[PyMOL] Displaying hydrophobic contacts

Hi everyone, I am trying to find a way to display hydrophobic (non-polar) interactions in PyMOL, the same way as we can display polar contacts. I am pretty sure this can be done. Does anyone know the command? Many thanks in advance. Angela -- Angela Gray -- Angela Gray

[PyMOL] How does PyMol add hydrogen atoms?

Hello all, I've been looking at Pymol's code for sometime time now and yet the algorithm for addition of hydrogen atoms to molecules in Pymol is not clear to me.. I've traced the h_add function to OMOP_AddHydrogens in layer2/Executive.c: op.code = OMOP_AddHydrogens;/* 4 passes comple

[PyMOL] DSS

Hi all, Is there a way to get an output from PyMol's DSS command (like a dssp output)? -- Bradley J. Hintze Graduate Student Duke University School of Medicine 801-712-8799 -- ThinkGeek and WIRED's GeekDad team up for t

Re: [PyMOL] DSS

Hi Bradley, PyMOL uses its own internal routine for secondary structure classification. The iterator token is "ss". Check out http://pymolwiki.org/index.php/Ss and http://pymolwiki.org/index.php/Iterate_sses and http://pymolwiki.org/index.php/WriteSS. Cheers, -- Jason On Tue, Jun 22, 2010 at

[PyMOL] Question about ray

Dear Pymol-Users, I tried to ray my protein to get a good looking picture. I tried set ray_trace_mode, 0 and ray 1200, 1200. I always go a square around my protein and parts where not visible. How can I get rid of that black border line and how can I ray my protein so it is on the whole page

Re: [PyMOL] Question about ray

Try setting your Pymol viewer to square dimensions first: Viewport 600,600 Then try the ray command This should work Joel _ Joel Tyndall, PhD Senior Lecturer in Medicinal Chemistry National School of Pharmacy University of Otago PO Box 56 Dunedin 9054 New Zeala

Re: [PyMOL] Question about ray

Hi all, Joel's correct: to get the ray traced image to match the viewport, you must set the viewport to the same aspect ratio as the output image: # setup the viewport viewport 800, 600 # zoom on the visible zoom visible # ray the scene ray 800,600 # scale it up ray 1600, 1200 Cheers, -- Jas