February 2008 - Chimera-users - RBVI Mailing Lists

Re: [Chimera-users] [chimera-dev] change hand ?
by Tom Goddard 20 Feb '08

20 Feb '08

Hi Stefan, You can flip the hand of the map by making the grid spacing negative along one axis. Chimera wasn't intended to do this so I'm not sure everything will work correctly. To make this change use the volume dialog Coordinates panel and change voxel size from (for example) 0.37 to 0.37 0.37 -0.37. The three numbers are grid plane spacing along the x, y, z axes. If they are all the same Chimera just shows one number. In Chimera 1.2470 the volume surface will become dark. To remedy this use the volume dialog Surface and Mesh options panel and turn off "two-sided surface lighting". A current Chimera daily build will not have that problem. Chimera won't correctly save the flipped map. So this is not an ideal way to proceed. I don't know of software that will write out the flipped map though it must exist. Tom Stefan Backstrom wrote: > Hi. > > Is it possible to flip the hand of a cryo-EM map in chimera ? > > Best wishes, > > Stefan Bäckström > Medical Biochemistry and Biophysics > Umeå University > Sweden > > _______________________________________________ > Chimera-dev mailing list > Chimera-dev(a)cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-dev >

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volume rendering depth issue with multiple volumes (segmented layers)
by William Jeffrey Triffo 19 Feb '08

19 Feb '08

hello, I remember past posts mentioning depth issues when rendering multiple volumes. I have several layers (6) that I have segmented out individually. Last night, they appeared to render 'in order' (the layers are parallel, and up to 6 thus overlap if rotated into the correct view). this morning, though, I notice that 'volume 2' is rendering 'on top' of everything else. is there a way I can trick this to work, or is there something I may be missing / clicked wrong? thanks, -Jeff -- ------------------------------------------------------------- Jeff Triffo Auer Group, Donner Lab, Lawrence Berkeley National Laboratory Raphael Group, Bioengineering Department, Rice University Medical Scientist Training Program (MSTP), Baylor College of Medicine phone (Berkeley): 510-486-7940 fax (Berkeley): 510-486-6488

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menssage error
by DRT/BA - Elias Silva dos Santos 19 Feb '08

19 Feb '08

Hi!! I am preparing a molecule for docking that he has two centers of iron sulphur [ 4FE-4S]+2 and one molecule of FAD. When trying to place loads I am recebeno error messages (DOCK Prep). As I must proceed to decide the problem Elias

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Mac OSX install issue: SOLVED
by Greg Williams 19 Feb '08

19 Feb '08

Thanks for the help. An upgrade from X11 1.1.1 to 1.1.3 solved the problem. GW

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Raytracing
by Bernard Heymann 19 Feb '08

19 Feb '08

Hi I'm trying to use povray directly from Chimera and everything works. However, the isosurface of my density comes out practically black, even though the clipping plane is rendered fine. I played a bit with lighting, but that does not seem to make a difference. Could you give me some guidance? I can send an output picture if needed. Bernard Heymann Rm 1515, 50 South Dr, NIH, Bethesda, 20892-8025 Tel 301-451-8241, Fax 301-480-7629

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Mac OSX install issue
by Greg Williams 19 Feb '08

19 Feb '08

I am running OSX 10.4.10 on an iMac with a 2.16 GHz Intel Core 2 Duo, 1 GB 66h MHz DDR2 SDRAM. I have installed X11 1.1.1 XFree86 4.4.0. I have downloaded the current production release of Chimera for Mac X11. The application doesn't open, either on a double click from the desk top or from the dock. I have also tried the Snapshot release dated 2-11-8, with the same result. The application will not open. I have also tried the Mac OSX (Aqua) version of 6-21-7. This version does open, and it works well, in limited doses. However, it is very unstable and closes spontaneously after a few minutes of work. Any ideas what may be incompatible between the X11 versions and my Mac? Thanks, Greg Williams

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surface color and coloring particular residues
by Michael DiMattia 19 Feb '08

19 Feb '08

hello, Is there a way to both color a surface-rendered protein by radius AND simultaneously color certain residues of the same chain with a distinct color? I have figured out how to do each one of these tasks, but can't seem to get both colorings to remain at the same time on the same protein. If I color by radius using "surface color" and then decide to highlight a particular residue, the particular residue is indeed colored, but at the expense of losing the color by radius to whatever color the protein was before that. thanks. mike

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Viewing mode
by James Fethiere 19 Feb '08

19 Feb '08

Hi, I'm trying to save an image of an EM map with atomic models fitting in and can't get pov-ray to write-out the displayed image. Using the side view panel, I cut out part of the surface and models to get the view I want. When I save the image without pov-ray, I get what is displayed but when I try using the pov-ray option, I get the full map and models without the clipping I imposed using the side view mode. What would be the right procedure? Thanks James

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color by radius and other color simultaneously
by Michael DiMattia 18 Feb '08

