Re: [PyMOL] how to create a new .pdb from 3 pdb's?

Hi Tsjerk, It did work! Thanks! Afonso On Sun, Mar 28, 2010 at 7:05 PM, Tsjerk Wassenaar wrote: > Hi Afonso, > > If you want to connect one object to another, you want to check out > the fuse command (help fuse) > > fuse atom_to_be_connected_from_object1, atom_to_be_connected_from_object2 > > H

[PyMOL] PYNMR or NMR support in Pymol

Hello Jayson, as I saw you are starting to implement crystallographic specific elements like fetching maps from the EDS, what about putting some NMR related features on top. The most important would be to get something like the old pyNMR plugin to show NOE restrains. What do you think about this i

[PyMOL] raw_input is not working in pymol command line

Hi, I had the idea that PyMol command line would respond to python commands. but today I tried raw_input('something: ') and it just gave error. PyMOL>raw_input('something: ') something: Traceback (most recent call last): File "/Users/koray/Downloads/MacPyMOL.app/pymol/modules/pymol/parser.p

[PyMOL] Transparency vs. Selection

Hi All, I'm not sure if this is a bug in PyMOL but I found that when you make a selection, show it as spheres representation, and then turn on the transparency (to anything but "off"), none of the now transparent spheres be selected via a mouse-click in the viewing area. Thus, if I selected

Re: [PyMOL] Transparency vs. Selection

Sean, Keen eye, there. Some representations are not selectable, like surfaces, and apparently transparent spheres. One trick/workaround is to show sticks and then spheres with transparency. If you need to hide the sticks, just set stick_transparency to 1.0. Here's an example, load $TUT/1hpv.p

[PyMOL] odd rendering with pdbqt files containing multiple molecules

Hi, Has anyone come across odd rendering problems with MacPyMol when loading pdb/pdbqt files with multiple molecules? For example, bonds span the length of an entire molecule; invisible bonds; impossible orientations, etc. Single molecule pdb/pdbqt are rendered correctly, however. Thanks, Paul

Re: [PyMOL] Atom Connections

Brett, > Thank you for your help Jason. I think this will work for my needs. > By one side vs. the other, I mean let's say we just look at the backbone of > a protein consisting of 5 residues, numbered 0, 1, 2, 3, 4 > I want to click on the C-a atom of residue 3, and generate 2 selections, one >

Re: [PyMOL] PYNMR or NMR support in Pymol

Justin, If this interests you, please send it to h...@schrodinger.com and also add your vote to http://www.pymolwiki.org/index.php/Ideas. I think this idea currently only has two supporters. Thanks, -- Jason On Wed, Mar 31, 2010 at 8:28 AM, Justin Lecher wrote: > Hello Jayson, > > as I saw yo