Re: [Jmol-users] show isosurface for water molecule sasurface freezes GUI

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shame shame.

On Mon, Jun 25, 2012 at 11:03 AM, Daniel Aioanei <aio...@gm...> wrote:

> Thanks for looking into this issue. The pqr file I sent you was
> created using Gromacs like this:
>
> g_editconf -f drgfin_GMX.tpr -mead drgfin_GMX.pqr
>
> On 25 June 2012 18:48, Robert Hanson <ha...@st...> wrote:
> > whatever software is creating that "PQR" file is not putting the
> information
> > in the correct columns:
> >
> > 0         1         2         3         4         5         6
> > 7
> >
> 01234567890123456789012345678901234567890123456789012345678901234567890123456789
> >                               xxxxxxxxyyyyyyyyzzzzzzzz
> > ATOM     84  CA  VAL A  28       2.806   7.385   9.363  1.00 99.99
> > C
> > ATOM      1 OAB  DRG     1     -13.46000   9.99000  -8.27000 -0.7840
> > 1.5332
> >
> >
> > Jmol uses this:
> >
> > setAtomCoord(atom, parseFloat(line, 30, 38), parseFloat(line, 38, 46),
> > parseFloat(line, 46, 54));
> >
> >
> > So, for example, the first atom's coordinates are being read as
> > (-13.46,0,9000)
> >
> > Take a look at the PDB specs. PQR is supposed to follow those.
> >
> >
> >
> > On Sun, Jun 24, 2012 at 11:10 PM, Daniel Aioanei <aio...@gm...>
> wrote:
> >>
> >> Thanks for the sasurface/vdw explanation.
> >>
> >> I'm attaching the pdb and pqr files for a water molecule.
> >>
> >> On 25 June 2012 06:48, Robert Hanson <ha...@st...> wrote:
> >> >
> >> >
> >> > On Sun, Jun 24, 2012 at 8:40 PM, Daniel Aioanei <aio...@gm...>
> >> > wrote:
> >> >>
> >> >> Dear Richard,
> >> >
> >> > [Bob]
> >> >>
> >> >>
> >> >> Let me see if I got it right. What I need is "set solventProbe 1.4;
> >> >> isosurface sasurface", which is also equivalent to "isosurface
> >> >> sasurface 1.4". But while that works for larger molecules, it doesn't
> >> >> work for the water molecule.
> >> >>
> >> > I think I said that wrong. For water you need
> >> >
> >> > isosurface vdw +1.4
> >> >
> >> > that's different from
> >> >
> >> > isosurface vdw 1.4  # 1.4 ang each
> >> >
> >> >
> >> >>
> >> >> You mentioned in a previous reply that "That's a bug when the number
> >> >> of vertices is 0. That's fixed, but for now just don't do that." I
> >> >> just updated jmol to the latest svn version (rev. 17329) and for
> water
> >> >> "sasurface 1.4; show isosurface" doesn't freeze the GUI any longer,
> >> >> but the surface is still not there. Are there any plans to make
> >> >> sasurface work for very small molecules in the near future?
> >> >>
> >> >
> >> > no. It is very important that sasurface not work for solvent. Use VDW
> >> > +1.4
> >> >
> >> >>
> >> >> As for PQR, I'm using the GAFF force field, and I'm not getting any
> >> >> zero radii so far. But how can I load the pqr file? I tried "load
> >> >> 'pqr::drgfin_GMX.pqr'", but the molecule just disappears when I do
> >> >> that.
> >> >>
> >> >
> >> > ?? send me the file, please.
> >> >
> >> >
> >> >>
> >> >> Thanks,
> >> >> Daniel
> >> >>
> >> >>
> >> >>
> >> >>
> >> >>
> ------------------------------------------------------------------------------
> >> >> Live Security Virtual Conference
> >> >> Exclusive live event will cover all the ways today's security and
> >> >> threat landscape has changed and how IT managers can respond.
> >> >> Discussions
> >> >> will include endpoint security, mobile security and the latest in
> >> >> malware
> >> >> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
> >> >> _______________________________________________
> >> >> Jmol-users mailing list
> >> >> Jmo...@li...
> >> >> https://lists.sourceforge.net/lists/listinfo/jmol-users
> >> >
> >> >
> >> >
> >> >
> >> > --
> >> > 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
> >> >
> >> >
> >> >
> >> >
> >> >
> ------------------------------------------------------------------------------
> >> > Live Security Virtual Conference
> >> > Exclusive live event will cover all the ways today's security and
> >> > threat landscape has changed and how IT managers can respond.
> >> > Discussions
> >> > will include endpoint security, mobile security and the latest in
> >> > malware
> >> > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
> >> > _______________________________________________
> >> > Jmol-users mailing list
> >> > Jmo...@li...
> >> > https://lists.sourceforge.net/lists/listinfo/jmol-users
> >> >
> >>
> >>
> >>
> ------------------------------------------------------------------------------
> >> Live Security Virtual Conference
> >> Exclusive live event will cover all the ways today's security and
> >> threat landscape has changed and how IT managers can respond.
> Discussions
> >> will include endpoint security, mobile security and the latest in
> malware
> >> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
> >> _______________________________________________
> >> Jmol-users mailing list
> >> Jmo...@li...
> >> https://lists.sourceforge.net/lists/listinfo/jmol-users
> >>
> >
> >
> >
> > --
> > 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
> >
> >
> >
> >
> ------------------------------------------------------------------------------
> > Live Security Virtual Conference
> > Exclusive live event will cover all the ways today's security and
> > threat landscape has changed and how IT managers can respond. Discussions
> > will include endpoint security, mobile security and the latest in malware
> > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
> > _______________________________________________
> > Jmol-users mailing list
> > Jmo...@li...
> > https://lists.sourceforge.net/lists/listinfo/jmol-users
> >
>
>
> ------------------------------------------------------------------------------
> Live Security Virtual Conference
> Exclusive live event will cover all the ways today's security and
> threat landscape has changed and how IT managers can respond. Discussions
> will include endpoint security, mobile security and the latest in malware
> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
> _______________________________________________
> Jmol-users mailing list
> Jmo...@li...
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>

-- 
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

Re: [Jmol-users] show isosurface for water molecule sasurface freezes GUI

An interactive viewer for three-dimensional chemical structures.

Re: [Jmol-users] show isosurface for water molecule sasurface freezes GUI