plugin allows me to move one structure relative to another. (I want
>> to do manual docking of one structure into another).
>>     
>
> You don't need a plugin to move objects.  Just use SHIFT-middle-mouse
> button drag, while in editing mode.  If you're starting from one
> object (eg. protein and ligand come from one file) then split them up:
>
> # example
> fetch 1oky, async=0
>
> # the protein and ligand are one object; now make them two
> extract myLigand, org
>
> Now you can move the myLigand object independently of other objects.
>
> Good luck,
>
> -- Jason
>
>   
>> Maia
>>
>> Jason Vertrees wrote:
>>     
>>> PyMOLers,
>>>
>>> Due to the popularity of using PyMOL as a portal to other programs and
>>> integrating programs with PyMOL, we are developing a new Plugin
>>> Architecture for PyMOL.  We have dedicated a page on the PyMOLWiki
>>>    http://www.pymolwiki.org/index.php/PluginArchitecture
>>> for this discussion.
>>>
>>> If you have a desire to be involved in how the architecture is
>>> developed please add your contact information to that page (or email,
>>> personally).  Even if you don't care much about helping out, you might
>>> want to stop by and let us know which plugin systems you like and
>>> which you don't.
>>>
>>> Thanks,
>>>
>>> -- Jason
>>>
>>>
>>>       
>
>
>
>