- Chimera-users - RBVI Mailing Lists

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 user, about 'turn' command
by Aguang Dai 15 Feb '08

15 Feb '08

Dear Mr./Ms. I'm a Chimera user in FSU. I would like to use Chimera to build some models. I used 'turn' command to rotate the model around the z axis. The command and option was: turn z 27.6923. The model is from a PDB file. But the result was that it should have be, not what I wanted. The atoms should be always in the circle centered in the Z axis, respectively. So my question is: When Chimera open a PDB file recording a protein structure, whether the coordinate axis is exactly the same as that in the PDB file? Thank you for your information in advance. Best, Daniel

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zone tool in volume rendering
by William Jeffrey Triffo 14 Feb '08

14 Feb '08

I've been using the new mask tool to extract features along surfaces, which is useful in its own right for generating separate maps of segmented areas. but, if I wish to color a region around a surface (or between surfaces) without generating a new map, I am not sure how to do this - the 'zone' and 'color zone' tools in Volume viewer expect atoms or marker files. I had thought about loading multiple files of these surface regions after segmenting them out, each with their own color, but loading them together produces the ordering problem with the volume rendering. also, loading multiple volumes consumes a lot of memory and I run short of memory. is there currently a way to color arbitrary regions in a volume rendering? for example, rendering all data within 60 A of a surface with a different color than the rest of the volume, or coloring a region between two surfaces a different color, analogous to the 'sandwich' option of the mask tool. thanks, -Jeff

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save volume histogram transfer function
by William Jeffrey Triffo 14 Feb '08

14 Feb '08

hello, is there a way for me to save the histogram transfer function that is displayed in Volume Viewer? I see that I can write down where the nodes are placed as these values appear in the "Level" dialog, but do not see a place to input magnitude (or write it down) of each node on the line. Ideally, I would just like to save it out, to apply the identical transform to multiple segmented areas of a volume. thanks, -jeff

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Per-model clipping plane flickering
by Tom Goddard 14 Feb '08

14 Feb '08

Hi Jeff, I think you need to increase the "cap to clip plane distance" in the Surface Capping dialog from its default value of 0.001 to maybe 0.01 or 0.1. I guess you have surface capping turned on. Sometimes the clip plane partially clips the surface cap causing a fractured appearance of the cap. The OpenGL clip plane is offset from the cap by a small amount to prevent this but the needed displacement depends on the precision of the OpenGL depth buffer. Chimera should figure out the right value for this offset but currently it is specified by the user. Tom Jeff wrote: > hi Tom, > > I am getting odd output using the per-model clipping plane - I have a > volume loaded w/ precomputed subsamplings, and have generated a > surface depiction of the volume. when I enable the per-model clipping > plane, there is a lot of blinking in the model at the interface with > the per-model clipping plane. > > this volume is a membrane that I masked out using contours (as I > explained a couple of emails ago, where I have a bunch of contours > plotted along a surface, and then use the zone tool along those > contours). this means that there are a lot of zeros where the masked > volume ends; could that be part of the problem? > > I am using Chimera build 2492, MacBookPro 2GB (identical model to > yours), and Leopard with the latest X11 patch. > > best, > > -Jeff >

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Opaque volume planes
by Tom Goddard 12 Feb '08

12 Feb '08

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?

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Split into models
by Sadler, Evan 12 Feb '08

12 Feb '08

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

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