very possible, can you send me the script? > On Nov 27, 2015, at 10:58 PM, Smith Liu <[email protected]> wrote: > > By Jordan, > > by > > find ~/ -name “newpdb.pdb” or by > > find / -name “newpdb.pdb” > > still does not work. Is any possibility the original "save_transformed.py" > does not work? > > > Smith > > > > > > At 2015-11-28 13:11:25, "Jordan Willis" <[email protected]> wrote: > try running > > > find ~/ -name “newpdb.pdb” > > >> On Nov 27, 2015, at 9:08 PM, Smith Liu <[email protected] >> <mailto:[email protected]>> wrote: >> >> >> Dear All, >> >> Osvaldo is new here for this question, so I repeat it a little. By pymol I >> open a pdb and orient it and I want to save the oriented pdb. First I input >> command "orient" after load the pdb, then I input command "run >> save_trannsforme.py all, newpdb.pdb". I have tried to locate the newpdb.pdb >> by locate newpdb.pdb or find newpdb.pdb, even as the root user, but I cannot >> find the outpur newpdb.pdb. My pymol is Linux Open-Source PyMOL 1.6.X. >> >> I am looking forward to getting a reply from you on how to get the oriented >> pdb, which should be different from the original PDB I load. >> >> Smith >> >> >> >> >> >> >> At 2015-11-28 00:44:07, "Shane Caldwell" <[email protected] >> <mailto:[email protected]>> wrote: >> Hi Smith, >> >> It will be in whatever folder pymol is launched from. If you launched pymol >> from a specific place, it will be that folder. If not, it might be in the >> system files for pymol, which will depend on your operating system and >> architecture. >> >> Shane >> >> >> Shane Caldwell >> McGill University >> >> On Fri, Nov 27, 2015 at 12:59 AM, Smith Liu <[email protected] >> <mailto:[email protected]>> wrote: >> Dear All， >> >> Once a molecule displayed in pymol, first I input command "orient", then I >> input command "run save_trannsforme.py all, newpdb.pdb", I cannot get the >> oriented newpdb.pdb. >> >> Will you please show me how to get the oriented newpdb.pdb? >> >> Smith >> >> >> >> >> >> At 2015-11-26 18:58:48, "Spencer Bliven" <[email protected] >> <mailto:[email protected]>> wrote: >> Smith– >> >> The code is intended to be saved to a file ("save_transformed.py") and then >> loaded into pymol using `run /path/to/save_transformed.py`. There's some >> general info on running pymol scripts: Simple_Scripting >> <http://pymolwiki.org/index.php/Simple_Scripting> Running_Scripts >> <http://pymolwiki.org/index.php/Running_Scripts> >> >> The script defines a new command which can be run e.g. `save_transformed >> <object>, <file>`. You don't have to replace anything in the script yourself. >> >> Note that the save_transformed command modifies the object it's run on, so >> you might want to run it on a backup copy by first calling `create >> <object>_backup, <object>` >> >> -Spencer >> >> On Thu, Nov 26, 2015 at 8:33 AM, Smith Liu <[email protected] >> <mailto:[email protected]>> wrote: >> Dear All, >> >> For get view, we get something like >> >> set_view (\ >> 0.999876618, -0.000452542, -0.015699286,\ >> 0.000446742, 0.999999821, -0.000372844,\ >> 0.015699454, 0.000365782, 0.999876678,\ >> 0.000000000, 0.000000000, -150.258514404,\ >> 11.842411041, 20.648729324, 8.775371552,\ >> 118.464958191, 182.052062988, 0.000000000 ) >> >> For save trasformed pdb file, we need sonething like >> >> ttt = [m[0], m[1], m[2], 0.0, >> m[3], m[4], m[5], 0.0, >> m[6], m[7], m[8], 0.0, >> 0.0, 0.0, 0.0, 1.0] >> Will you please show me how to replace m[0], m[1].... from what we get by >> get_view? Which item is which item? >> >> In addition, for the save_transformed.py, the last sentence is >> "cmd.extend('save_transformed',save_transformed)". Should we replace the >> second save_transformed with something, for example *.pdb? Ortherwise how to >> get the output modified PDB? >> >> >> I am looking forward to getting a reply from you. >> >> Smith >> >> >> >> >> >> >> >> >> >> >> >> >> At 2015-11-26 14:24:15, "Andreas Forster" <[email protected] >> <mailto:[email protected]>> wrote: >> http://www.pymolwiki.org/index.php/Modeling_and_Editing_Structures >> <http://www.pymolwiki.org/index.php/Modeling_and_Editing_Structures> >> >> >> Andreas >> >> >> On Thu, Nov 26, 2015 at 2:24 AM, Smith Liu <[email protected] >> <mailto:[email protected]>> wrote: >> Dear Shane, >> >> >> get_view is a nice command. Is any way to change the original PDB based on >> what we get by set_view to get the new pdb? >> >> Smith >> >> >> >> >> >> >> At 2015-11-26 03:54:32, "Shane Caldwell" <[email protected] >> <mailto:[email protected]>> wrote: >> Hi Smith, >> >> You can type >> >> >get_view >> >> and copy the output into a txt file for later use. The output set_view >> command will return the window to the same camera settings >> >> Shane >> >> Shane Caldwell >> McGill University >> >> On Tue, Nov 24, 2015 at 9:45 PM, Smith Liu <[email protected] >> <mailto:[email protected]>> wrote: >> Dear All, >> >> Suppose the original PDB was not oriented. Once we have it oriented by >> pymol, is any way we can save the new PDB oriented? >> >> Smith >> >> >> >> >> ------------------------------------------------------------------------------ >> Go from Idea to Many App Stores Faster with Intel(R) XDK >> Give your users amazing mobile app experiences with Intel(R) XDK. >> Use one codebase in this all-in-one HTML5 development environment. >> Design, debug & build mobile apps & 2D/3D high-impact games for multiple OSs. >> http://pubads.g.doubleclick.net/gampad/clk?id=254741551&iu=/4140 >> <http://pubads.g.doubleclick.net/gampad/clk?id=254741551&iu=/4140> >> _______________________________________________ >> PyMOL-users mailing list ([email protected] >> <mailto:[email protected]>) >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> <https://lists.sourceforge.net/lists/listinfo/pymol-users> >> Archives: http://www.mail-archive.com/[email protected] >> <http://www.mail-archive.com/[email protected]> >> >> >> >> >> >> ------------------------------------------------------------------------------ >> Go from Idea to Many App Stores Faster with Intel(R) XDK >> Give your users amazing mobile app experiences with Intel(R) XDK. >> Use one codebase in this all-in-one HTML5 development environment. >> Design, debug & build mobile apps & 2D/3D high-impact games for multiple OSs. >> http://pubads.g.doubleclick.net/gampad/clk?id=254741551&iu=/4140 >> <http://pubads.g.doubleclick.net/gampad/clk?id=254741551&iu=/4140> >> _______________________________________________ >> PyMOL-users mailing list ([email protected] >> <mailto:[email protected]>) >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> <https://lists.sourceforge.net/lists/listinfo/pymol-users> >> Archives: http://www.mail-archive.com/[email protected] >> <http://www.mail-archive.com/[email protected]> >> >> >> >> >> >> ------------------------------------------------------------------------------ >> Go from Idea to Many App Stores Faster with Intel(R) XDK >> Give your users amazing mobile app experiences with Intel(R) XDK. >> Use one codebase in this all-in-one HTML5 development environment. >> Design, debug & build mobile apps & 2D/3D high-impact games for multiple OSs. >> http://pubads.g.doubleclick.net/gampad/clk?id=254741551&iu=/4140 >> <http://pubads.g.doubleclick.net/gampad/clk?id=254741551&iu=/4140> >> _______________________________________________ >> PyMOL-users mailing list ([email protected] >> <mailto:[email protected]>) >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> <https://lists.sourceforge.net/lists/listinfo/pymol-users> >> Archives: http://www.mail-archive.com/[email protected] >> <http://www.mail-archive.com/[email protected]> >> >> >> >> >> >> >> >> >> ------------------------------------------------------------------------------ >> _______________________________________________ >> PyMOL-users mailing list ([email protected] >> <mailto:[email protected]>) >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> <https://lists.sourceforge.net/lists/listinfo/pymol-users> >> Archives: http://www.mail-archive.com/[email protected] >> <http://www.mail-archive.com/[email protected]> > > >
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