[PyMOL] Help with autodock plugin for PyMOL

I have a problem when running the autodock plugin for PyMOL. I followed the tutorial at http://www.pymolwiki.org/index.php/Autodock_plugin. When I prepare the ligand I get the following error output: Batch: /usr/lib/python2.7/site- packages/MGLToolsPckgs/AutoDockTools/Utilities24/prepare_ligand4.

Re: [PyMOL] Rotation of entire helix

Hi Alex, You have a couple options. First, use the rotate command: # rotate the selected atoms 4.5 degrees about the x axis. rotate x, 4.5, (sele) If you specifically know the axis of rotation, supply it as a vector. Next, PyMOL can also do rotations about an axis defined by two picked atoms.

[PyMOL] Rotation of entire helix

Hi All, So I have a structure that's fully modeled, but I have one alpha helix that is turned in a non-optimal way. Is there anyway to "rotate" the entire helix along its barrel while keeping everything else fixed? The objective is to turn it such that a critical side chain that was facing inward

Re: [PyMOL] cctbx and pymol version 1.41

On Fri, Oct 26, 2012 at 10:37 AM, joseph Lyons wrote: > I currently source cctbx from /usr/local/xtal/cctbx/cctbx_build/setpath.sh > with pymol in /usr/local/xtal/pymol_1.41/pymol > > I have tried the getting pymol to recognise the cctbx.python however I have > run into difficulties. > > I tried m

[PyMOL] cctbx and pymol version 1.41

Hi, I am currently trying to run the plugin SuperSymPlugin12.py. However it requires cctbx. I currently source cctbx from /usr/local/xtal/cctbx/cctbx_build/setpath.sh with pymol in /usr/local/xtal/pymol_1.41/pymol I have tried the getting pymol to recognise the cctbx.python however I have run in

Re: [PyMOL] Volume visualization

Thanks, it works beautifully Cheers /Per 26 okt 2012 kl. 16:42 skrev Jason Vertrees: > Hi Per, > >> So, to add to that, the version that is available through eg MacPorts (v 1.5 >> iirc) should give me what I want? >> I watched a Youtube-video showing some of the rendering capabilities in the

Re: [PyMOL] Volume visualization

Hi Per, > So, to add to that, the version that is available through eg MacPorts (v 1.5 > iirc) should give me what I want? > I watched a Youtube-video showing some of the rendering capabilities in the > Volume-interface, and it seems to be really nice. Volume rendering came out in v1.4 of PyMOL

Re: [PyMOL] Volume visualization

Hi Jason Thank you! So, to add to that, the version that is available through eg MacPorts (v 1.5 iirc) should give me what I want? I watched a Youtube-video showing some of the rendering capabilities in the Volume-interface, and it seems to be really nice. Cheers /Per 26 okt 2012 kl. 06:15 s