RE: [PyMOL] ca trace

Jason, In version 0.90, there is a ribbon_trace setting which allows you to do this for the ribbon representation. In versions 0.91+, I've added the same thing for cartoons "cartoon_trace". Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist

RE: [PyMOL] Electrostatic potential maps in PyMOL

Okay, scratch that -- I fixed the problem, relying on "standard" Fortran unformatted IO conventions to automatically determine endianness and map size. PyMOL should now be able to read a PHI map of any dimensionality, so long as record size is implicitly and correctly specified in the map file.

RE: [PyMOL] Electrostatic potential maps in PyMOL

Yes, you have identified the problem: PyMOL 0.90 currently only reads PHI files in one of the two endian formats (not sure if it is big or little). The problem is, how it PyMOL to determine which format the incoming map is in? The file format is so darn implicit, I haven't yet come up with any

RE: [PyMOL] pymol on OSX

John, The "native" OSX port is incomplete with respect to the user interface. You can get the complete package if you use the Fink version under X11. PyMOL doesn't export 3D data well at present. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Pr

RE: [PyMOL] Electrostatic potential maps in PyMOL

Hi! As far as I can see from the pymol source code, the Phimap loading routine requires the map to be big-endian (also on little-endian hardware). I guess this means that maps from SGI versions of Delphi or from GRASP (which only runs on SGI) works fine, but maps created with Linux (i386 or other

Re: [PyMOL] Electrostatic potential maps in PyMOL

Yu Chen, I have attached the output from the load command (which loads the phimap). I don't see the error that you describe. Does this output mean that it is working fine? I can generate a surface and color it with the electrostatic potential too. But I am not sure if I can trust the result

Re: [PyMOL] Electrostatic potential maps in PyMOL

Hello, Kaushik Yeah, we do had problems with DelPhi to PyMoL. I don't know what your mean by "modified version of Delphi..." We bought the latest Delphi from their website, and used the data from all the example folders comes with Delphi. The calculation all went well. When we tried to read the ph

Re: [PyMOL] Electrostatic potential maps in PyMOL

There has been some talk on the list regarding failure of PyMOL in reading Delphi generated potential maps that I missed. I have generated phimap using a modified version of Delphi in the GRASP format that PyMOL reads and displays without any problem. So I am not sure what the problem is. C

[PyMOL] ca trace

Hello: I think this was asked before but the list archives are down: If I have a pdb of Ca's only, is there a way to trace through them without iteratively bonding them all (change allowed bond distance??) Can the tube cartoon recognize this? If I bond all the Ca together iteratively, the carto

[PyMOL] Electrostatic potential maps in PyMOL

Hi PyMOL users, MEAD's potential maps can be used in PyMOL, but it requires a little more than a bit of tweaking, as the maps are in the AVS .fld format, which can not be read by PyMOL. (These maps can be read by Dino, as Paulo just mentioned). Also, PyMOL reads (as far as I can see) only big-endi

RE: [PyMOL] Further functionality

Quoting "Warren L. DeLano" : > > 1- calculation of surface potentials- will this be coming soon? > > Creation of a Possion-Boltzman solver is a bit of work, so this will not > happen very soon -- probably not until we accumulate enough sponsorship > to contract with someone to perform the task.

RE: [PyMOL] Further functionality

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 | Message: 4 From: "Warren L. DeLano" |>> 1- calculation of surface potentials- will this be coming soon? | | Creation of a Possion-Boltzman solver is a bit of work, so this will | not happen very soon -- probably not until we accumulate enough | sp