VMD-L Mailing List

From: Zampighi, Lorenzo (LZampighi_at_mednet.ucla.edu)
Date: Wed Jun 04 2003 - 13:46:54 CDT

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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