- Chimera-users - RBVI Mailing Lists

benchmark results 1.2422-linux_x86_64
by Damir Perisa 23 Aug '07

23 Aug '07

hi there, i just set up my new laptop with archlinux 64bit and since i'm going to use everything 64bit on this machine (no 32bit libraries), i tried first time chimera 64bit. details on machine: Thinkpad x61t (Tablet Laptop) Linux Apollon 2.6.22-ARCH #1 SMP PREEMPT Wed Aug 15 22:51:57 CEST 2007 x86_64 Intel(R) Core(TM)2 Duo CPU L7500 @ 1.60GHz GenuineIntel GNU/Linux graphics: Intel integrated graphics 965GM VideoRam: 262144 KB (xorg version 1.3.0 xf86-video-intel version 2.1.1) ram total: [damir@Apollon ~]$ free total used free shared buffers cached Mem: 1002364 570780 431584 0 9524 142080 -/+ buffers/cache: 419176 583188 Swap: 979924 372324 607600 benchmarks: surface 130 mesh 129 contour 158 solid 128 recolor 129 Molecule (Atoms): Null Wire Stick BStick Ribbon Sphere Ops 1GCN (246): 762.0 677.0 150.0 150.0 736.0 109.0 7634.0 1YTI (798): 981.0 554.0 50.0 48.0 702.0 36.0 2305.0 2GBP (2575): 877.0 375.0 17.0 17.0 609.0 16.0 713.0 1GOT (6449): 601.0 213.0 6.0 6.0 468.0 9.0 216.0 2HMG (12189): 254.0 134.0 3.0 3.0 291.0 6.0 87.0 2PDA (18894): 165.0 91.0 2.0 2.0 191.0 4.0 51.0 1YNJ (24369): 132.0 67.0 5.0 10.0 217.0 3.0 40.0 1F4H (33805): 97.0 53.0 1.0 1.0 128.0 2.0 28.0 quite low scores, no? ... in addition i'm observing that only 50% of cpu is used (means only one core). chimera is not multi-threaded? greetings, Damir

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A problem
by EFFICIENT ECON AND ENVIR FRIENDLY PRD OF KEY INTER OFMJ ANTI 22 Aug '07

22 Aug '07

Dear Sir/Madam, I am very interested in your UCSF Chimera. Unfortunately I don't know how to use it to open my PDB files derived from molecular modelling. Could you help me? Your reply will be greatly appreciated. Best wishes, Qi Zhang ------------------------------------------------- This e-mail is sent by CUHK WebMail http://webmail.cuhk.edu.hk

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copy and paste a model
by William Jeffrey Triffo 22 Aug '07

22 Aug '07

is there a way to 'copy and paste' an entire model? for example, I have a volume data map with some surface and volume renderings that I would like to display in a few different orientations (same map, maybe rotated by 45 deg) side by side in the same scene/window. -- ------------------------------------------------------------- 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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Fitting informations
by Magali Cottevieille 21 Aug '07

21 Aug '07

Hi, Could you tell me where I can find informations of the fitting procedure of Chimera (Fit model in map)? I would particularly like to know if it is in real or Fourier space. Thank you, Magali.

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stereo view
by Rutledge, Robert (NIH/NCI) [V] 21 Aug '07

21 Aug '07

I have been trying to get chimera to work with stereo. I now have an NVidia Quadro FX 1500 card, and I start Chimera with the --stereo option. The program starts fine, but produces the following error: "can not open camera mode". Stereo will not work when I try to select it from the camera tab. My computer has 3 monitors; two are connected to the Quadro card. The first monitor (the one active during boot) is connected to an NVidia 7800GTX. Do I need to swap my cards so that the Quadro becomes the first card or is there another solution? Thanks, Robert Rutledge

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New benchmark
by David Konerding 21 Aug '07

21 Aug '07

Hello, here is a new benchmark HP xw9400 2 dual core Opteron 2220 8GB RAM Quadro FX3500 256MB nvidia driver 100.14.11 Chimera version 2422 Molecule (Atoms): Null Wire Stick BStick Ribbon Sphere Ops 1GCN (246): 15318.0 12309.0 1401.0 1313.0 15107.0 3208.0 6848.0 1YTI (798): 8422.0 7090.0 469.0 453.0 11649.0 900.0 2585.0 2GBP (2575): 448.0 2287.0 122.0 127.0 1443.0 289.0 536.0 1GOT (6449): 172.0 559.0 39.0 43.0 590.0 87.0 186.0 2HMG (12189): 173.0 254.0 26.0 27.0 246.0 52.0 78.0 2PDA (18894): 96.0 172.0 18.0 14.0 208.0 33.0 40.0 1YNJ (24369): 75.0 128.0 14.0 13.0 184.0 24.0 30.0 1F4H (33805): 46.0 114.0 9.0 8.0 72.0 25.0 21.0 surface 842 mesh 846 contour 153 solid 477 recolor 153 Dave

