[Chimera-users] Chimera-users Digest, Vol 81, Issue 21 - chopped ccp4 maps in chimera

[Elaine Meng]

If the problem is what Boaz suggests, you can extend the map using the  
"vop cover" command:

<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#cover>

Elaine


On Jan 28, 2010, at 2:11 PM, Boaz Shaanan wrote:

> Hi,
>
>  The possible reason for the chopped ccp4 maps when they are  
> displayed in Chimera (whereas they're fine Coot) may have to do with  
> the fact that as far as I know Chimera does not apply the  
> crystallographic symmetry operations to the ccp4 map (at least  
> that's how it used to be in v1.3), whereas Coot does. So if the map  
> is defined for the asymmetric unit only, it has to be expanded in  
> order to cover all the region which one wants to display before  
> being read into Chimera. There could of course be other reasons for  
> the chopped maps.
>
>    Cheers,
>
>
> >
> > Message: 4
> > Date: Wed, 27 Jan 2010 16:25:55 -0800
> > From: Hector Viadiu <viadiu at ucsd.edu>
> > To: chimera-users at cgl.ucsf.edu
> > Subject: [Chimera-users] Contouring ED Maps
> > Message-ID: <0BD410EF-3FD0-4C63-B1E1-635D884ADBB1 at ucsd.edu>
> > Content-Type: text/plain; charset="us-ascii"; Format="flowed";
> > DelSp="yes"
> >
> > Hi,
> >
> > Also regarding contouring ED maps: we have ccp4 maps that are
> > fine in
> > coot, but as soon as you display them in chimera they are
> > sharply
> > chopped in one direction, as if there is any problem with a
> > border.
> > Any suggestion, the effect it's particularly bad for a
> > surface
> > representation, but it's also obvious when you display it as a mesh.
> >
> > Thank you!
> >
> > Hector Viadiu
> > viadiu at ucsd.edu
> >
> > Message: 5
> > Date: Wed, 27 Jan 2010 16:34:10 -0800
> > From: Tom Goddard <goddard at cgl.ucsf.edu>
> > To: Hector Viadiu <viadiu at ucsd.edu>
> > Cc: chimera-users at cgl.ucsf.edu
> > Subject: Re: [Chimera-users] Contouring ED Maps
> > Message-ID: <4B60DB82.1080501 at cgl.ucsf.edu>
> > Content-Type: text/plain; charset="iso-8859-1"; Format="flowed"
> >
> > Hi Hector,
> >
> >   Not sure what "sharply chopped" means without a
> > picture.  But we have
> > seen a problem where the map surface looks like sliced
> > bread.  It is
> > caused by a bug in old Mesa OpenGL (3-d graphics) libraries on
> > Linux,
> > and is not a Chimera bug.  The solution is to install a
> > graphics driver
> > which will also give you much faster rendering.  Or you can
> > disable
> > Vertex Buffer Objects in the Chimera Debug Graphics Driver tool.
> >
> >     http://plato.cgl.ucsf.edu/trac/chimera/ticket/7201
> >
> >
> > http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/debug/debug.html
> >
> > If this is not your problem you can submit a bug report with
> > Chimera
> > menu entry Help / Report a Bug and attach an image.
> >
> >   Tom