18 Feb '08

hello, Is there a way to both color a surface-rendered protein by radius AND simultaneously color certain residues of the same chain with a distinct color? I have figured out how to do each one of these tasks, but can't seem to get both colorings to remain at the same time on the same protein. If I color by radius using "surface color" and then decide to highlight a particular residue, the particular residue is indeed colored, but at the expense of losing the color by radius to whatever color the protein was before that. thanks. mike

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selection of different part of the protein through the sequence prompt
by Jean Didier Pie Marechal 16 Feb '08

16 Feb '08

Hi guys, I'd like to select two precise beta strands of my prot and I thought it would be easier to do so from the sequence editor. Unfortunately, I can't find a way to select different parts of the same protein in the sequence editor; I alwys select the full length between first and last selected residues whatever combo I use (shift, ctrl and so on). Is it possible to do this in the sequence editor? Cheers, JD Dr. Jean-Didier Maréchal Professor Lector Unitat de Química Física Departament de Química Universitat Autònoma de Barcelona Edifici C.n. 08193 Cerdanyola (Barcelona) Tel: +34.935814936 e-mail: JeanDidier.Marechal(a)uab.es ----- Missatge original ----- De: chimera-users-request(a)cgl.ucsf.edu Data: Dimecres, Febrer 13, 2008 9:00 pm Assumpte: Chimera-users Digest, Vol 58, Issue 15 > Send Chimera-users mailing list submissions to > chimera-users(a)cgl.ucsf.edu > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > or, via email, send a message with subject or body 'help' to > chimera-users-request(a)cgl.ucsf.edu > > You can reach the person managing the list at > chimera-users-owner(a)cgl.ucsf.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Chimera-users digest..." > > > Today's Topics: > > 1. Split into models (Sadler, Evan) > 2. Re: Split into models (Elaine Meng) > 3. Opaque volume planes (Tom Goddard) > 4. Re: Opaque volume planes (William Jeffrey Triffo) > 5. Re: Opaque volume planes (Tom Goddard) > > > -------------------------------------------------------------------- > -- > > Message: 1 > Date: Tue, 12 Feb 2008 17:51:30 -0600 > From: "Sadler, Evan" <ESADLER(a)dom.wustl.edu> > Subject: [Chimera-users] Split into models > To: "chimera-users(a)cgl.ucsf.edu" <chimera-users(a)cgl.ucsf.edu> > Message-ID: <C3D78D22.18B15%esadler(a)dom.wustl.edu> > Content-Type: text/plain; charset="iso-8859-1" > > Recent email address change caused the first try to bounce, so I > resent it. > > I've loaded a file (2rjp.pdb) with 4 chains and want to split it > into 4 > models so I can align them. But "split" returns: > > unrecognized command: "split" > > What am I doing wrong? > > Evan > > -- > J. Evan Sadler, M.D., Ph.D. > Howard Hughes Medical Institute > Washington University > 660 S. Euclid Ave., Box 8022 > St. Louis, MO 63110 > Tel: 314-362-9067 > FAX: 314-454-3012 > email: esadler(a)im.wustl.edu > > > > > ------------------------------ > > Message: 2 > Date: Tue, 12 Feb 2008 16:09:22 -0800 > From: Elaine Meng <meng(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] Split into models > To: "Sadler, Evan" <ESADLER(a)dom.wustl.edu> > Cc: chimera BB <chimera-users(a)cgl.ucsf.edu> > Message-ID: <84C5F9DD-BED6-4476-B29C-F39C322D4BEB(a)cgl.ucsf.edu> > Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed > > Hi Evan, > You must be using a version of Chimera older than the "split" > command. If you use the documentation that came with your download > > (opened from the Help menu) it should be fairly synchronized with > your software and you won't get confused by features you don't > have! > However, in this case, just get a newer version. > > The pages at our web site under http://www.cgl.ucsf.edu/chimera/ > docs/UsersGuide/ > > are "development documentation," which I am constantly changing as > Chimera changes. It will generally have newer things than your > downloaded software. > > The pages under http://www.cgl.ucsf.edu/chimera/current/docs/ > UsersGuide/ > > are documentation for the most recent production release (currently > > Nov 2007) and I see it also lists "split". So to use that feature > you can get that production release: > http://www.cgl.ucsf.edu/chimera/download.html#production > > There are also much newer "daily builds" although they are > essentially untested and exist mainly to provide access to the very > > latest developments. > http://www.cgl.ucsf.edu/chimera/download.html#production > > I just tried your structure in the production release and last > night's daily build; "split" worked in both, so you should be all set! > Elaine > ----- > Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu > UCSF Computer Graphics Lab and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > http://www.cgl.ucsf.edu/home/meng/index.html > > > On Feb 12, 2008, at 3:51 PM, Sadler, Evan wrote: > > > Recent email address change caused the first try to bounce, so I > > resent it. > > > > I've loaded a file (2rjp.pdb) with 4 chains and want to split it > > into 4 > > models so I can align them. But "split" returns: > > > > unrecognized command: "split" > > > > What am I doing wrong? > > > > Evan > > > > -- > > J. Evan Sadler, M.D., Ph.D. > > Howard Hughes Medical Institute > > Washington University > > 660 S. Euclid Ave., Box 8022 > > St. Louis, MO 63110 > > Tel: 314-362-9067 > > FAX: 314-454-3012 > > email: esadler(a)im.wustl.edu > > > > > > _______________________________________________ > > Chimera-users mailing list > > Chimera-users(a)cgl.ucsf.edu > > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > > ------------------------------ > > Message: 3 > Date: Tue, 12 Feb 2008 17:41:06 -0800 > From: Tom Goddard <goddard(a)cgl.ucsf.edu> > Subject: [Chimera-users] Opaque volume planes > To: William Jeffrey Triffo <triffo(a)rice.edu>, "'Chimera BB'" > <chimera-users(a)cgl.ucsf.edu> > Message-ID: <47B24AB2.3060501(a)cgl.ucsf.