Ah, I just remembered! If you add this line at the top of your file, it
will read PQR without need for pqr::
REMARK 1 PQR
exactly those spaces.
Atom size. Shouldn't be a problem.
On Fri, Mar 22, 2013 at 3:32 AM, Andrea Magro <[email protected]> wrote:
>
>
> >
> >Indeed, Jmol is perfect and has been used like this before. (For,
> example, electron probability plots.)
> >
> >
> >Because PQR and PDB have the same format, you will need to preface your
> file name with "pqr::" to force Jmol to read PQR format. If you can scale
> your coordinates down by a factor of 50, this would look about the size of
> a molecule. But it should work even with this large range.
> >
> >Bob Hanson
> >
> >
>
> Hi Bob,
>
> Sorry, I'm not familiar with jmol. I don't understand were to write that
> command. I'm using jmol as a GUI application under Windows and I load the
> file by clicking File>Open in the program menu.
>
> However the problem is not in opening the file. The format is recognized
> and spheres are displayed in the correct positions. The only problem is
> their radii that are not connected to the values written in the pqr file,
> but they seem absolutely random.
>
>
> Meanwhile I made a new discovery. If I open Preferences there is a slider
> by which I can modify the percentage of Van der Waals radii. When I slide
> it from left (0%) to right (100%) the spheres increase in size but when
> they reach a given size they pop (disappear) and a new sphere starts to
> grow from zero. It seems like there is a size limit in atom radius......
>
>
> >
> >
> >
> >On Thu, Mar 21, 2013 at 1:27 PM, Andrea Magro <[email protected]>
> wrote:
> >
> >I want to visualize a random sphere packing. They are not atoms, just
> generic spherical particles but I don't know a suitable software to do it
> so I thougth I could use jmol.
> >>I have a file with lines in the following format:
> >> x y z r
> >>
> >>
> >>where x,y,z are the coordinates of the centers of the spheres, which are
> contained in a cubic box, and r are the radii (different for each sphere).
> >>Since jmol can read pqr files, which are a modification of pdb files
> where the last column is the atom radius, I converted my output file to a
> "pseudo pqr" file.
> >>Here an example of a few lines from my pqr file:
> >>
> >>
> >>ATOM 1 X THR 1 -403.3 -445.3 -72.6 0.00000 20.9
> >>ATOM 2 X THR 1 429.2 285.4 -132.2 0.00000 11.6
> >>ATOM 3 X THR 1 -304.5 -270.2 351.6 0.00000 49.0
> >>ATOM 4 X THR 1 292.5 -208.9 -35.7 0.00000 20.5
> >>ATOM 5 X
> THR 1 -175.3 4.3 -103.2 0.00000 54.1
> >>
> >>
> >>(currently coordinates range from -500 to +500, but they can be easily
> rescaled if required)
> >>
> >>
> >>The problem is that when I select Display-Atom-100% Van der Waals I
> obtain spheres with radii which are absolutely random and not the values
> written in the pqr file...
> >>
> >>
> >>where is the mistake?
> >>Thank you in advance
> >>
>
>
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--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Chemistry Department
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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