Re: [PyMOL] Outlines thickness

s black and less infill. > > 3. Setting the Ray_trace_slope_factor higher, will also reduce the infill > black. 0.9 Ray_trace_slope_factor and ray_trace_gain of 0.2 at 1500dpi > looks fairly good. > > It seems that PyMOL doesn’t have a way to easily control the ray traced > black

[PyMOL] Outlines thickness

Hi, is there a proper way to increase outlines thickness in PyMol? I noticed that increasing ray_trace_gain setting outlines are drawn thicker but increasing this setting increases also the number of outlines. Is there a way to increase thickness without increasing the outlines number? __

[PyMOL] How to store primitives number in a variable

Hi, I would like to store in a variable the primitives number gained from cmd.ray(renderer=2). I am trying to redirect output using StringIO module but seems not to work. Is there an other way to do this? ___ PyMOL-users mailing list Archives: http://www.

[PyMOL] Ambient occlusion on isosurface

Hi, is it possible to set ambient occlusion for isosurfaces? -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot

[PyMOL] interior color always white

Hi, I have found that with this settings the rendering keeps always white the interior color. fetch 1c0k, async=0 as spheres, clip near , -50 set ray_interior_color, pink set direct,off set spec_direct,1 set light_count, 1 ray If you change the light_count to 2 or try to shut down spec_direct, th

[PyMOL] Export vmrl as single object

Hi, when I try to export a sphere representation as a vrml file and then import it into blender, the file is imported as multiple objects. When a lot of spheres are present int the representation, blender imports the file very slowly.. is there a way to export the representation as a single object

[PyMOL] Assembly comparison between cif/pdb and mmtf file format

Hi, I was trying to set assembly 1 and load 1C0K (and other structures) in pdb, cif and mmtf format. I noticed that when I split_states and get each model, model_0001 of cif and pdb format corresponds to model_0002 of mmtf format.

Re: [PyMOL] Load mmtf data

am missing? 2017-06-22 17:52 GMT+02:00 Gianluca Tomasello : > Thank you very much! > > 2017-06-22 13:11 GMT+02:00 Thomas Holder : > >> Hi Gianluca, >> >> Yes this is possible, assuming you're using PyMOL 1.8.6. Use something >> like this: >> >&

[PyMOL] Increase label outline size

Hi, Is there a way to control the size of label outline in pymol? -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot___

[PyMOL] show nonbonded atoms with stick representation

Hi, is it possible to render nonbonded atoms as small spheres using only stick representation? -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot__

Re: [PyMOL] Valence bonding ray trace in batch mode

Cheers, > Thomas > > > > > > On Jul 4, 2017, at 3:39 PM, Gianluca Tomasello > wrote: > > > > Hi Thomas, > > > > the script below reproduce the behavior for me. I don't use pymolrc file > or k flag. > > > > I loaded the script like this a

Re: [PyMOL] Valence bonding ray trace in batch mode

o you pass -k flag > (ignores pymolrc files) in batch mode? > > Cheers, > Thomas > > > On Jul 2, 2017, at 5:32 PM, Gianluca Tomasello > wrote: > > > > Hi, I am trying to execute a script that sets valence bonding on sticks > and then it gives me back a rendered i

[PyMOL] Valence bonding ray trace in batch mode

Hi, I am trying to execute a script that sets valence bonding on sticks and then it gives me back a rendered image. There seems there is a difference when i try to run the script normally or in batch mode (pymol -cq script.py). If i run it in batch mode, each atom with a double bond is rendered wi

[PyMOL] Load mmtf data

Hi, I am using read_pdbstr function to load a strucutres into pymol. Is there a way to do the same for mmtf file formats? (I mean without using temporary files) -- Check out the vibrant tech community on one of the world's

Re: [PyMOL] ball stick representation problem

It works with: > > - Incentive PyMOL (all rendering modes) > - Open Source PyMOL in ray tracing and with use_shaders=0 > > Cheers, > Thomas > > > > On Jun 15, 2017, at 11:32 AM, Gianluca Tomasello > wrote: > > > > Hi, I am following the instructu

[PyMOL] ball stick representation problem

Hi, I am following the instructuions on https://pymolwiki.org/index.php/Ball_and_Stick to make a ball and stick representation. I would like to use only stick representation to accomplish this task, and I finded the last method in the page is not working properly on my version of pymol (1.8.4.0) s