[PyMOL] hydrogen bonds

Hi, I am a new PyMOL user and I am impressed indeed by the characteristics of this program! Since I am about preparing a paper, I would like to include some pictures prepared with PyMOL. I have a complex ligand/protein and I would like to show the hydrogen bonds interaction between them. I l

[PyMOL] selecting atoms from a mask

Dear users, I would like to select atoms from file.pdb which are - at the same time - inside the volume of a map. In other words, I would like to make to make a selection like: select file.pdb AND map.ccp4 I would like to know what would be the correct way to do it in PyMOL. Many thanks in ad

RE: [PyMOL] selecting atoms from a mask

Ricardo, Your suggestion sounds great -- enable creation of atom selections based on map value. Here is a further refinement: select (prot and map1 < 1) select (prot and map1 1 3) select (prot and map1 >= 3) select (prot and map1 = 5) Unfortunately, the code isn't yet written, but it won't tak

[PyMOL] About Surface

Hi List, PyMol is really amazing. Besides what we can do with it now, there is a great potential of evolution. I'm particularly interested in how pymol generate surface (a internal algorithm?) and how to compare it to vdW, solvent, Connolly and MSMS surfaces. Moreover, I know Del

[PyMOL] Participation

All PyMOL users please read. > From: Alan Wilter Sousa da Silva [mailto:a...@biof.ufrj.br] > PyMol is really amazing. Besides what we can do with it now, > there is a great potential of evolution. That is the key difference between PyMOL and any comparable closed-source project. PyMOL can

RE: [PyMOL] About Surface

Now, on to Alan's specific questions: > I'm particularly interested in how pymol generate surface (a > internal algorithm?) and how to compare it to vdW, solvent, > Connolly and > MSMS surfaces. PyMOL's surfacing algorithm is just something I cooked up over a weekend a couple years back.

Re: [PyMOL] About Surface

Warren, I've used Varshney's surface code (written at UNC) for many years now. There are some legal statements but I checked with UNC and they told me they didn't care who used copied or modified the code, so I consider it public domain at this point. I would be happy to send you a copy. It is C-co

[PyMOL] display of densities, electrostatic maps

Hi out there, Pymol is really amazing, I started to write a module to create and manipulate densities for pymol. Is it possible to create surfaces from contours (additional to isomesh and isodot) something like isosurf ??? Ingo -- In