Re: [PyMOL] new ideas

[Jason V. <jas...@sc...>]

For the sale of PyMOL, we had to take down FreeMOL temporarily.  I
will put it back up soon.  I think you can still get access to the
code from bioinformatics.org.

I'll update the list when I've posted the FreeMOL code.

Thanks,

-- Jason

On Wed, Jan 20, 2010 at 10:27 PM, David Hall <dwa...@ya...> wrote:
> In my incentive build, freemol is present with the following readme:
>
> This is a binary distribution of the FreeMOL Open-Source Compilation.
>
> The FreeMOL project home page can be found at:
>
>    http://bioinformatics.org/freemol
>
> Complete source code for building FreeMOL and its various components
> can be browsed via:
>
>    http://www.bioinformatics.org/websvn/listing.php?repname=freemol
>
> and fetched via:
>
>    svn co svn://bioinformatics.org/svnroot/freemol/trunk
>
> Licensing information can be found in LICENSE.txt
>
> If you have any questions about FreeMOL, please contact:
>
> Warren L. DeLano, Ph.D.
> DeLano Scientific LLC
> wa...@de...
>
> Thank You!
>
> I don't have any instructions how to incorporate this into building from pymol trunk necessarily though.  In the incentive builds, the freemol folder is not inside ext or modules or anything, but instead is a top level directory like those.  You will have to build the sources of the things that come with it (apbs, mengine, mpeg_encode, pdb2pqr).
>
> I think pymol autodetects the presence of freemol based on this grep output on the pymol source.
>
> modules/pymol/__init__.py:        # auto-detect bundled FREEMOL (if present)
> modules/pymol/__init__.py:        if not os.environ.has_key("FREEMOL"):
> modules/pymol/__init__.py:            test_path = os.path.join(os.environ['PYMOL_PATH'],"freemol")
> modules/pymol/__init__.py:                os.environ['FREEMOL'] = test_path
> modules/pymol/__init__.py:        # include FREEMOL's libpy in sys.path (if present)
> modules/pymol/__init__.py:        if os.environ.has_key("FREEMOL"):
> modules/pymol/__init__.py:            freemol_libpy = os.path.join(os.environ['FREEMOL'],"libpy")
> modules/pymol/__init__.py:            if os.path.isdir(freemol_libpy):
> modules/pymol/__init__.py:                if freemol_libpy not in sys.path:
> modules/pymol/__init__.py:                    sys.path.append(freemol_libpy)
>
>
> Hopefully this all helps.
>
> -David
>
>
>
> ----- Original Message ----
>> From: Maia Cherney <ch...@ua...>
>> To: Jason Vertrees <jas...@sc...>
>> Cc: pym...@li...
>> Sent: Wed, January 20, 2010 9:37:46 PM
>> Subject: Re: [PyMOL] new ideas
>>
>> Thanks,
>>
>> But I could not find the download site for FreeMol.
>>
>> Could somebody send me a link to FreeMol?
>>
>> Maia
>>
>> Jason Vertrees wrote:
>> > Maia,
>> >
>> > You can already move structures independently.  If you install
>> > PyMOL+FreeMOL you can have access to the MMFF-enabled PyMOL that will
>> > allow you to do small molecule cleanup and editing.
>> >
>> > Try putting your mouse into "Editing Mode" and moving atoms around.
>> > It's not hard.  Check this out:
>> > http://pymolwiki.org/index.php/Molecular_Sculpting for some help.
>> >
>> > Regards,
>> >
>> > -- Jason
>> >
>> >
>> > On Wed, Jan 20, 2010 at 11:52 AM, Maia Cherney wrote:
>> >
>> >> Hi Jason
>> >>
>> >> I need such features. I open two different pdbs and I want to manually move
>> >> one structure relative to another. I want to dock one structure into another
>> >> or superpose 2 structures manually. Is it possible?
>> >>
>> >> Or I want to move a fragment of the molecule relative to the rest of the
>> >> molecule.
>> >> Is it possible?
>> >>
>> >>
>> >> Maia
>> >>
>> >>
>> >>
>> >
>> >
>> >
>> >
>>
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>
>
>
>
>
> ------------------------------------------------------------------------------
> Throughout its 18-year history, RSA Conference consistently attracts the
> world's best and brightest in the field, creating opportunities for Conference
> attendees to learn about information security's most important issues through
> interactions with peers, luminaries and emerging and established companies.
> http://p.sf.net/sfu/rsaconf-dev2dev
> _______________________________________________
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-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

(e) Jas...@sc...
(o) +1 (603) 374-7120