VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Jun 04 2003 - 14:03:56 CDT

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
>
> **---------------------------------** 

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