Re: [PyMOL] on PDB

try running find ~/ -name “newpdb.pdb” > On Nov 27, 2015, at 9:08 PM, Smith Liu 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 lo

Re: [PyMOL] on PDB

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 newp

Re: [PyMOL] on PDB

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, No

Re: [PyMOL] on PDB

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 Blive

Re: [PyMOL] on PDB

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 Running_Scripts

Re: [PyMOL] on PDB

Dear All, For get view, we get something like set_view (\ 0.999876618, -0.000452542, -0.015699286,\ 0.000446742,0.99821, -0.000372844,\ 0.015699454,0.000365782,0.999876678,\ 0.0,0.0, -150.258514404,\ 11.842411041, 2

Re: [PyMOL] on PDB

http://www.pymolwiki.org/index.php/Modeling_and_Editing_Structures Andreas On Thu, Nov 26, 2015 at 2:24 AM, Smith Liu 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 20

Re: [PyMOL] on PDB

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" wrote: Hi Smith, You can type >get_view and copy the output into a txt file for later use. The outpu

Re: [PyMOL] on PDB

http://pymolwiki.org/index.php/Save ?? -David > On Nov 24, 2015, at 9:45 PM, Smith Liu 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 > > > > > --

Re: [PyMOL] on PDB

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 wrote: > Dear All, > > Suppose the original PD

[PyMOL] on PDB

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 amaz

Re: [PyMOL] on PDB display and calculation

Hi Smith - Check out the `orient` and `clip` commands. http://www.pymolwiki.org/index.php/Orient http://www.pymolwiki.org/index.php/Clip Cheers, Jared — Jared Sampson Graduate Student Department of Biochemi

Re: [PyMOL] on PDB display and calculation

Hi Smith, are you looking to visualize symmetrie axes? Then this might be a starting point: http://www.pymolwiki.org/index.php/SuperSym Cheers, Julian On Mon, Nov 23, 2015 at 4:15 PM, Smith Liu wrote: > Dear All, > > Once I have displayed a tetramer PDB by pymol, is any way I can get the > cen

[PyMOL] on PDB display and calculation

Dear All, Once I have displayed a tetramer PDB by pymol, is any way I can get the central axis of the tetramer and display it? Is any way I can get the cross-section of the tetramer (perpendicular to the central axis) and display it? If the tetramer is asymmetric, then how to get the central a