Re: [PyMOL] sphere_scale

Hi Jon, I'm stumped too, because that's the correct syntax. Can you send me a copy of your session file? The only thing I can think of at present is that a selection might need: set sphere_scale, 5, (selection_name) Cheers, -- Jason On Mon, Nov 26, 2012 at 2:53 PM, Jonathan Grimes wrote: > >

Re: [PyMOL] (no subject)

Hi Mary, Just a hint for any future lists you might be on: most modern email lists, including pymol-users, have footers with links to subscription options. You simply click that to get to a subscription page where you can unsubscribe. In this case, I removed you from the list to save you the hass

[PyMOL] (no subject)

How do I remove myself from the PyMOL users list? I'd like to stop receiving emails. Thank you. M. Hall -- Monitor your physical, virtual and cloud infrastructure from a single web console. Get in-depth insight into apps

Re: [PyMOL] rigimol (morph)

Morphing toward a target .pdb, or end-point analysis and 1) solvent box; or 2) vacuum? g...@ohsu.edu On Nov 26, 2012, at 12:42 PM, "Hasan Demirci" wrote: > Dear all, > I am trying to morph two protein-protein complex pdb files. > Everything looks fine but somehow during the morphing the comple

[PyMOL] Fuse gaps

Hi All, I recall asking a bunch of questions here about Fuse earlier this year, but I haven't needed to come back to it until now. Apologies if this has already been addressed elsewhere. When I fuse, the two objects are manually attached in a reasonable way, correct? Does the cartoon representati

Re: [PyMOL] pymol contact_map_visualizer plugin

Hi Balaji, the latest incentive builds (since v1.4, as far as I know) from Schrödinger are shipped with python 2.7. If you are looking for the open-source version, Christoph Gohlke has Windows builds with python2.7 as described on the PyMOLWiki: http://pymolwiki.org/index.php/Windows_Install#Pre-

[PyMOL] sphere_scale

I wanted to changed the size of sphere_scale for all atoms in an object, a selection of Calpha atoms. I thought I could use the command set sphere_scale, 5, object_name this doesnt seem to work and am unclear as to the reason. thanks jon does the command Dr. Jona

[PyMOL] pymol contact_map_visualizer plugin

Dear Thomas Which version of pymol has python 2.7. Is it free for academics or I have to purchase license from schrodinger. Kindly advice. Many Thanks Balaji -- Monitor your physical, virtual and cloud infrastructure fr

Re: [PyMOL] cgo object tutorials

Hi Heng, > Hi, I am just wondering if there are some useful pymol cgo tutorials > available ? such as how to visualize a 3D triangle object(vertex and > triangle files are known ) in Pymol? See https://www.google.com/?q=pymol%20cgo. There is a chapter subsection on CGOs and also a few scripts th

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

Hi Per, You'll probably want to use something like this: # load the file load http://molecules.gnu-darwin.org/html/00150001_00175000/153919/153919.pdb, myMolecule # ray trace and save the image; you need to do this since you're running # PyMOL headlessly png ~/foo.png, height=768, width=1024,

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

On Mon, Nov 26, 2012 at 8:28 AM, Per Larsson wrote: > 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

Re: [PyMOL] was: Mobile PyMOL Problem and Solution/ Now: pdb or related libraries

Hi Mike, > I was trying to figure out what to eat today so naturally I started looking > for PDB libraries > with food components. I was looking for garlic related chemicals when I came > across this, > > http://molecules.gnu-darwin.org/ > > which seems to have many pdb files. My question I gue

[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

[PyMOL] cgo object tutorials

Hi, I am just wondering if there are some useful pymol cgo tutorials available ? such as how to visualize a 3D triangle object(vertex and triangle files are known ) in Pymol? In addition, is the pymol volume visualize (http://pymol.org/volume) available for educational use ?

Re: [PyMOL] Reducing VRML file size

Another tips is to open the vrml file with 3D modelling program (for example, Blender) and remove redundant vertices. It is called "Remove Doubles" in Blender. PyMOL tends to define discrete vertices even when their coordinates are identical. See http://www.pymolwiki.org/index.php/Blender for de

Re: [PyMOL] Reducing VRML file size

Gzip it and rename the gzipped file with a "wrl" extension. The VRML standard specifies that the file can be gzipped and still be readable. You could also turn down the "quality" settings for "sticks" "cylinders" "cartoons" etc. Good luck! Darrell Sent with Xobni Mobile - http://xobni.com/mob

[PyMOL] Reducing VRML file size

Hi folks, we are currently facing problems with large VRML files. We have a quite complex .pse file with several molecules in surface representation. Once we save this .pse file as VRML it has a size of about 1.2 gigabyte. We could reduce the file size to about 700mb after combining all molecul