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VRML output
by Andrew Carter 17 Aug '07

17 Aug '07

I have been testing the vrml output from chimera (for loading into cinema 4d) and I can get a ribbon representation to work ok. However when I try a surface rendering it looses all the color. Am I dong something wrong. Also with the surface rendering is there a way to change how course the vrml output is? Many thanks Andrew

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potential bug in saving sessions using IMOD import
by William Jeffrey Triffo 17 Aug '07

17 Aug '07

not sure if this has already been reported, but if I save a session in which I have imported IMOD models (surface meshes + contours), and then reload the session, only the contours appear - the surface meshes do not. this is using build 2416, May 30 2007 release. -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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NRAMM workshop
by Thomas Goddard 16 Aug '07

16 Aug '07

Hi Scooter, Bridget Carragher suggests I give a demo of Chimera at the NRAMM (National resource for automated molecular microscopy) workshop on November 14. I think I will do that. Do you have special interest in talking with Bridget and Clint Potter about our proposed collaboration to use Chimera as a viewer of their EM database? Tom Bridget Carragher wrote: > Hi Tom, > We are hoping that we might be able to persuade you to come to our > upcoming workshop: "Workshop on advanced topics in EM structure > determination" which will be held during November 10-16, 2007 at NRAMM. > We will have a number of afternoon demonstrations of various relevant > software and we would be delighted if you would agree to give a half > hour presentation of the most relevant aspects of Chimera to the cryoE > community during the afternoon of Wednesday November 14. We will of > course, cover your airfare, as well as accommodation and all meals while > you are here and we'd encourage you to stay for as much of the workshop > as you can manage. I'm attaching a draft agenda of the workshop so you > can get an idea of the basic outlay - all except the highlighted talks > are conformed. > Best regards, > Bridget and Clint > > > ------------------------------------------------------------------------ > > > ---------------------------------------------------------------------------------------------------------------------------------- > Bridget Carragher, Associate Professor > Automated Molecular Imaging Group, Department of Cell Biology > The Scripps Research Institute, MC CB129,10550 North Torrey Pines Road, > La Jolla, CA 92037 > tel: (858) 784-9070; fax: (858) 784-9090; bcarr(a)scripps.edu; > http://ami.scripps.edu > National Resource for Automated Molecular Microscopy: > http://nramm.scripps.edu > ---------------------------------------------------------------------------------------------------------------------------------- > > > >

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Re: [Chimera-users] sym command in Chimera
by Thomas Goddard 16 Aug '07

16 Aug '07

Hi Nevin, The sym command places molecule copies relative to the coordinate frame of a density map. If you do not have a density map open it will not work. The solution is to open a density map, any map will do even if it is not related to your system -- it is just providing a coordinate frame. Here's a density map (potassium ion channel electron microscope data) if you don't have one. ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-1094/map/emd_1094.map.gz You'll need to uncompress it (for example, with gunzip, or on the Mac it will offer to uncompress automatically when you download it) before opening it in Chimera. Once it is open in Chimera and you use the sym command you can undisplay it with Favorites / Model Panel. You also use Model Panel to freeze the map (uncheck the "active" button) in order to make motions of the molecule generate new positions for the molecule copies. Here is why a map is needed to define a coordinate frame. You might think the positioning matrices could just be applied in the global coordinate frame. But when you rotate the Chimera models with the mouse to get a different view point, that moves all the models around in the global frame, and that would cause all the monomers to assume a new arrangement if the matrices were applied to the rotated reference model. So in order to be able to see you models from different view points without changing their relative positions the symmetries are applied relative to the coordinate frame of a density map. (Could be relative to any other model but the command was created for people fitting molecules into density maps.) If you rotate the density map and molecules together then the matrices still keep the same relative positions of the molecules. Tom Z. Nevin Gerek wrote: > > Hello, > I am having another problem with sym command. When I test on some > proteins including the example (1i84) provided in the website, I get > 'No opened volume or reference model specified" error. > I used sym and then sym #0 but they give same error. Do I need to copy > another feature for this command? Is there anyway I can fox this problem? > > Thanks again, > > > Z. Nevin Gerek, Ph.D. > Postdoctoral Fellow > ----------------------------------------------------- > The Center for Biological Physics > Arizona State University > PO Box 871504 > Tempe, AZ 85287-1504 > Phone: (480) 727-8897 > nevin.gerek(a)asu.edu <mailto:nevin.gerek@asu.edu>

