From: Paul T. Bauman (pbauman_at_ices.utexas.edu)
Date: Fri Dec 08 2006 - 15:24:48 CST

Oh OK. Even better, I guess I missed that in the manual. Thanks!

Peter Freddolino wrote:
> As an aside, if your primary interest is being able to color things by a
> floating point number, you can fill in the beta or occupancy fields of a
> pdb file with floating point values; these are read by VMD.
> Peter
>
> Marcos Sotomayor wrote:
>
>> Hi Paul,
>>
>> Have a look at the appendices of the NAMD tutorial available at:
>>
>> http://www.ks.uiuc.edu/Training/Tutorials/
>> http://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-unix-html/index.html
>>
>> http://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-unix-html/node21.html
>>
>>
>> Marcos
>>
>> On Fri, 8 Dec 2006, Paul T. Bauman wrote:
>>
>>
>>> Hello,
>>>
>>> I'm trying to generate .psf file from my own molecular simulation
>>> code and I can't find the specific detais of the file format so VMD
>>> will accept it. Does anyone know where I can look to get the most
>>> detailed account of what VMD wants in the .psf file?
>>>
>>> Basically, I'm visualizing position of atoms as well as covalent
>>> bonds using a .pdb format. Now, I want to color the atoms according
>>> to a real valued number that I give it and I gather the best way to
>>> hack it is to use a .psf file and specify my number as the charge and
>>> plot the color according to charge. I've found a few examples here
>>> and there of a .psf but I haven't gotten the format right yet (i.e.
>>> VMD errors when it trys to read my version of the .psf file). Any
>>> help is most appreciated. Thanks,
>>>
>>> Paul
>>>
>>>