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@ucsd.edu> To: chimera-users@cgl.ucsf.edu Subject: [Chimera-users] Contouring ED Maps Message-ID: <0BD410EF-3FD0-4C63-B1E1-635D884ADBB1@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@ucsd.edu
Message: 5 Date: Wed, 27 Jan 2010 16:34:10 -0800 From: Tom Goddard <goddard@cgl.ucsf.edu> To: Hector Viadiu <viadiu@ucsd.edu> Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] Contouring ED Maps Message-ID: <4B60DB82.1080501@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