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)

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Message: 1 Date: Wed, 27 Jan 2010 12:51:19 -0800 From: Tom Goddard To: Bridget Carragher 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

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OK, thanks Tom.  Any tips on how to do all three planes

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rather keep the others constant while eating though the side

at once - or plane.  I

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have sen movies like this but can;t seem to figure out how to do it in Chimera. Bridget

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Message: 2 Date: Wed, 27 Jan 2010 19:12:31 -0500 From: Veer Bhatt To: chimera-users@cgl.ucsf.edu Subject: [Chimera-users] Contouring ED Map: Sigma versus Chimera thresholds Message-ID: 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