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Manually assigning secondary structure to residues
by Oren Shalev 16 Aug '07

16 Aug '07

Dear Chimera team and users, I'm modeling chains with gaps using in-house software. When opening in Chimera a model in which a secondary structure element is broken or flanked by the start/end of a gap, the secondary structure of the residue adjacent to the gap is assigned to be 'coil'. I guess this is expected, since one needs to know both Phi and Psi angles to determine the secondary structure of a given residue, yet I always have knowledge that the residue adjacent to the gap does indeed belong to a secondary structure element. My question is this: is there a way to assign the secondary structure of a given residue to either 'helix' or 'strand'? I'm interested in this for imaging purposes, so potential negative consequences on other aspects of Chimera's operation (perhaps on analysis tools?) don't matter to me. Thank you, Oren

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sym command in Chimera
by Z. Nevin Gerek 15 Aug '07

15 Aug '07

Dear Chimera team, I am trying to use sym command to generate symmetry related copy of a protein. I followed this link: http://www.cgl.ucsf.edu/chimera/experimental/symmetrycopies/ symcopies.html The version I am using is 1.2422. When I write sym, I get this error: "unrecognized command: "sym" Then I found this link http://www.cgl.ucsf.edu/pipermail/chimera- users/2005-September/000464.html and put necessary files to Chimera.app/Contents/Resources/share folder. Then I restart Chimera, I get same error. Is there another way to use sym command in Chimera? Thanks for your help, Z. Nevin Gerek, Ph.D. Postdoctoral Fellow ----------------------------------------------------- The Center for Biological Physics Arizona State University PO Box 871504 Tempe, AZ 85287-1504 Phone: (480) 727-8897 nevin.gerek(a)asu.edu On Aug 11, 2007, at 12:00 PM, 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. transposing a pdb structure ("copy & paste") (Ben Keshet) > 2. Re: transposing a pdb structure ("copy & paste") (Elaine Meng) > 3. Re: transposing a pdb structure ("copy & paste") (Eric > Pettersen) > 4. Re: chimera on AMD workstation (Vinay Kumar) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 10 Aug 2007 15:53:33 -0400 > From: "Ben Keshet" <keshet1(a)umbc.edu> > Subject: [Chimera-users] transposing a pdb structure ("copy & paste") > To: <chimera-users(a)cgl.ucsf.edu> > Message-ID: <000001c7db88$238da8b0$29ad5582@umbc80a173302c> > Content-Type: text/plain; charset="us-ascii" > > Dear Chimera fans and team, > > I have a pdb file of a fragment of an amyloid fibril constructed of > 8 layers > (8 parallel strands of beta sheet). I would like to overcome the end > effects when modeling it, so I would like extend the existing > structure by > duplicating it at its end. > > Does Chimera has a tool do the following: duplicate existing pdb > molecule > coordinates, position the duplicated molecule at a desired > location, and > then align it reasonably with respect to the original molecule? > > Thank you very much for your time and help. > > Ben > > > > > ------------------------------ > > Message: 2 > Date: Fri, 10 Aug 2007 16:04:20 -0700 > From: Elaine Meng <meng(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] transposing a pdb structure ("copy & > paste") > To: "Ben Keshet" <keshet1(a)umbc.edu> > Cc: chimera-users(a)cgl.ucsf.edu > Message-ID: <8f3e5fad823ed51cc9da3fa7677864cc(a)cgl.ucsf.edu> > Content-Type: text/plain; charset=US-ASCII; format=flowed > > Dear Ben, > Chimera doesn't have the ability to figure out for you the proper > position of one copy relative to another. You could open multiple > copies, perform manual positioning, and then write out all the > coordinates, but I imagine it might be difficult to get the right > position of one copy relative to another, even manually/interactively. > > To manually position a structure relative to another, you could > interactively rotate/translate and/or use the "move" (translation) and > "turn" (rotation) commands. You can freeze/unfreeze a copy using the > Active checkbox in the Model Panel (in the Favorites menu by default), > the command "select," or the little checkboxes under the Command Line > (also under Favorites). > > If you did manage to position copy 2 relative to copy 1 to your > liking, > you could write the transformation matrices out (see "matrixget" > command). From those you could calculate the transformation of 2 > relative to 1 and also generate appropriate matrices that would then > position 3, 4, ... correctly (see "matrixset" command). I admit I > don't know