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Hi Jeff, > > The trouble obtaining opaque volume planes is not related to > volume > plane display being built into the volume dialog. It is related to > a > change I made in how transparency is handled in solid mode back in > Aug 2007. > > Today I changed transparency in "solid" style volume rendering so > it > is easier to obtain completely opaque data planes. In tonight's > builds > (if they succeed, may not since we are switching to Python 2.5 > today) > you can obtain completely opaque volume planes by using the > "Brightness > and Transparency" panel of the volume dialog to set transparency to > 0. > This transparency value represents the fraction (0-1) of the depth > of > the volume required to produce opacity to the degree indicated by > the > height of the yellow curve on the histogram. In other words it > modulates the overall transparency. But until today it was > arbitrarily > deciding not to modulate the transparency if this depth was less > than > one grid spacing. This meaning of the transparency factor was > introduced in August 2007, and prior to that the transparency > factor > just scaled the opacity given by the yellow curve. > > Tom > > Jeff wrote: > > hi Tom, > > > > in the older (plug-in) volume planes tool, I was able to generate > > images that were opaque planes. I don't seem to be able to do > this > > anymore, even with transparency = 0. is there a way for me to do > this > > in the current Chimera? > > > > ------------------------------ > > Message: 4 > Date: Tue, 12 Feb 2008 17:47:37 -0800 > From: William Jeffrey Triffo <triffo(a)rice.edu> > Subject: Re: [Chimera-users] Opaque volume planes > To: "'Chimera BB'" <chimera-users(a)cgl.ucsf.edu> > Message-ID: <47B24C39.10306(a)rice.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > thanks, > > do you know when tonight's builds will go through, I will test it > at > that point to see if the functionality made it in > > -Jeff > > > Tom Goddard wrote: > > Hi Jeff, > > > > The trouble obtaining opaque volume planes is not related to > volume > > plane display being built into the volume dialog. It is related > to a > > change I made in how transparency is handled in solid mode back > in Aug > > 2007. > > > > Today I changed transparency in "solid" style volume rendering > so it > > is easier to obtain completely opaque data planes. In tonight's > > builds (if they succeed, may not since we are switching to Python > 2.5 > > today) you can obtain completely opaque volume planes by using > the > > "Brightness and Transparency" panel of the volume dialog to set > > transparency to 0. This transparency value represents the > fraction > > (0-1) of the depth of the volume required to produce opacity to > the > > degree indicated by the height of the yellow curve on the > histogram. > > In other words it modulates the overall transparency. But until > today > > it was arbitrarily deciding not to modulate the transparency if > this > > depth was less than one grid spacing. This meaning of the > > transparency factor was introduced in August 2007, and prior to > that > > the transparency factor just scaled the opacity given by the > yellow > > curve. > > > > Tom > > > > Jeff wrote: > >> hi Tom, > >> > >> in the older (plug-in) volume planes tool, I was able to > generate > >> images that were opaque planes. I don't seem to be able to do > this > >> anymore, even with transparency = 0. is there a way for me to do > this > >> in the current Chimera? > > > > > > -- > ------------------------------------------------------------- > Jeff Triffo > Auer Group, Donner Lab, Lawrence Berkeley National Laboratory > Raphael Group, Bioengineering Department, Rice University > Medical Scientist Training Program (MSTP), Baylor College of Medicine > phone (Berkeley): 510-486-7940 > fax (Berkeley): 510-486-6488 > > > > ------------------------------ > > Message: 5 > Date: Tue, 12 Feb 2008 18:10:01 -0800 > From: Tom Goddard <goddard(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] Opaque volume planes > To: William Jeffrey Triffo <triffo(a)rice.edu> > Cc: 'Chimera BB' <chimera-users(a)cgl.ucsf.edu> > Message-ID: <47B25179.5050005(a)cgl.ucsf.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > The Chimera nightly builds usually run around 9 pm pacific standard > time > (california). The nightly build download web page has the date for > each > build, and that will not be updated if code checked in during the > day > does not compile. Code changes checked in before about 8 pm makes > it > into that night's build. > > http://www.cgl.ucsf.edu/chimera/alpha-downloads.html > > Tom > > > > ------------------------------ > > _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > End of Chimera-users Digest, Vol 58, Issue 15 > ********************************************* >

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Chimera-users February 2008