[PyMOL] Get dihedral angle of multiple objects

Hi, I'm trying to use this script to get a specific dihedral angle from all the objects and write into a file: PyMOL>f = open('dih.txt','w') PyMOL>for obj in cmd.get_object_list():\ PyMOL>dih = cmd.dihedral('dih','/obj///655/CA','/obj///655/CB','/obj///655/CG','/obj///655/CD1')\ PyMOL>f.w

Re: [PyMOL] Get dihedral angle of multiple objects

Hi, I am assuming it is because, when you pass the arguments on the cmd.dihedral() command, the "obj" is being read as a string, instead of the variable obj. I think your problem will be solved if you use something like, for your first example: "/"+obj+"///655/CA" Note the quotation marks pla

[PyMOL] how to show PBC box?

Hello: I am visualizing a MD simulation system in PyMOL. It contains the PBC information. I am just wondering how can we show the PBC box in PyMOL? As far as I know the PBC box can be shown in VMD using the following command line: >pbc box Is there any similar command line in PyMOL? Thank y

Re: [PyMOL] how to show PBC box?

Hi Albert, You can do: show cell Cheers, Tsjerk On Dec 7, 2016 8:44 PM, "Albert" wrote: > Hello: > > I am visualizing a MD simulation system in PyMOL. It contains the PBC > information. I am just wondering how can we show the PBC box in PyMOL? > As far as I know the PBC box can be shown in V

Re: [PyMOL] how to show PBC box?

Dear Tsjerk: Thanks a lot for such prompt reply. It works very well. Cheers. Albert On 12/07/2016 08:46 PM, Tsjerk Wassenaar wrote: Hi Albert, You can do: show cell Cheers, Tsjerk -- Developer Access Program