VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Jun 04 2003 - 17:36:45 CDT

Lorenzo,
  I made a 3 line change in the VMD source code force it to renormalize
normals given to us by 'draw' commands and that cured the problem with
your Situs file displaying badly.

Can you send an email to the Situs guys to let them know that it would
be best if they pre-normalized the surface normals before generating the
VMD script, for future versions? The forced-renormalization change will
be in the final version of VMD 1.8.1, so that should cure your problem
with this type of Situs output regardless whether they fix it in Situs
itself.

Regarding VMD's isosurface rep: I'm hoping to add smoothed surface
  normals to the isosurface rep (and various other improvements) in the
  next major version of VMD. For VMD 1.8.1 I didn't have time, but its
  on the list of things to improve.

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Jun 04, 2003 at 01:21:42PM -0700, Zampighi, Lorenzo wrote:
>
> Hi John,
>
> Here is the one of the files. I don't know if it makes any difference how
> you load the file into vmd (I have only been able to load it this one way)
> but to load these files I type into the vmd console (assuming nothing else
> is loaded already):
>
> draw color green
> source <filename>
>
> The file formats that are supported are largely used in the X-ray field. In
> my field of single particle the dominate file formats are either spider,
> imagic, or raw data. I am planning on writing new file readers for those
> formats but that will have to wait until July. Right now converting to ccp4
> (which isn't a problem) seems to be the only way for me to use that feature.
>
> The only thing that I don't like is the surface of the model when
> isosurfaced should be smoothed. The surface looks like a bunch of triangles
> joined together rather than a smooth surface rendering. I have no idea how
> you would be able to "fix" this but if I can help in any way just let me
> know.
>
> Other than this I really think this is a great software package. Very
> intuative and simple yet extremely powerful. I think the use of both the
> menus and the console window was a great idea. And the functionality is
> very impressive.
>
> Thanks,
>
> Lorenzo
>
> -----Original Message-----
> From: John Stone
> To: Zampighi, Lorenzo
> Cc: 'Suzanne Brewerton '; 'vmd-l_at_ks.uiuc.edu'
> Sent: 6/4/03 12:03 PM
> Subject: Re: Situs
>
>
> Hi Lorenzo,
> Thanks for your input on this. By the way, do you have one of the
> Situs-produced files that gets "whited out"? If you can send that
> to me, I'd like to take a look at it. The newer versions of VMD are
> much more picky about getting normalized vertex normals in triangle
> meshes such as Situs may be generating. If you've got surfaces that
> look white, my guess is that its a vertex normal re-normalization issue,
> as non-unit-lenth surface normals will commonly cause objects to look
> washed out/white, etc. Anyway, if you've got files that exhibit the
> problem, I'd love to get a copy. By the way, let us know what you guys
> think of the new electron density map reader plugins, etc.
>
> Thanks,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Wed, Jun 04, 2003 at 11:46:54AM -0700, Zampighi, Lorenzo wrote:
> > Suzanne -
> >
> > I have some experience and there could be several fixes. First, the
> new
> > beta version 1.8.1 can natively read ccp4 format and I would suggest
> using
> > that instead and avoid any conversion.
> >
> > Second, if you are doing a solid rendering I have also noticed that my
> > models get "whited out", and are without any features after converting
> to
> > vmd. I assumed that it was a OpenGL problem with my Maxtor G550 card
> but
> > curiously it is able to display it without problem using vmd 1.7.1.
> So you
> > can either use vmd 1.7.1 or do wireframe rendering.
> >
> > Third, Situs 2.1 seems to have some problems with the conformat
> program
> > which don't appear present in Situs 2.0. I haven't had the time to
> test it
> > more throughly and send a bug report to the Situs people but I plan to
> in a
> > week or two. When I convert from Situs -> ccp4 parts of the model get
> > cropped out or reversed (seems to be an ordering problem of some
> sort). For
> > that one I just convert from Situs -> Spider and in another program
> convert
> > to ccp4.
> >
> > Hope this helps.
> >
> > Lorenzo
> >
> > -----Original Message-----
> > From: Suzanne Brewerton
> > To: vmd-l_at_ks.uiuc.edu
> > Sent: 6/4/03 7:22 AM
> > Subject: Situs
> >
> >
> > I am trying to use vmd with Situs (for docking models into electron
> > microscopy data). I have a CCP4 format map and I have converted it to
> > the
> > situs format using conformat and then to vmd format so that I can view
> > it.
> > However the conversion is not working as the map looks extremely
> > peculiar
> > when I open it. Does anyone have any experience in this?
> >
> > Thanks
> > Suzanne
> >
> > **---------------------------------**
> >
> > Suzanne Brewerton
> > PhD Candidate
> >
> > Department of Biochemistry
> > University of Cambridge
> > Old Addenbrookes site
> > 80 Tennis Court Road
> > Cambridge CB2 1GA
> > United Kingdom
> >
> > Tel: 01223 766030
> > Email: suzanne_at_cryst.bioc.cam.ac.uk
> >
> > **---------------------------------**
>
> --
> 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