how to do those calculations. Anyone? > > Yet another snag depends on how you will be using these coordinates. > Does it require all the PDB files to be merged into one? If so, can > they be in a multi-MODEL form, or in a single model? Chimera can > output separate PDB files or a single multi-MODEL PDB file. If you > need all the coordinates to be in one model, however, you would > have to > edit the PDB output from Chimera so there are not atoms with duplicate > atom numbers and chain IDs. However, it all depends on what the > *next* > program you will be using requires and expects. If you will just be > using Chimera, however, no further editing would be required (in fact, > you could just save a session rather than writing out coordinates). > > Maybe someone else will have a smarter and less discouraging set of > suggestions! Best, > Elaine > > On Aug 10, 2007, at 12:53 PM, Ben Keshet wrote: > >> Dear Chimera fans and team, >> >> I have a pdb file of a fragment of an amyloid fibril constructed of 8 >> layers >> (8 parallel strands of beta sheet). I would like to overcome the end >> effects when modeling it, so I would like extend the existing >> structure by >> duplicating it at its end. >> >> Does Chimera has a tool do the following: duplicate existing pdb >> molecule >> coordinates, position the duplicated molecule at a desired location, >> and >> then align it reasonably with respect to the original molecule? >> >> Thank you very much for your time and help. >> >> Ben > > > > ------------------------------ > > Message: 3 > Date: Fri, 10 Aug 2007 16:53:36 -0700 > From: Eric Pettersen <pett(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] transposing a pdb structure ("copy & > paste") > To: Ben Keshet <keshet1(a)umbc.edu> > Cc: Chimera BB <chimera-users(a)cgl.ucsf.edu> > Message-ID: <E5C1411A-58C1-49A8-8899-24816E53E043(a)cgl.ucsf.edu> > Content-Type: text/plain; charset="us-ascii" > > On Aug 10, 2007, at 4:04 PM, Elaine Meng wrote: > >> To manually position a structure relative to another, you could >> interactively rotate/translate and/or use the "move" (translation) >> and >> "turn" (rotation) commands. You can freeze/unfreeze a copy using the >> Active checkbox in the Model Panel (in the Favorites menu by >> default), >> the command "select," or the little checkboxes under the Command Line >> (also under Favorites). >> >> If you did manage to position copy 2 relative to copy 1 to your >> liking, >> you could write the transformation matrices out (see "matrixget" >> command). From those you could calculate the transformation of 2 >> relative to 1 and also generate appropriate matrices that would then >> position 3, 4, ... correctly (see "matrixset" command). I admit I >> don't know how to do those calculations. Anyone? > > It's a little tricky. Basically, you want to get copy 1's matrix to > be the identity matrix while keeping copy 2 in the same relative > position. Here's one way to do it (and maybe someone can suggest > something better): > > 1) open yet another copy (copy 3) as a reference > 2) use "matrixset" to set copy 3's matrix to be the identity matrix > 3) use the "match" command with the 'active' keyword to match copy 1 > onto the reference (copy 3) while also moving copy 2 appropriately > 4) use "matrixget" to get copy 2's new transformation matrix > > I would imagine that copy 2's matrix is essentially all translation > components (i.e. the upper 3x3 is all zeroes or near-zeroes) so all > you need to do to place additional copies to multiply the translation > components by 2, 3, etc. > > --Eric > > Eric Pettersen > UCSF Computer Graphics Lab > pett(a)cgl.ucsf.edu > http://www.cgl.ucsf.edu > > >

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Request
by Rajendra P. OJHA 14 Aug '07

14 Aug '07

Dear Sir, After installation on a AMD opetron machine(64 bit) it gives the following error message Pease rectify the problem and oblige. Thanks Ojha ************************** Message ********************** ./chimera-1.2422-linux_x86_64.exe UnZipSFX 5.41 of 16 April 2000, by Info-ZIP (Zip-Bugs(a)lists.wku.edu) Original path: '/home/rpo/CHIMERA' inflating: chimera_install_KUOeVj/installer inflating: chimera_install_KUOeVj/chimera.exe ./installer: /lib64/tls/libc.so.6: version `GLIBC_2.4' not found (required by ./ installer) result code from installer: 256 Installer returned unexpected return code '256' Cleaning up extract dir, 'chimera_install_KUOeVj' Installation is done; press return. ____________________________________________________________________________________ Choose the right car based on your needs. Check out Yahoo! Autos new Car Finder tool. http://autos.yahoo.com/carfinder/

