VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Aug 28 2003 - 19:58:15 CDT

Ioana,
  Have you verified that the atom coordinates in the actual PDB file
are correct? I suspect that the "centering" you're doing in Amber may
not be affecting the coordinates as they are written out in the actual
PDB file. It should be very easy for you to verify this by finding the
atom(s) of interest in your PDB file in a simple text editor. The coordinates
VMD uses are verbatim what it reads in from the PDB file, so I suspect that
Amber is not actually writing out the transformed atom coordinates.
Perhaps I'm missing something about the actual operations you're
performing, but if you're just comparing coordinates between structures,
I'd be quite surprised if VMD is doing something wrong there.

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Aug 28, 2003 at 03:55:35PM -0700, Ioana Cozmuta wrote:
> Hi John,
>
> Thanks for your reply. I am not doing anything at all in VMD other than
> loading the pdb structure, selecting atoms, calculating the center and
> printing out the coordinates of the center. For such a structure
> previously centered in zero in amber, vmd gives a non zero value for the
> center (40A at least shifted).
>
> I found a way around this but I was just curious why the difference??
> I will send you some example files after the 9th of September, I have a
> deadline for that week as well...
>
> If you have any time to help me with the question I've submited about the
> forces I would appreciate that a lot!
>
> Thanks and have a nice trip,
> Ioana
>
> On Thu, 28 Aug 2003, John Stone wrote:
>
> >
> > Ioana,
> > Without the actual files to look at, its very hard for me to guess
> > why you might be having the problem you describe. VMD loads structures
> > in the same world coordinate system, so unless you've done various
> > manipulations on one of the structures with some of the others toggled
> > as "Fixed" in the main VMD windows, I can't think of a reason that
> > they wouldn't retain exactly the same relative orientations and positioning
> > (thus centering) that you had external to VMD. To eliminate any possible
> > issues with temporary "fixing" followed by scaling/rotation/translation,
> > make sure to do a Display->Reset View if they aren't lining up properly.
> > This undoes any inadvertent molecule-specific viewing transformations
> > you may have caused by using the "Fixed" toggle in the main VMD window.
> >
> > If this doesn't solve your problem, please email us some example files,
> > and I'll help you solve your problem when I return from being out of town.
> > I'll be out until September 9th, so it'll be a while, but if you post
> > to VMD-L, perhaps someone else can help solve your problem while I'm away.
> >
> > Thanks,
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> > On Mon, Aug 25, 2003 at 05:29:55PM -0700, Ioana Cozmuta wrote:
> > > Hi John,
> > >
> > > What I am actually tying to do is the following:
> > > I have to structures: a protein and a box with water.
> > > I want to center them in zero, align them with the z axis and remove
> > > all the atoms from the box that overlap with the protein.
> > > The problem is the following: if I center both structures in amber (tleap)
> > > in zero when I view them in VMD their centers do not overlap and also
> > > their centers is not zero anymore (although I've especially done that in
> > > amber).
> > > I am just curious why this difference? I wrote a code that does the
> > > removal of the overlaping molecules, that's what I need the radii for.
> > > I will add there the centering but then again I might want to vizualize
> > > the centered structure and vmd may show them again shifted from each
> > > other...
> > >
> > > Thanks,
> > > Ioana
> > >
> > > On Mon, 25 Aug 2003, John Stone wrote:
> > >
> > > > Dear Ioana,
> > > > VMD reads and interprets only the PDB columns it knows how
> > > > to make use of. As such, when writing out PDB files from VMD,
> > > > some of the columns get default values, or are left blank,
> > > > particularly for fields that VMD doesn't store. According to
> > > > the PDB file spec, the last two fields of the ATOM recard
> > > > are supposed to contain the element symbol (cols 77-78) and
> > > > the charge (cols 79-80). Which actual fields/columns are you
> > > > storing the radii and charge in?
> > > >
> > > > In any case, I suspect that there's no easy way for you to preserve
> > > > the custom radii/charge info unless you were to store it in the
> > > > occupancy and tempFactor fields, which VMD does actualy store and
> > > > should also save.
> > > >
> > > > Since VMD isn't intended specifically to work with just PDB files,
> > > > there are many PDB record types and fields that VMD doesn't process,
> > > > so this is only one example of all kinds of similar limitations with PDB
> > > > and potentially with other formats,
> > > >
> > > > Thanks,
> > > > John Stone
> > > > vmd_at_ks.uiuc.edu
> > > >
> > > > On Mon, Aug 25, 2003 at 04:24:27PM -0700, Ioana Cozmuta wrote:
> > > > > Hi vmd users,
> > > > >
> > > > > I am reading in VMD a pdb file and in the last two columns of the file I
> > > > > have the charge and radii. However after I recenter the structure and
> > > > > select all atoms, when I write the selection into a pdb file the last two
> > > > > columns loose the information. Is there a way to preserve the charge/radii
> > > > > information when I write the atomselection into the pdb file?
> > > > >
> > > > > Thank you,
> > > > > Ioana
> > > >
> > > > --
> > > > NIH Resource for Macromolecular Modeling and Bioinformatics
> > > > Beckman Institute for Advanced Science and Technology
> > > > University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> > > > Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> > > > WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
> > > >
> >
> > --
> > NIH Resource for Macromolecular Modeling and Bioinformatics
> > Beckman Institute for Advanced Science and Technology
> > University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> > Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> > WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
> > 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349              
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078