VMD-L Mailing List

From: Suzanne Brewerton (suzanne_at_cryst.bioc.cam.ac.uk)
Date: Thu Jun 05 2003 - 03:44:51 CDT

Thankyou very much from your help on this. It sounds like the third issue
that Lorenzo mentioned - that the data has been reversed or something of
that sort. I will try using situs 2.0 and also vmd 1.8.1.
Thanks again
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

**---------------------------------**

On Wed, 4 Jun 2003, 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
>
> **---------------------------------**
>