VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Feb 25 2002 - 17:26:28 CST

Laurence,
  To deal with those PDB warnings specifically, yes.
For this particular application though, I think that rendering the
surfaces as point clouds is still much more appropriate than
loading a fake molecule. When I get the rendering code done to
support options 4) and 5), I think they are the best options to
pursue for the long term. But, I do agree with your point on
getting the CONECT record reading in there. Now that we've got
file reader plugins going in VMD 1.8, I think that will be
easier to do without risking breaking the code, since testing
new file I/O code will become MUCH MUCH easier than it used to be.

This and a few other PDB reader improvements are definitely on our
TODO list :-)

  John

On Mon, Feb 25, 2002 at 06:20:34PM -0500, Laurence F. Wood wrote:
> However the best way to deal with this is to implement CONECT record
> support. :)
>
> -----Original Message-----
> From: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu]On Behalf
> Of John Stone
> Sent: Monday, February 25, 2002 2:18 PM
> To: Alan Wilter Sousa da Silva
> Cc: vmd-l_at_ks.uiuc.edu; vmd_at_ks.uiuc.edu
> Subject: Re: Plotting elect. pot. surface
>
>
>
> Dear Alan,
> I have a couple of immediate suggestions that will give you better
> results than your current method using PDB files, for the reasons below.
>
> PDB file method:
> The behavior you describe with making a PDB file containing surface
> points is to be expected, VMD assumes that the contents of the PDB
> file are actually atoms, not just arbitrary points, so it attempts to
> find bonds between the atoms, leading to the messages you describe
> complaining about too many bonds (points are too close together, so
> VMD thinks they are all bonded...)
>
> Improved methods:
> From the information you've given me, it seems that the best immediate
> solution would be to use the VMD graphics commands to draw points at the
> positions extracted from your data files. This will not have any of the
> problems of the PDB method, and will be easy to convert to using more
> advanced methods such as I mention in options 4) and 5) in my original
> reply. Since the output format from your Connelly subtroutine does not
> include potential values, I assume that you are assigning these through the
> use of a separate program or script? If you can output potential values
> in a 3-D grid, then you can use option 4) as soon as I have it running,
> and you could also use the potential grid to color any other VMD
> representations you like. We can talk about this more as I make progress
> on the new rendering code to do this. In the mean time, here's an easier
> way to get a point cloud representation from VMD without making intermediate
> PDB files (and their attendant difficulties), in pseudo-Tcl:
>
> # (loop over all surface points)
> for {set i} {$i < numpoints} {incr i} {
> # map potential values to colors here...
> # see "tricolor_scale" and other routines in user's guide examples...
> # http://www.ks.uiuc.edu/Research/vmd/vmd-1.7.1/ug/node186.html
> draw color $c
>
> # extract surface points from files or lists here
> # see Tcl guides for reading files in Tcl scripts..
> # set x, y and z
>
> # draw geometry here...
> # http://www.ks.uiuc.edu/Research/vmd/vmd-1.7.1/ug/node167.html
> draw point { $x $y $z }
> }
>
>
> Let us know if you need help getting your script going, this should
> be an easy one to bang out.. You can use the same sorts of scripts to
> draw quite complex stuff in VMD, adding your own geometry into molecular
> scenes. It gets tricky if you want to have multiple simultaneous graphics
> molecules, but its not too bad.
>
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Mon, Feb 25, 2002 at 03:40:57PM -0500, Alan Wilter Sousa da Silva wrote:
> > Dear Dr. Stone,
> >
> > I should worship you.
> >
> > We use a subroutine done by Connelly and one of the output is (the
> > most complete) something like that:
> >
> > 3 2 -0.46880871 -2.60773206 -4.40835810
> 0.18325105 -0.85492104 0.29627359 0.42583075 0
> > (1)(2) ( 3 ) ( 4 )
> ( 5 ) (6)
> >
> > c Where:
> > c The first field (I5) contains the atom number. The second
> > c field (I2) is 1 for convex surface, 2 for saddle surface, 3 for
> > c concave surface. The third through fifth fields give the coordinates
> > c of the surface point. The remaining fields are optional and depend
> > c on the attention number specified for the atom. The remaining fields
> > c are: area, normal vector, buried flag. The records of this file are
> > c not in atom number order, so they must be sorted if the user desires
> > c to reference the surface points by atom number.
> >
> > The particularly important about this program is one can plot only
> > intermolecular surface if one wants.
> > Normally, we reformat this output to a pdb format without 'CONECT'.
> > When one loads it in VMD many errors messages appears (since VMD 1.7,
