Re: [PyMOL] `selection` argument in load_traj

Hi Lorenzo, You are correct, it's doing nothing for most trajectory formats. Only the implementation for AMBER .trj files uses it. It looks like it allows selecting a subset of atoms. Cheers, Thomas > On Jun 25, 2019, at 4:05 PM, Lorenzo Gaifas wrote: > > Dear pymol users, > > What is the

Re: [PyMOL] Thermal ellipsoid plot

Mr. Thomas Holder, Many thanks for your help. I can manage it. Best regards, Koji 2019年6月26日(水) 18:56 Thomas Holder : > Hi Koji, > > Yes it is my understanding that sphere_scale 1.1932 would correspond to > 30% probability. > > Cheers, > Thomas > > > On Jun 25, 2019, at 12:26 PM, koji naka

Re: [PyMOL] Thermal ellipsoid plot

Hi Koji, Yes it is my understanding that sphere_scale 1.1932 would correspond to 30% probability. Cheers, Thomas > On Jun 25, 2019, at 12:26 PM, koji naka wrote: > > Dear Mr. Thomas Holder, > > Thank you very much for your kind reply. > I am very happy to know the scale factor for the 50%

Re: [PyMOL] set transparency for selected elements of secondary structure

OK, with latest pymol this works fine set cartoon_transparency, 0.5, object this does not work set cartoon_transparency, 0.5, ss H+S how I can select for example all of the objects in the current session + ss H+S ? ср, 26 июн. 2019 г. в 11:13, Thomas Holder : > > Hi James and Ali, > > Are you u

Re: [PyMOL] set transparency for selected elements of secondary structure

Hi James and Ali, Are you using PyMOL 2.3 yet? "As of PyMOL version 2.3, cartoon transparency is now an atom-level setting." https://pymolwiki.org/index.php/Cartoon_transparency Cheers, Thomas > On Jun 26, 2019, at 10:26 AM, Ali Kusay wrote: > > Hi James, > > I am not sure what the exact

Re: [PyMOL] Export molecule does not keep changes

Hi Jesse, I am not aware of a structure file (i.e. PDB) which can store information such as color and thus when you load a PDB file pymol applies the default colors to it. You can however make it so that all proteins loaded into pymol are automatically assigned the grey colour, this is done by

Re: [PyMOL] set transparency for selected elements of secondary structure

Hi James, I am not sure what the exact cause of your issue is but I think if you make a selection first then apply the transparency to the selection that should work, i.e.: sele ss H+S set cartoon_transparency, 0.5, sele Something to do with selection based transparency settings not enabling n

[PyMOL] Export molecule does not keep changes

Hello! (English is not my native language; please excuse typing errors.) Goal is to recolor molecule so it stays that way after the edit. This is how I thought it would work: Lets start by opening any molecule (like downloading 5jh0.cif from https://www.rcsb.org/structure/5jh0) Changed the c

[PyMOL] set transparency for selected elements of secondary structure

Dear pymol users! I am trying to set transparency based on the secondary structure using pymol selection algebra # set transparency to all helix and sheets but not loops set cartoon_transparency, 0.5, ss H+S which produce the following output PyMOL>set cartoon_transparency, 0.5, ss H+S Setting: