VMD-L Mailing List

From: Giovanni Bellesia (gbellesia_at_chem.ucsb.edu)
Date: Fri Jun 22 2007 - 14:24:11 CDT

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
>>>
>>
>>