Re: [PyMOL] Corrupted IDTF file from small molecule (sticks representation)

I'm sorry for the news.. I did not know about DeLano's death ... in November of 2009, I read: I did not know about the "Open Source PyMOL Fellowship projects" of which Jared has spoken, so I made a web search, finding this web page, and so the news, with the date .

Re: [PyMOL] Corrupted IDTF file from small molecule (sticks representation)

Hi Riccardo - I guess you are asking if "layer1/Ray.c" is the only place you'd have to write code to implement IDTF export of spheres, cylinders, etc.? Then I believe the answer is "yes." I'm working on a COLLADA implementation as one of my PyMOL Open Source Fellowship projects this year, and

Re: [PyMOL] Corrupted IDTF file from small molecule (sticks representation)

Riccardo, like me, I think you forgot to "reply all." (I gather that from your addressing two of us and not just me.) Yes, Jmol does that. It's not perfect, but it's a respectable amount of PyMOL functionality. This is actually something that Warren and I talked about not too long before his unti

Re: [PyMOL] Corrupted IDTF file from small molecule (sticks representation)

So in the mean time, Riccardo, I guess what you are already using: xxx.pse -- JmolData.jar --> idtf is your best bet. Q: What sort of size of PDF file are you seeing in the end? Q: Do you see this a practical and useful in some way? If so, in what way? Bob Hanson --

Re: [PyMOL] Corrupted IDTF file from small molecule (sticks representation)

Hi Riccardo - Looking at the source (pymol/layer1/Ray.c, in RayRenderIDTF(), starting around line 2254) I can confirm that Sphere, Cone, Cylinder and Sausage representations are not implemented in the IDTF exporter. Currently only triangle mesh representations (cartoon, surface) are supported.

[PyMOL] RNA stick depiction with filled-out rings

Hi Pymol users, I am trying to depict RNA as sticks, however with filled-out rings (bases and ribose). I have been going about doing this by combining cartoon view for the filled-out bases, using set_cartoon_radius=0 and stick view for the backbone. When doing this I am always left with a fine