VMD-L Mailing List

From: Arneh Babakhani (ababakha_at_mccammon.ucsd.edu)
Date: Fri Jun 22 2007 - 14:38:42 CDT

Yes, you're right, thanks. So the amount of whitespace in a pdb file
must be exact? I thought most readers can parse that out? That's a
very important lesson! Thanks for your help,

Arneh

Giovanni Bellesia wrote:
> looks like your pdb is not formatted correctly:
> Try this:
>
> ATOM 1 H XXX 1 2.00 2.00 0.00 H
> ATOM 2 H XXX 1 0.00 2.00 0.00 H
> END
>
> it worked for me.
>
> You also might want to take a look at this:
>
> http://www2.cs.uh.edu/~chandler/chem/PDBSpec.html
> (9. Coordinate Section)
>
>> Thanks, let me try to clarify.
>>
>> Assuming the pdb is formatted correctly, when I load it up and query
>> the coordinates of say the first atom, I get this:
>> >Main< (PracticeVMD) 67 % [atomselect top "index 0"] get {x y z}
>> {2.0 0.0 0.0}
>>
>> But this does not match up with the coordinates in the actual pdb
>> file, where the coordinates for the first atom are {2.0 2.0 0.0}, b/c
>> of what you stated below (the viewing transformation is independent
>> of the atom coordinates).
>>
>> My question is, how can I load up the pdb without such a viewing
>> transformation? In other words, when I do 'get {x y z}', I want the
>> result to be the exact coordinates found in the pdb file.
>>
>> Thanks,
>>
>> Arneh
>>
>>
>>
>> John Stone wrote:
>>> Hi,
>>> I'm not sure what you're asking here. VMD preserves the original
>>> coordinates of the structures after they are loaded. The viewing
>>> transformations applied for graphical scaling/rotation/translation
>>> are completely independent from the atom coordinates. You can
>>> query the atom coordinates using a selection to verify this for
>>> yourself:
>>> set sel [atomselect top all]
>>> $sel get {x y z}
>>>
>>> If you're writing PDB files by hand, you need to make absolutely
>>> sure that you've got the PDB columns lined up since it is a column
>>> based format. If you write the coordinates into the wrong columns,
>>> you'll get gibberish from VMD (and any other program....)
>>>
>>> Cheers,
>>> John Stone
>>> vmd_at_ks.uiuc.edu
>>>
>>>
>>> On Fri, Jun 22, 2007 at 11:10:06AM -0700, Arneh Babakhani wrote:
>>>
>>>> Hello,
>>>>
>>>> I have a brief question about loading up pdb files in VMD. I
>>>> noticed that when I load up a pdb file, one of the atoms is placed
>>>> at the origin {0 0 0} and the rest are plotted around that. For
>>>> instance, for the simple pdb file:
>>>> ATOM 1 H XXX A 1 2.00 2.00 0.00 H
>>>> ATOM 2 H XXX A 1 0.00 2.00 0.00 H
>>>> END
>>>>
>>>> the fist hydrogen atom is placed at {0 0 2}, the second is placed
>>>> at {0 0 0}. So the distance between the two atoms is correct, but
>>>> they're coordinates are different from what actually appears in the
>>>> pdb file.
>>>> So my question is, how can I load up the pdb file such that the
>>>> atoms are placed in the 'absolute' coordinates of file? And how
>>>> can I do that from the TCL command line, is there an option to 'mol
>>>> load pdb whatever.pdb' ?
>>>> Thanks,
>>>>
>>>> Arneh
>>>>
>>>
>>>
>