From: Warren D. <wa...@de...> - 2005-07-18 18:02:24
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Sebastien, Yes, you can do with with a "p1m" file, which is like a "pml" file, but = data can be included as well. Also note that p1m files are intended for = web publishing, so embedded Python is disallowed. In p1m files, there = is an "embed" command that enables this for PDB, MOL, MOL2, SDF, and = XPLOR data. It works like this: embed tag, format ****REPLACE THIS LINE WITH YOUR DATA FILE**** embed end load_embedded tag where tag is some identifier of your choice. 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 > Sebastien Moretti > Sent: Monday, July 18, 2005 5:03 AM > To: pymol-users > Subject: [PyMOL] Mix pml script and PDB file >=20 > Hello, > Is there a way to get one file with pymol commands (pml=20 > script) and with the structure (PDB file) ? >=20 > I can get this with Rasmol and the ras script file. > Can I get the same kind of file with PyMOL ? >=20 > Thanks >=20 > -- > S=E9bastien Moretti > http://www.igs.cnrs-mrs.fr/ > CNRS - IGS > 31 chemin Joseph Aiguier > 13402 Marseille cedex >=20 >=20 > ------------------------------------------------------- > SF.Net email is sponsored by: Discover Easy Linux Migration Strategies > from IBM. Find simple to follow Roadmaps, straightforward articles, > informative Webcasts and more! Get everything you need to get up to > speed, fast. http://ads.osdn.com/?ad_idt77&alloc_id=16492&op=3Dick > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users >=20 >=20 >=20 |
From: <tan...@st...> - 2005-07-18 20:48:56
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Hi, web publishing? Sounds like a nice feature... are there any documentations about that? regards Yusuf Quoting Warren DeLano <wa...@de...>: > Sebastien, > > Yes, you can do with with a "p1m" file, which is like a "pml" file, > but data can be included as well. Also note that p1m files are > intended for web publishing, so embedded Python is disallowed. In > p1m files, there is an "embed" command that enables this for PDB, > MOL, MOL2, SDF, and XPLOR data. It works like this: > > embed tag, format > ****REPLACE THIS LINE WITH YOUR DATA FILE**** > embed end > > load_embedded tag > > where tag is some identifier of your choice. > > Cheers, > Warren > > -- > Warren L. DeLano, Ph.D. > Principal Scientist > > . DeLano Scientific LLC > . 400 Oyster Point Blvd., Suite 213 > . South San Francisco, CA 94080 USA > . Biz:(650)-872-0942 Tech:(650)-872-0834 > . Fax:(650)-872-0273 Cell:(650)-346-1154 > . mailto:wa...@de... > > >> -----Original Message----- >> From: pym...@li... >> [mailto:pym...@li...] On Behalf Of >> Sebastien Moretti >> Sent: Monday, July 18, 2005 5:03 AM >> To: pymol-users >> Subject: [PyMOL] Mix pml script and PDB file >> >> Hello, >> Is there a way to get one file with pymol commands (pml >> script) and with the structure (PDB file) ? >> >> I can get this with Rasmol and the ras script file. >> Can I get the same kind of file with PyMOL ? >> >> Thanks >> >> -- >> S=E9bastien Moretti >> http://www.igs.cnrs-mrs.fr/ >> CNRS - IGS >> 31 chemin Joseph Aiguier >> 13402 Marseille cedex >> >> >> ------------------------------------------------------- >> SF.Net email is sponsored by: Discover Easy Linux Migration Strategies >> from IBM. Find simple to follow Roadmaps, straightforward articles, >> informative Webcasts and more! Get everything you need to get up to >> speed, fast. http://ads.osdn.com/?ad_idt77&alloc_id=16492&op=3Dick >> _______________________________________________ >> PyMOL-users mailing list >> PyM...@li... >> https://lists.sourceforge.net/lists/listinfo/pymol-users >> >> >> > > > ------------------------------------------------------- > SF.Net email is sponsored by: Discover Easy Linux Migration Strategies > from IBM. Find simple to follow Roadmaps, straightforward articles, > informative Webcasts and more! Get everything you need to get up to > speed, fast. http://ads.osdn.com/?ad_idt77&alloc_id=16492&op=3Dclick > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users > |
From: Sebastien M. <seb...@ig...> - 2005-07-19 10:04:54
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> Sebastien, >=20 > Yes, you can do with with a "p1m" file, which is like a "pml" file, but= data can be included as well. Also note that p1m files are intended for= web publishing, so embedded Python is disallowed. In p1m files, there i= s an "embed" command that enables this for PDB, MOL, MOL2, SDF, and XPLOR= data. It works like this: >=20 > embed tag, format > ****REPLACE THIS LINE WITH YOUR DATA FILE**** > embed end >=20 > load_embedded tag >=20 > where tag is some identifier of your choice. >=20 > Cheers, > Warren Warren, It is the format I sought for. E.g.: embed 1H1S, pdb HEADER TRANSFERASE 21-JUL-02 1H1S TITLE STRUCTURE OF HUMAN THR160-PHOSPHO CDK2/CYCLIN A COMPLEXED ... CONECT 9002 9000 MASTER 531 0 4 64 20 0 8 6 9701 4 82 88 END embed end load_embedded 1H1S ... I load structure and PyMOL instructions in one file. Thanks >>Hello, >>Is there a way to get one file with pymol commands (pml=20 >>script) and with the structure (PDB file) ? >> >>I can get this with Rasmol and the ras script file. >>Can I get the same kind of file with PyMOL ? >> >>Thanks --=20 S=E9bastien Moretti http://www.igs.cnrs-mrs.fr/ CNRS - IGS 31 chemin Joseph Aiguier 13402 Marseille cedex |