[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 save_transformed.py

Dear Smith, The line cmd.extend('save_transformed',save_transformed) adds a new command to PyMOL, this command is named save_transformed and what is does is to call the save_transformed function. This function takes two arguments save_transformed(object, file), hence the newly created command also

[PyMOL] on save_transformed.py

Dear All, In http://pymolwiki.org/index.php/Modeling_and_Editing_Structures there is "save_transformed.py". Will you please show me how to use this script? There is no problem to do "run save_transformed.py". But after click that command, how to get and save the transformed pdb file? Smith-

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