February 2008 - Chimera-users - RBVI Mailing Lists

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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selection shadow is fixed
by jean-francois menetret 11 Feb '08

11 Feb '08

Recompiling the driver for the graphical card took care of the "selection shadow" Jean-Fran�ois M�n�tret, PhD Boston University School of Medicine Physiology and Biophysics Department 700 Albany Street W315 Boston, MA 02118 Email: menetret(a)bu.edu Mailing address: 715 Albany Street On Mon, 11 Feb 2008, chimera-users-request(a)cgl.ucsf.edu wrote: > 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. selection shadow (jean-francois menetret) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 11 Feb 2008 08:49:42 -0500 (EST) > From: jean-francois menetret <menetret(a)bu.edu> > Subject: [Chimera-users] selection shadow > To: chimera-users <chimera-users(a)cgl.ucsf.edu> > Message-ID: <Pine.A41.4.63.0802110846190.146120(a)acsrs3.bu.edu> > Content-Type: text/plain; charset="x-unknown" > > > I am using the latest nightly build installed on our linux machine. If I > select a PDB and move it around, the selection leaves a "shadow" behind > (see attached snapshot). > Thanks > > > > Jean-Fran?ois M?n?tret, PhD > Boston University School of Medicine > Physiology and Biophysics Department > 700 Albany Street W315 > Boston, MA 02118 > Email: menetret(a)bu.edu > Mailing address: 715 Albany Street >

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Dual display Mac problem moving Chimera window
by Tom Goddard 11 Feb '08

11 Feb '08

Jeff reports that with 2 displays on Mac OS 10.5 the Chimera window gets stuck when being dragged from one display to the other. Fixed by updating X11. Jeff wrote: > hi Tom, > > I thought since you also have a MacBookPro you might know the answer > to this question - I just bought a 24" monitor to extend the display > on my MBP (running Leopard). for all my other applications, I am able > to drag the application window onto the adjacent desktop space that > now exists on the new monitor (am still using the screen on my laptop > as well). however, the chimera window "gets stuck" - after I launch > it, the window spawns on my laptop screen, and when I try to move it > onto the new monitor, it stops halfway and I can't drag it any further. > > is there a properties file or something that Chimera / X uses to set > the bounds on the desktop? I took a screenshot but it saved 2 separate > files (one for each screen); the new 24" screen is set up on the left > side of the MBP. > Jeff wrote: > hi Tom, > > I downloaded the latest X11 update from macosforge (xquartz project) > and this relieved the Chimera window location problem, am now able to > move the window onto my attached 24" screen. > > -Jeff >

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selection shadow
by jean-francois menetret 11 Feb '08

11 Feb '08

I am using the latest nightly build installed on our linux machine. If I select a PDB and move it around, the selection leaves a "shadow" behind (see attached snapshot). Thanks Jean-Fran�ois M�n�tret, PhD Boston University School of Medicine Physiology and Biophysics Department 700 Albany Street W315 Boston, MA 02118 Email: menetret(a)bu.edu Mailing address: 715 Albany Street

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split-map
by Gatsogiannis, Christos 08 Feb '08

08 Feb '08

Hello chimera team, is there any memory-limitation for the split-map tool? When i perform a segmentation of a density-map larger than ~100MB i always get a chimera-error. In order to perform the segmentation, i have to coarse the density-map with a factor of 2, as example in imagic, and then split-map works fine with the new map. The result is of course density maps with a lower resolution. My Linux-PC has 4GB of memory and my first thought was that this should be enough for the segmentation of the density map as example in 10 parts (10x100=1GB). Is there any way to circumvent this problem and perform the segmentation with the original map? Thanks Christos Gatsogiannis Christos Dipl.Biol. Cryo-EM Lab Institut for Zoology Johannes Gutenberg University 55128, Mainz Germany Tel: +49(0)6131-39-23091

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Chimera-users February 2008