VMD-L Mailing List

From: Arneh Babakhani (ababakha_at_mccammon.ucsd.edu)
Date: Fri Jun 22 2007 - 14:26:12 CDT

This is my pdb file (just two hydrogen atoms, with a fake residue name XXX):

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

John Stone wrote:
> Hi,
> I think you must have a misformatted file if you're getting a different
> coordinate from the atom selection than what you see in the file.
> The viewing transformations only affect the _display_ of the molecule,
> and do not affect the atom selections, coordinates, or measuring parts
> of the program at all. Please check that your PDB file is correctly
> formatted, or else send me a copy and I'll check it for you.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Fri, Jun 22, 2007 at 11:50:59AM -0700, Arneh Babakhani wrote:
>
>> 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
>>>>
>>>>
>>>
>>>
>
>