[PyMOL] Volume visualization

Also, are there any differences between incentive v 1.4 and 1.5 in terms of volume visualization? Thanks /Per Larsson-- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDyn

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

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

[PyMOL] Ray-trace of volume visualization

Hi! Following up on my earlier post http://sourceforge.net/mailarchive/message.php?msg_id=30017929, I have managed to make some very nice volume visualizations in Pymol. I now wonder about the possibilities of ray-tracing the volume? I should add that I'm not a graphics guru, so maybe this doe

Re: [PyMOL] Ray-trace of volume visualization

ring I'd love to see what you came up with. > > Cheers, > > -- Jason > > On Fri, Nov 2, 2012 at 1:19 PM, Per Larsson wrote: >> Hi! >> >> Following up on my earlier post >> http://sourceforge.net/mailarchive/message.php?msg_id=30017929, I have &g

[PyMOL] Controlling colors in volume object

Hi pymol-users I have previously been able to make quite nice visualizations of my volume object, containing the time-averaged density of atoms from a MD-simulation. For making even more improvement, I'd like to be able to use a script (either python or pml) to control which regions of density g

Re: [PyMOL] Controlling colors in volume object

(2,(0.39,0.67,1,0.01),0) r.addColor(130,(0,1,0.50,0.25),0) r.addColor(192,(1,0.0,0.0,0.25),0) r.addColor(255,(1,0,0,0.25),0) ramp_colors = r.getRamp() cmd.volume_color("density",ramp_colors) 21 nov 2012 kl. 17:30 skrev Per Larsson: > Hi pymol-users > > I have previously been ab

[PyMOL] Pymol in command mode - no output

Hi Pymol-users, I'm running a pml-script file to render some images on a remote server, using pymol 1.4, but I do not get any output at all. And no error message, so it is hard to troubleshoot, unfortunately. To reduce the complexity of my script, I have reduced it to basically just loading a

Re: [PyMOL] Pymol in command mode - no output

d delete this > e-mail immediately. Thank you. > > -Original Message- > From: Jason Vertrees [mailto:jason.vertr...@schrodinger.com] > Sent: 26. november 2012 17:48 > To: Per Larsson > Cc: pymol-users@lists.sourceforge.net > Subject: Re: [PyMOL] Pymol in comma

[PyMOL] Per residue rms?

Dear people Is there somewhere in pymol that will allow me to print or otherwise get access to per-residue rms-values when doing a structural superposition? Regards /Per Larsson

[PyMOL] Per residue rms

Dear people Is there somewhere in pymol an option that will allow me to see the per-residue rms-values when doing a structural alignment with align? Regards /Per Larsson

[PyMOL] Change location of measurement label

Hi! I need to make some pictures of very simple di-peptide systems, and need to include values (from wizard->measurement->dihedrals) of certain dihedral angles. However, the two labels end up very close, with the values almost on top of each other making them un-readable. Is there a way to