Re: [PyMOL] PyMOL 1.6 pre-release announcement

2013-06-14 Thread Robert Campbell
Hello Thomas and David, Was there any resolution of this? I've just compiled the latest version from SVN and I have the same problem opening files created under version 1.5.0. This is on Debian testing (32-bit). Cheers, Rob On Fri, 2013-04-26 19:15 EDT, David Hall wrote: > Hi Thomas, > >

Re: [PyMOL] Distorted secondary structure using 'alter' command

2013-06-14 Thread Thomas Holder
Hi Ritu, do I understand correctly that resi 3-9 are *not* in helix conformation, and you want to perform a modelling task? Altering the ss property is not sufficient, that's just an annotation and not a modelling constraint. PyMOL is primarily a visualization tool and less a modelling tool, altho

Re: [PyMOL] Isomesh plot in Pymol vs Coot

2013-06-14 Thread Thomas Holder
Hi Partha, load your structure and map into PyMOL like this: PyMOL> load your.pdb PyMOL> load your_2fofc.map, format=ccp4 or: PyMOL> load your_2fofc.ccp4 Hope that helps. Cheers, Thomas Munshi, Parthapratim wrote, On 06/13/13 21:20: > Hi > > I am having some issues with the isomesh plot in

Re: [PyMOL] Visualizing sp3-hybridized electron orbital

2013-06-14 Thread Thomas Holder
Hi Yury, if you have the electron cloud as map data, you can load it into PyMOL and use any map visualization (volume, isosurface, isomesh). Once the map is loaded into PyMOL, use the "A" (Action) button next to the object name in the object menu panel on the right. Supported map formats include: