Re: [PyMOL] Compile error svn 4162

Dear Thomas, Yes, confirmed fixed in rev 4163. Thank you. Best, Quyen On Tue, Oct 18, 2016 at 5:41 AM, Thomas Holder < thomas.hol...@schrodinger.com> wrote: > Hi Quyen, > > This should be fixed in svn rev 4163. > > Cheers, > Thomas > > On 18 Oct 2016, at 01:05, QT wrote: > > > Dear all, > >

Re: [PyMOL] Using 'python' and 'python end' in pymol scripts

Rename the script from .py to .pml Regards, Gabriel Marques PyMOL > On Oct 19, 2016, at 4:39 PM, #YEO JINGJIE# wrote: > > Dear Users, > > I am trying to implement a script which uses a mix of pymol and python > scripting. I enclosed the main portion within the 'python' and 'python end' > com

[PyMOL] Using 'python' and 'python end' in pymol scripts

Dear Users, I am trying to implement a script which uses a mix of pymol and python scripting. I enclosed the main portion within the 'python' and 'python end' commands. This runs perfectly fine in Pymol GUI mode, however when I tried it with 'pymol -cg my_script.py', it generates an error: Tra

Re: [PyMOL] problem saving the transformed coordinate after alignment

Thanks Gabriel and David for the useful suggestion. Best Regards, Subha On Wed, Oct 19, 2016 at 12:11 PM, David Hall wrote: > I think the answer is to just use save, not that save_transformed function. > > -David > > On Oct 19, 2016, at 1:47 PM, Subha K wrote: > > Hi there, > > I am trying to

Re: [PyMOL] Adding a new internal GUI to Pymol for Leap motion support

Hi Johan and Casper, You can create a menu above the mouse mode panel by writing a wizard. There is no API documentation for wizards, so you have to learn from existing wizards as examples. You can create an external menu or panel with Tkinter and/or Pmw. See for example eMovie as an example f

Re: [PyMOL] problem saving the transformed coordinate after alignment

I think the answer is to just use save, not that save_transformed function. -David > On Oct 19, 2016, at 1:47 PM, Subha K wrote: > > Hi there, > > I am trying to save the transformed coordinates of an object after performing > an alignment. I came across the save_transformed.py > [https://py

Re: [PyMOL] problem saving the transformed coordinate after alignment

Subha K, You can just call cmd.save or save on the object name as so: fetch 1oky 1t46, async=0 align 1oky, 1t46 save /tmp/1oky_transformed.pdb, 1oky PyMOL will write out the transformed coordinates of 1oky into the pdb file. The structure of the alignment command is such that pymol transforms t

[PyMOL] problem saving the transformed coordinate after alignment

Hi there, I am trying to save the transformed coordinates of an object after performing an alignment. I came across the save_transformed.py [ https://pymolwiki.org/index.php/Modeling_and_Editing_Structures], but, this seems to give a completely different coordinate of the object and not the one th