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 produce a set of data like spin up+down and spin up-down. How can i access different data in pymol? Thanks again Best Wei-Bing On 29/04/2015, Thomas Holder <thomas.hol...@schrodinger.com> wrote: > 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 <weibingzhang...@gmail.com> wrote: > >> Dear Thomas >> >> Thanks very much for your prompt reply and kindness. I am using VASP >> to do some DFT calculation and want to use pymol to visualize the >> geometry structure (i.e. POSCAR/CONTCAR file) and charge density >> (CHGCAR). The corresponding VASP plugins for VMD has been developed >> and integrated in official VMD. The VASP geometry is always periodic. >> The related files of a simple example (a relax CO molecule,the main >> output file : POSCAR/CONTCAR, CHGCAR/CHG) are enclosed. The >> corresponding help file can be also found at >> http://cms.mpi.univie.ac.at/vasp/vasp/POSCAR_file.html;http://cms.mpi.univie.ac.at/vasp/vasp/CHGCAR_file.html >> >> Thanks very much for your help again. >> >> Best wishes >> >> On 24/04/2015, Thomas Holder <thomas.hol...@schrodinger.com> wrote: >>> Hi Wei-Bing, >>> >>> support to load topology files with the vmd plugins was added in PyMOL >>> 1.7.4 >>> (previous versions only supported trajectories and maps). >>> >>> Unfortunately, every supported filetype has to be registered in PyMOL, >>> right >>> now only CMS files (Desmond topology) are registered to be passed to the >>> vmd >>> plugin loader. You could of course modify open-source PyMOL yourself to >>> add >>> a filetype, but you have to edit about 5 files! >>> >>> If you send me example input files (topology and trajectory) I can >>> register >>> their extensions and check it in to the SVN repo. >>> >>> Cheers, >>> Thomas >>> >>> On 24 Apr 2015, at 06:13, Wei-Bing Zhang <weibingzhang...@gmail.com> >>> wrote: >>> >>>> Dear all >>>> >>>> Recently, i plan to use the pymol as my main visualize tools. I have >>>> complied the latest version successfully and the vmd plugin seems to >>>> be complied as well at least the stage of build (i did not find these >>>> during the install ). However, when i open the pymol and i find i >>>> still can not load some format geometry such as vasp POSCAR which is >>>> included in vmd pludins. Could you tell me how to enable and use the >>>> vmd plugin in pymol. >>>> >>>> Best >>>> >>>> Wei-Bing >> >> -- >> ---------------------------------------------------------------------- >> Dr. Wei-Bing Zhang >> >> School of Physics and Electronic Sciences >> Changsha University of Science and Technology, Changsha 410004, >> People's Republic of China >> Phone : +86 186 73108538 >> E-mail: zhan...@csust.edu.cn, weibingzhang...@gmail.com >> ---------------------------------------------------------------------- >> <CHGCAR><POSCAR><XDATCAR><OUTCAR> > > -- > Thomas Holder > PyMOL Principal Developer > Schrödinger, Inc. > > -- ---------------------------------------------------------------------- Dr. Wei-Bing Zhang School of Physics and Electronic Sciences Changsha University of Science and Technology, Changsha 410004, People's Republic of China Phone : +86 186 73108538 E-mail: zhan...@csust.edu.cn, weibingzhang...@gmail.com ---------------------------------------------------------------------- ------------------------------------------------------------------------------ One dashboard for servers and applications across Physical-Virtual-Cloud Widest out-of-the-box monitoring support with 50+ applications Performance metrics, stats and reports that give you Actionable Insights Deep dive visibility with transaction tracing using APM Insight. http://ad.doubleclick.net/ddm/clk/290420510;117567292;y _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
