VMD-L Mailing List

From: Arneh Babakhani (ababakha_at_mccammon.ucsd.edu)
Date: Fri Jun 22 2007 - 13:50:59 CDT

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
>>
>
>