Re: [Chimera-users] Chimera-users Digest, Vol 81, Issue 21 - chopped ccp4 maps in chimera
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,
Boaz
----- Original Message ----- From: chimera-users-request@cgl.ucsf.edu Date: Thursday, January 28, 2010 21:11 Subject: Chimera-users Digest, Vol 81, Issue 21 To: chimera-users@cgl.ucsf.edu
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Today's Topics:
1. Re: Chimera movie question (Tom Goddard) 2. Contouring ED Map: Sigma versus Chimera thresholds (Veer Bhatt) 3. Re: Contouring ED Map: Sigma versus Chimera thresholds (Elaine Meng) 4. Contouring ED Maps (Hector Viadiu) 5. Re: Contouring ED Maps (Tom Goddard) 6. H Bonds in MD simulation (snoze pa) 7. Re: H Bonds in MD simulation (Elaine Meng)
Message: 1 Date: Wed, 27 Jan 2010 12:51:19 -0800 From: Tom Goddard goddard@cgl.ucsf.edu To: Bridget Carragher bcarr@scripps.edu Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] Chimera movie question Message-ID: 4B60A747.5030705@cgl.ucsf.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Hi Bridget,
I put an example animation on the Chimera web site in the animation gallery called "Herpes virus slices". There is also a link to a command script which makes this movie. You just use File/Open... in Chimera to run the command script.
http://www.cgl.ucsf.edu/chimera/animations/animations.html Tom
OK, thanks Tom. Any tips on how to do all three planes
at once - or
rather keep the others constant while eating though the side
plane. I
have sen movies like this but can;t seem to figure out how
to do it in
Chimera. Bridget
Message: 2 Date: Wed, 27 Jan 2010 19:12:31 -0500 From: Veer Bhatt veer82@gmail.com To: chimera-users@cgl.ucsf.edu Subject: [Chimera-users] Contouring ED Map: Sigma versus Chimera thresholds Message-ID: C41C6E8E-343B-4FA1-BB71-49BAADB32DF2@gmail.com Content-Type: text/plain; charset="us-ascii"; Format="flowed"; DelSp="yes"
Hi, This in context of using Chimera to view *ccp4 format electron density maps. How does Chimera 'Threshold Level' ('Level' in Volume viewer) equate or relate to sigma level reported by some other programs. For example a 'Level' of 0.4 seems like a map contoured at 1.5 sigma or so. I was wondering if someone could point out how these two are related, more precisely.
Thanks
Veer Sandeep Bhatt
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/7201http://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
participants (2)
-
Boaz Shaanan -
Elaine Meng