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

[Wei-Bing Z. <wei...@gm...>]

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 <tho...@sc...> 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 <wei...@gm...> 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 <tho...@sc...> 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 <wei...@gm...>
>>> 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: zh...@cs..., wei...@gm...
>> ----------------------------------------------------------------------
>> <CHGCAR><POSCAR><XDATCAR><OUTCAR>
>
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
>
>


-- 
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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: zh...@cs..., wei...@gm...
----------------------------------------------------------------------