[PyMOL] Ray Trace of Icosahedral Viral Capsids using NVIDIA GE Force

Hi all I am trying to ray trace my icosahedram viral capsid, a 75 MB .pse file. I am running this on a 16 GB windows 64 bit machine with 2 GB NVIDEA GEFORCE graphics. But the memory still seems to be low as for some reason PyMOL's virtual memory is still low. I have tried set hash_max but does

Re: [PyMOL] Is Ball & Stick models of molecules possible?

Yes, now know how to build surface. But it appears that there is very little activity on the forum. Anyway, thanks. Regards On 23/04/2015, bkpsusmitaa wrote: > Corrigendum: Are instead of Is in the title/header. > as the cases could be(to add a comma) > Apologies for the typos. > Regards, > Rajib

[PyMOL] Is cyclododecene in the database of PyMol?

Hello, Dr. Thomas and members, Is cyclododecene in the database of PyMol? How to search for a molecule in Pymol database? How to confirm that any particular we have built is feasible? Eager to hear, Regards Rajib & Yuktimmana

Re: [PyMOL] Is cyclododecene in the database of PyMol?

Dear Rajib & Yuktimmana Molecules in PyMOL are stored as .pkl files. Those files are located inside the “pymol/data/chempy/fragments” folder. I guess the only way to get a confident estimation on the feasibility of a theoretical molecule is to perform quantum chemical computations. Nevertheless,

Re: [PyMOL] Ray Trace of Icosahedral Viral Capsids using NVIDIA GE Force

Hi, Did you try with this recipe ? Did you try doing the ray-traicing from a script (and not using the GUI)? Cheers, Osvaldo. On Tue, Apr 28, 2015 at 11:46 AM, Rallapalli, Pavithra < pavithra.rallapalli...@ucl.ac.uk> wrote: Hi all > > > > I am

[PyMOL] moving objects

Hi Pymol Users, I have 2 objects (objects 1 and 2) and I would like to re-orient object 1 so that the distance from either end of object 1 becomes the same to object 2 (see image). Is there a way to achieve this in PyMol? I have tried using the mouse in edit mode and I have tried using the rot

Re: [PyMOL] How to use vmd molfile_plugin in pymol?

Hi Wei-Bing, thank you for the example files. I added support for CHGCAR, POSCAR and OUTCAR. In theory there is also XDATCAR support, but that didn't work for me. The changes are available as of SVN rev 4118. Cheers, Thomas On 24 Apr 2015, at 10:05, Wei-Bing Zhang wrote: > Dear Thomas > >

Re: [PyMOL] Raw map access

Hi Filip, there is no function to query map values with 3D coordinates. There is, however, a cmd.get_volume_field() function that returns the raw map data on the grid (works with maps and volumes, PyMOL 1.7.4). With cmd.get_extend() you could put together a mapping from 3D coordinate to grid ce

Re: [PyMOL] rms_cur

Hi Bharat, your residue numbers don't match. Read about the "matchmaker" argument here: http://pymolwiki.org/index.php/Fit Cheers, Thomas On 27 Apr 2015, at 05:46, bharat gupta wrote: > Hi, > > I am using rms_cur for calculating rmsd for two sets of structures. It works > for the first set

Re: [PyMOL] How to use vmd molfile_plugin in pymol?

Dear Thomas Thanks very much. Great, It works well. I think it will attract more people to switch from VMD to Pymol. Possibly, since the new version of VASP have change the format of XDATCAR, a update of VMD plugin may be needed. A stupid question: When the pymol read the CHGCAR file, it will pr