> > before not):
> > >ERROR) Residue exceeded maximim number of bonds (4).
> > ...
> >
> > >Unusual bond between residues 83 and 110
> > ...
> > But it's not quite relevant since I believe you've change VMD, so
> > psf file can be neglected. And it works since I can view a cloud of a lot
> > of points resembling the Connelly surface of the molecule, and using
> > appropriate colour method I can see electrostatic potential distribution.
> > Summarising, if VMD could connect the points by small surfaces...
> >
> > So, we don't have connectivity and no order.
> >
> > I'm studying potsurf script and I'm figuring out that I have to
> > use the command 'mol volume .....' but I can't find much about it (even
> > in the new Manual VMD 1.7.1).
> >
> > Anyway, methinks option (4) and (5) should be what I'm looking
> > for.
> >
> >
> > On Mon, 25 Feb 2002, John Stone wrote:
> >
> > >
> > >
> > > Dear Alan,
> > > From what you describe in your email, it shouldn't be too hard to get
> > > VMD to render what you want. Off the top of my head, there are two
> obvious
> > > routes to getting this done. The appropriate method will depend on how
> > > your program works, and what data it outputs:
> > > 1) If your program outputs a regularly spaced rectilinear grid of data
> > > points, with potential values at the grid points, then the best
> method
> > > would be to write a simple Tcl script to read in the potential map,
> > > and apply it as the coloring on an MSMS surface, as is done in the
> > > potsurf script.
> > >
> > > 2) If your program outputs a list of discrete points (not in a grid,
> just
> > > list of points which are not on a regular sample interval) then you
> could
> > > use a Tcl script to read in the list of points, and draw them with
> the
> > > VMD graphics commands. This assumes that your list of points does
> not
> > > include any connecttivity information.
> > >
> > > 3) Similar to 2), but if you have connectivity information, you can
> > > draw a solid surface much like MSMS, or Surf. Instead of reading
> in
> > > the sample points as points, they are used as vertices in a
> triangle
> > > mesh with the face/edge/vertex connectivity information.:w
> > >
> > > 4) Similar to 1), but using a feature I'm still developing, which
> would
> > > allow any molecular geomtry to be colored by volumetric data, using
> > > 3-D texture mapping.
> > >
> > > 5) Similar to 2) but using a feature I'm still developing, which will
> > > allow VMD to draw big point clouds efficiently. May also implement
> a
> > > mode for displaying vector fields...
> > >
> > > Let me know which of these options interests you the most, and I'll work
> with
> > > you to get your program and scripts working with VMD.
> > >
> > > Thanks for using VMD!
> > > John Stone
> > > vmd_at_ks.uiuc.edu
> > >
> > >
> > > On Mon, Feb 25, 2002 at 01:15:52PM -0500, Alan Wilter Sousa da Silva
> wrote:
> > > > Hi VMD-list.
> > > >
> > > > Amazing, fantastic VMD!
> > > >
> > > > But I have a problem. Since I don't have Insight/Delphi, I'm
> > > > trying to plot elect. pot. molecular surface with what I have.
> > > > (1) First, loading a pdb file with charges (using beta or
> > > > occupancy column). Then using MSMS and change colour represantation
> (RWB)
> > > > to beta (or occupancy, whatever I set in the pdb file) results look
> fine
> > > > but I don't think it's right, I mean, (2) I would like to see a
> surface
> > > > composed of discretes points and had accounted every atom charge
> > > > interaction (Coulomb, epslon=80) over every point of the grid surface.
> > > > Maybe, it's what potsurf script does, but not what (1) does.
> > > > So, I have a Connolly adapeted program to our situation, which
> > > > calculates a point-surface (Connolly, probe 1.4) with charges values
> > > > attributed as desired in (2) but now I'm looking for a way to show it
> as
> > > > a graphic surface.
> > > > I'm sorry if I couldn't make myself clear, but I want to find a
> > > > way to make VMD represents my data source in a surface.
> > > > My point-surface data is built by as many as need points to cover
> > > > the molecular Connolly surface with each point having its 3 spatial
> > > > coordnates and its charge value (using pdb format I can see a sketch
> of
> > > > what I expect).
> > > > I would thank in advance any attention dedicated to my problem.
> > > >
> > > > Sincerely,
> > > >
> > > > -----------------------
> > > > Alan Wilter S. da Silva
> > > > -----------------------
> > > > Laboratório de Física Biológica
> > > > Instituto de Biofísica Carlos Chagas Filho
> > > > Universidade do Brasil/UFRJ
> > > > Rio de Janeiro, Brasil
> > >
> > >
> >
> > --
> > -----------------------
> > Alan Wilter S. da Silva
> > -----------------------
> > Laboratório de Física Biológica
> > Instituto de Biofísica Carlos Chagas Filho
> > Universidade do Brasil/UFRJ
> > Rio de Janeiro, Brasil
>
> --
> 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