[Chimera-users] Chimera-users Digest, Vol 81, Issue 21 - chopped ccp4 maps in chimera
Boaz Shaanan
bshaanan at bgu.ac.il
Thu Jan 28 14:11:52 PST 2010
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 at cgl.ucsf.edu
Date: Thursday, January 28, 2010 21:11
Subject: Chimera-users Digest, Vol 81, Issue 21
To: chimera-users at 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 at cgl.ucsf.edu>
> To: Bridget Carragher <bcarr at scripps.edu>
> Cc: chimera-users at cgl.ucsf.edu
> Subject: Re: [Chimera-users] Chimera movie question
> Message-ID: <4B60A747.5030705 at 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 at gmail.com>
> To: chimera-users at cgl.ucsf.edu
> Subject: [Chimera-users] Contouring ED Map: Sigma versus Chimera
> thresholds
> Message-ID: <C41C6E8E-343B-4FA1-BB71-49BAADB32DF2 at 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
>
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> ------------------------------
>
> Message: 3
> Date: Wed, 27 Jan 2010 16:23:42 -0800
> From: Elaine Meng <meng at cgl.ucsf.edu>
> To: Veer Bhatt <veer82 at gmail.com>
> Cc: chimera-users at cgl.ucsf.edu
> Subject: Re: [Chimera-users] Contouring ED Map: Sigma versus Chimera
> thresholds
> Message-ID: <DD1CB9A9-7BCD-4617-86B9-25ED6A6CC616 at cgl.ucsf.edu>
> Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed
>
> Hi Veer,
> This previous reply may be useful:
>
> <http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-
> May/002651.html>
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
>
>
> On Jan 27, 2010, at 4:12 PM, Veer Bhatt wrote:
>
> > 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
>
>
>
> ------------------------------
>
> 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
>
>
>
>
> On Jan 27, 2010, at 4:12 PM, Veer Bhatt wrote:
>
> > 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
> >
> > <ATT00001..txt>
>
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> ------------------------------
>
> 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
>
>
> > 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
> >
>
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> ------------------------------
>
> Message: 6
> Date: Thu, 28 Jan 2010 12:51:14 -0600
> From: snoze pa <snoze.pa at gmail.com>
> To: chimera-users at cgl.ucsf.edu
> Subject: [Chimera-users] H Bonds in MD simulation
> Message-ID:
> <10f848911001281051se57f898x524890e61121102d at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Dear Chimera Users,
>
> I am analyzing a MD trajectory in chimera. After selecting
> H binds
> when I am playing the trajectory, then it always shows the hydrogen
> bond. Though some of the bonds are broken during the simulation
> but it
> always connect the step 1 h bonds connected.. How can I show the h
> bonds which breaks during the simulation.
>
> Thank you very much for your help.
> S
>
>
> ------------------------------
>
> Message: 7
> Date: Thu, 28 Jan 2010 11:09:56 -0800
> From: Elaine Meng <meng at cgl.ucsf.edu>
> To: snoze pa <snoze.pa at gmail.com>
> Cc: chimera-users at cgl.ucsf.edu
> Subject: Re: [Chimera-users] H Bonds in MD simulation
> Message-ID: <6CC6C6BE-EFCA-4568-8ABB-570DF5D961EC at cgl.ucsf.edu>
> Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes
>
> Hi S,
> The H-bonds do not automatically recalculate. Instead of
> using
> findhbond one time before playing the trajectory, it should be
> used at
> each step. This can be done with a per-frame script.
> On the MD Movie
> player dialog, choose "Per-Frame... Define script" and specify
> that
> the script is in "Chimera commands." Then enter whatever
> commands you
> want to execute at each step. The MD Movie documentation
> includes an
> example with calculating H-bonds:
> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/movie/movie.html#per-frame
> >
>
> In your case it could be as simple as one "findhbond"
> command. First,
> I recommend trying the command in the regular Command Line to
> figure
> out which keywords and options you want.
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/hbonds.html>
>
> If there are protein ribbons shown, another command you might
> want to
> include in your per-frame script is "ksdssp" to recalculate
> secondary
> structure assignments.
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/ksdssp.html>
>
> The Trajectories tutorial, part 1, also includes using a per-
> frame
> script to calculate H-bonds:
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ensembles2.html#part1
> >
>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
> On Jan 28, 2010, at 10:51 AM, snoze pa wrote:
>
> > Dear Chimera Users,
> > I am analyzing a MD trajectory in chimera. After selecting H binds
> > when I am playing the trajectory, then it always shows the hydrogen
> > bond. Though some of the bonds are broken during the
> simulation but it
> > always connect the step 1 h bonds connected.. How can I show
> the h
> > bonds which breaks during the simulation.
> > Thank you very much for your help.
> > S
>
>
>
>
>
>
>
>
>
>
> ------------------------------
>
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
>
>
> End of Chimera-users Digest, Vol 81, Issue 21
> *********************************************
>
Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben-Gurion University of the Negev
Beer-Sheva 84105
Israel
Phone: 972-8-647-2220 ; Fax: 646-1710
Skype: boaz.shaanan
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