RE: [PyMOL] Refinement in auto_sculpt

[Warren D. <wa...@de...>]

Jim,

(we discussed this at ACS, but just for the mailing list record).

PyMOL does not yet support real-space refinement internally.  However, I
suspect one could use cctbx to accomplish this with PyMOL.  Perhaps
someone familiar with both open-source projects would like to take a
stab at it?

Cheers,
Warren

--
Warren L. DeLano, Ph.D.                    =20
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> -----Original Message-----
> From: Jim Nettles [mailto:jn...@em...]=20
> Sent: Tuesday, August 30, 2005 6:00 AM
> To: Warren DeLano
> Cc: pym...@li...; Mathieu Coincon
> Subject: Re: [PyMOL] Refinement in auto_sculpt
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> Hello all,=20
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>         Perhaps I'm awaking from hibernation or something,=20
> but the communication below came as a surprise to me.=20
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>         Do I read this correctly that Pymol does real space=20
> refining into electron density using the sculpting function?=20
> If so, that is great! I apologize if this has been discussed=20
> before and I missed it. Could someone please clue me in as to=20
> how to best use this function?=20
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>         Thanks,=20
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>         Jim Nettles=20
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> On Aug 30, 2005, at 8:33 AM, Warren DeLano wrote:=20
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> Mathieu,=20
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>  =20
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> Deselect Sculpting from the builder menu or "unset sculpting"=20
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>  =20
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> Note that if you're doing this a lot, then create some custom=20
> on/off function keys as follows:=20
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>  =20
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> # F1 to turn on sculpting=20
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> cmd.set_key('F1',lambda=20
> :(cmd.set("sculpting"),cmd.set("auto_sculpt")))=20
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>  =20
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> # F2 to turn off sculpting=20
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> cmd.set_key('F2',lambda=20
> :(cmd.unset("sculpting"),cmd.unset("auto_sculpt")))=20
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>  =20
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> Cheers,=20
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> Warren=20
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> From: pym...@li... on behalf of=20
> Mathieu Coincon=20
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> Sent: Mon 8/29/2005 8:26 AM=20
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> To: pym...@li...=20
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> Subject: [PyMOL] Refinement in auto_sculpt=20
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> Hi,=20
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> i'm usinig pymol for modelling my protein in electron density.=20
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> I like it very much but there is one thing I would like to=20
> understand.=20
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> Is there a way to stop the refinement of the geometry:=20
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>     I'm using auto_sculpt and I protect/deprotect the protein=20
> but sometimes the=20
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> refinemt run during a long time I would like to stop it ? i=20
> played with the=20
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> number  of cycles and other parameters but it didn't work.=20
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