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stereo display
by Rutledge, Robert (NIH/NCI) [V] 14 Aug '07

14 Aug '07

I am trying to get stereo working with Chimera. I use the --stereo switch when I start up the program. This results in the following error: "unable to find hardware stereo support (Togl: couldn't choose stereo pixel format)". The graphics card connected to the CRT monitor is NVIDIA 7900GS. I run Chimera under Windows XP media center edition. I have a cheap pair of shutter glasses (edimensional), which work properly when tested by the test application on the graphics card. Do I need another graphics card or glasses, or is something else the problem? Robert Rutledge

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modeling non-standard amino acids
by Dan Wendt 14 Aug '07

14 Aug '07

Hello, My name is Daniel Wendt and I work for Biomarin Pharmaceuticals in Novato, Ca. I'm trying to use Chimera's modeling software to predict structural changes that are imparted on my 22 amino acid peptide by the insertion of two non-standard changes to the peptide bond. In one case, I am adding a methyl group to the backbone amide bond. In another case, I'm removing a carbonyl from the backbone amide bond. This peptide then needs to be cyclized by the formation of a intra-disulfide bond. I do have x-ray crystal structure data of my cyclized peptide bound to one of its receptors. Do you know how one goes about doing this? Do you have any references that might help? Thank you in advance! Daniel Wendt Senior Scientist BioMarin Pharmaceutical Novato, Ca 94949 (415) 506-6131 This message is intended only for the confidential use of the intended recipient(s). If you have received this communication in error, please notify the sender by reply e-mail, and delete the original message and any attachments. Any unauthorized disclosure, copying, or distribution of this message (including the attachments), or the taking of any action based on it, is strictly prohibited.

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mrc maps
by Gorelik, Tatiana 13 Aug '07

13 Aug '07

Dear Chimera-team, Can I load several .mrc maps at a time and rotate them one against another? Thanks, Tatiana ************************************ Tatiana Gorelik, PhD, Institut für Physikalische Chemie Johannes Gutenberg-Universität Mainz Welderweg 11 55099 Mainz Germany Tel.: 0049 6131 39 22347 Fax: 0049 6131 39 23768 e-mail:gorelik@uni-mainz.de ************************************

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macintosh/stereographics/boot camp
by Dougherty, Matthew T. 11 Aug '07

11 Aug '07

There are some difficulties deep in the apple graphics driver implementation that prevent X11 and openInventor and openGL stereographics. I can report that mac-bootcamp-windows running with a quadro fx 4500 (card supplied by apple, other cards have the wrong firmware); does correctly do stereographics under XP windows correctly with no noted problems. ========================================================================= Matthew Dougherty *** 713-433-3849 National Center for Macromolecular Imaging ========================================================================= =========================================================================

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chimera on AMD workstation
by Vinay Kumar 10 Aug '07

10 Aug '07

Hello all, recently we bought a AMD workstation. I tried to install chimera_linux x86_64 on it. But it did not install. went through installation instructions. still did not work. i would like you to give me some suggestions and some variations that i could try to install chimera. Thank you Elaine, for your post on spheres. shall inform when my adventures have a result. regards, Vinay

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Teaching with Chimera
by Fabian Glaser 09 Aug '07

09 Aug '07

Dear Chimera team, I'd like to use both chimera and chimera tutorials for a new "Structural Bioinformatics practical course" I am preparing here at the Technion in Israel. I will of course acknowledge appropriately. Is there any legal limitation for using chimera for this purpose? Thanks for creating such a fantastic tool Fabian Glaser, PhD Bioinformatics Knowledge Unit, The Lorry I. Lokey Interdisciplinary Center for Life Sciences and Engineering Technion - Israel Institute of Technology Haifa 32000, ISRAEL E-mail: fglaser(a)tx.technion.ac.il Tel: +972-4-829-3701 Cell: +972-52-2357731

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writing translation/rotation
by Thomas C. Marlovits 08 Aug '07

