Yes, but what you are describing, saving a new view is your purpose. All orient does is move the camera. It does not do anything to the x,y,z coordinates of the PDB. > On Nov 27, 2015, at 11:49 PM, Smith Liu <[email protected]> wrote: > > Dear Jordan, > > To save a new view is not my purpose, my purpose is to save a new set of PDB. > For example， if the original PDB does not orient well by pymol by default, > first I input "orient", and I want to save a set of new pdb, when I display > by pymol the new pdb, it will display as "oriented“. Is any way we can get > this oriented pdb? > > Smith > > > > > > At 2015-11-28 15:37:10, "Jordan Willis" <[email protected]> wrote: > get view takes in camera coordinates. You can’t open a PDB and it have know > anything about the camera view. You will have to grab the view, save it > somewhere, and then load it. You can’t code a view change within the PDB. > > >> On Nov 27, 2015, at 11:27 PM, Smith Liu <[email protected] >> <mailto:[email protected]>> wrote: >> >> Dear Jordan, >> >> My purpose is, once you move a molecule in pymol, I want to save a new pdb, >> when we open the new pdb, pymol will display the new position as default. >> >> The script is >> >> "# Adds the command save_transformed >> # Usage: save_transformed object, file >> def save_transformed(object,file): >> m = cmd.get_view(0) >> 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] >> cmd.transform_object(object,ttt) >> cmd.save(file,object) >> cmd.extend('save_transformed',save_transformed)" >> >> shown in http://pymolwiki.org/index.php/Modeling_and_Editing_Structures >> <http://pymolwiki.org/index.php/Modeling_and_Editing_Structures> >> >> Here I notice that once load a pdb, you move it a little, then you input >> "get_view", you will get the matrix like >> 0.448818117, 0.886667669, -0.111277729 >> -0.889764965, 0.454960942, 0.036454394 >> >> which should be the m[0] to m[5] in the above script. >> >> In addition, in http://www.pymolwiki.org/index.php/Transform_odb >> <http://www.pymolwiki.org/index.php/Transform_odb>, there is also a >> transcript. For matrix it uses *.odb file. Is this *.odb same as the >> get_view matrix, if not, can we convert get_view matrix to *.odb? >> >> Besides, in http://www.pymolwiki.org/index.php/Transform_selection >> <http://www.pymolwiki.org/index.php/Transform_selection> there is another >> script. >> >> I do not know how to use this scripts to realize my purpose. >> >> Smith >> >> >> >> >> >> >> >> >> At 2015-11-28 15:07:18, "Jordan Willis" <[email protected] >> <mailto:[email protected]>> wrote: >> very possible, can you send me the script? >>> On Nov 27, 2015, at 10:58 PM, Smith Liu <[email protected] >>> <mailto:[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] >>> <mailto:[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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