From: Warren D. <wa...@de...> - 2005-08-12 18:58:53
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Hi Carsten, This isn't yet possible from within PyMOL, but it will be soon since it is a recurring request. In the meantime unforutnately, you will need to truncate the maps outside of PyMOL in order to generate smaller session files. Sorry about that! Cheers, Warren -- Warren L. DeLano, Ph.D. =20 Principal Scientist . DeLano Scientific LLC =20 . 400 Oyster Point Blvd., Suite 213 =20 . South San Francisco, CA 94080 USA =20 . Biz:(650)-872-0942 Tech:(650)-872-0834 =20 . Fax:(650)-872-0273 Cell:(650)-346-1154 . mailto:wa...@de... =20 =20 > -----Original Message----- > From: pym...@li...=20 > [mailto:pym...@li...] On Behalf Of=20 > Schubert, Carsten [PRDUS] > Sent: Friday, August 12, 2005 11:56 AM > To: pym...@li... > Subject: [PyMOL] Saving a carved section of a map. >=20 > Hi=20 >=20 > I was wondering if it is possible to save a carved out=20 > section of a map and the read it back into pymol as a=20 > separate map. The background is that I'd like to distribute=20 > .psw files with a couple of maps, but they get rather large=20 > (>50 MB) since the map data is not compressed in pymol. I am=20 > only interested in a small portion of the map centered around=20 > a ligand and some residues, so the rest of the map would be=20 > unnecessary since it will not be shown anyway.=20 >=20 > I have tried if mapman could do the trick but apparently not.=20 > I could probably restrict the calculation of the map to be=20 > only centered around a region of interest, but was wondering=20 > if this would be possible in pymol. >=20 >=20 > Thanks=20 >=20 > Carsten=20 >=20 >=20 |
From: Warren D. <wa...@de...> - 2005-08-14 19:26:23
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> > I was wondering if it is possible to save a carved out section of a=20 > > map and the read it back into pymol as a separate map. > Pymol won't do it Not so, as of today (grin). =20 In 0.99beta11 and beyond, the newly implemented command to carry this out is "map_trim". (Windows build at http://delsci.com/beta or compile from source). map_trim map-name, selection-name, buffer Combined with the convenient new object-name wildcards (!!!), you could for example trim all your maps to 3 Angstroms around ligands with one commmand as follows map_trim *, organic, 3 With map size now reduced, the map_double command can come in handy to increase mesh density on your figure. map_double * Also in this new beta: Dunbrack rotamers, nucleic acid cartoons, new pop-up menus, etc. Cheers, Warren -- Warren L. DeLano, Ph.D. =20 Principal Scientist . DeLano Scientific LLC =20 . 400 Oyster Point Blvd., Suite 213 =20 . South San Francisco, CA 94080 USA =20 . Biz:(650)-872-0942 Tech:(650)-872-0834 =20 . Fax:(650)-872-0273 Cell:(650)-346-1154 . mailto:wa...@de... =20 =20 > -----Original Message----- > From: pym...@li...=20 > [mailto:pym...@li...] On Behalf Of Tim Fenn > Sent: Saturday, August 13, 2005 11:38 AM > To: Schubert, Carsten [PRDUS] > Cc: pym...@li... > Subject: Re: [PyMOL] Saving a carved section of a map. >=20 > On Fri, Aug 12, 2005 at 02:48:16PM -0400, Schubert, Carsten=20 > [PRDUS] wrote: > >=20 > > I was wondering if it is possible to save a carved out section of a=20 > > map and the read it back into pymol as a separate map. >=20 > Pymol won't do it, but if its something thats urgent,=20 > povscript+ saves maps in GTS format (including vertex colors): >=20 > http://gts.sf.net > http://www.stanford.edu/~fenn/povscript/gts_fileformat.html >=20 > HTH, > Tim >=20 > -- > --------------------------------------------------------- >=20 > Tim Fenn > fe...@st... > Stanford University, School of Medicine > James H. Clark Center > 318 Campus Drive, Room E300 > Stanford, CA 94305-5432 > Phone: (650) 736-1714 > FAX: (650) 736-1961 >=20 > --------------------------------------------------------- >=20 >=20 >=20 > ------------------------------------------------------- > SF.Net email is Sponsored by the Better Software Conference &=20 > EXPO September 19-22, 2005 * San Francisco, CA * Development=20 > Lifecycle Practices Agile & Plan-Driven Development *=20 > Managing Projects & Teams * Testing & QA Security * Process=20 > Improvement & Measurement * http://www.sqe.com/bsce5sf=20 > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users >=20 >=20 >=20 |