08 Aug '07

Hi, am looking for an analysis tool in Chimera that would write out - let's say a matrix for translation/rotation of a pdb-file in respect to another one. Usage: would like to align chain A and chain B present in a pdb-file and want to know which translation/rotation matrix has to be applied in order to convert the non-aligned pdb-coordinates of chain B to the 'new" aligned pdb-coordinates. Thanx for your help, -Thomas ------------------------------------------------------------------------ ------- Thomas C. Marlovits, PhD, M.A.S. IMP-IMBA Research Center - Research Institute of Molecular Pathology (IMP) - Institute of Molecular Biotechnology, Austrian Academy of Sciences (IMBA) Dr. Bohr-Gasse 3 Room IMBA/6.02 A-1030 Vienna Austria, Europe fone: (++43-1) 79044-4630 fax: (++43-1) 79044-4401 email: marlovits(a)imp.univie.ac.at

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how to select spheres for docking?
by Vinay Kumar 06 Aug '07

06 Aug '07

Hello all, I have a few queries to ask. hoping you all will reply. i use DOCK6.0, the dms program under DOCK, can create and execute a total of 9999 spheres. I would want to know, how do i selectively select spheres using chimera? Is it possible to select certain residues and generate the molecular surface for it? and use it for docking?? My previous problem with chimera got resolved. Thank you Greg. I had to change the OS from RHL9.0 to fedora core. with regards, Vinay ps- please ignore if off-topic. i have posted the same query on dock mailing list. still awaiting a reply there.

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Re: [Chimera-users] odd glare when volume rendering
by Tom Goddard 03 Aug '07

03 Aug '07

Hi Jeff, Aha! Now I see Chimera is working as expected and I can reproduce the glare on my computer. If you have depth cueing set to "No color", which is the default, *and* you use a light background color, then Chimera interprets "no color" as white. With a dark background color, I use black, "no color" for depth cueing is interpreted as black. So all I had to do was set by background color to a light shade to see the glare. So this is bad behavior. The white depth cue color does not work with volume rendering -- it is way too powerful -- all the far planes in the data become slightly white, and this ends up making a very white brick. Oddly, I have already fixed the problem, accidently! My current development version of Chimera (not on the web) has a new blending mode for volumes. I made the change to address a serious problem you raised earlier that the brightness in volume rendering changes a lot when you change step size. The new mode fixes that and will be the default in the next snapshot. Coincidentally the new blending mode also makes white fog work as expected without an overly powerful effect. I have also added better handling of large EM tomography maps -- file loads report progress and can be canceled, default initial display can show a single z plane, the z plane slider is built into volume viewer, hdf5 format map files can be written which contain subsampled versions of the map allowing rapid display of the data at any scale. I'm testing all this on an 2048^3 map. A snapshot should be out in a month or so, though if you really want bleeding edge stuff I could probably give you an earlier version for mac os. Tom William Jeffrey Triffo wrote: > hello, > > I am getting an odd glare when I use solid rendering in VolumeViewer - > it is orientation dependent, which makes me think it has to do with > lighting? I am using build 2416; is it possible to forward a screenshot > to the list? > > thanks, > >

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odd glare when volume rendering
by William Jeffrey Triffo 02 Aug '07

02 Aug '07

hello, I am getting an odd glare when I use solid rendering in VolumeViewer - it is orientation dependent, which makes me think it has to do with lighting? I am using build 2416; is it possible to forward a screenshot to the list? thanks, -- ------------------------------------------------------------- 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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Problem with Gasteiger charges of a formally charged ligand
by cdeligka＠purdue.edu 02 Aug '07

02 Aug '07

Dear all, I tried to calculate the Gasteiger charges of peroxynitrite anion using Chimera (I tried the version that was recently released as well as some previous ones). This is my PDB file: HEADER HETATM 1 O 2 2 1.225 0.000 1.819 HETATM 2 N 2 2 0.138 0.000 1.281 HETATM 3 O 2 2 0.138 0.000 -0.086 HETATM 4 O 2 2 1.359 0.000 -0.746 The formal charge of this molecule is -1. For some reason Chimera generates the Gasteiger charges for the molecule but these charges correspond to a formal charge of zero and not -1. If I try the other method AM1-BCC the charges that are calculated do correspond to a formal charge of -1. In my calculations I do need the Gasteiger charges and so I cannot use the ones that are calculated by AM1-BCC. If you have any suggestions please let me know. Are you aware of any other software that might be able to do this calculation? Thank you all, Christos

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Moving individual markers
by J. Evan Sadler 02 Aug '07

02 Aug '07

Is it possible to move single markers from the command line, instead of using the mouse under the Volume Path Tracer tool? If so, it would greatly simplify certain model constructions. Evan Sadler

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