September 2007 - Chimera-users - RBVI Mailing Lists

Frozen chimera
by hsosa＠aecom.yu.edu 28 Sep '07

28 Sep '07

I have the following problem: When rotating molecules or volumes the whole computer freezes for a while. Sometimes recover and will freeze again after a few more molecule movements. Sometimes the whole system crash, the blue screen appear and a whole reboot is needed. The problem most likely is graphic card related. I did reported it before and was suggested to change the driver. I did but it did not solve the problem. My system currently is as follow: Chimera 1.2422 Windows XP service pack-2 Dell Precision 530 with Dual Xeon 1.4 GHZ processors and 1 GB RAM Graphic Card: NVDIA Quadro 900 XGL Video BIOS version 4.25.0027.05 ForceWare version: 78.01 Before I had: ForceWare version 91.36 So both of these video driver had problems. I wonder if anybody has experienced something similar and found the right driver. Thanks Hernando

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reconstructing x-ray structure
by Nevin Gerek 27 Sep '07

27 Sep '07

Hello, I am wondering if there is an option in Chimera to reconstruct exact place for binding peptide. I do have x-ray structures and binding peptide was incorporated as a C-terminal extension. When I used these structures, I do not get protein-peptide contact information in our model. Is there any way to reconstruct x-ray structure data with the right peptide binding information? Any help would be appreciated. Thanks. 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

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sgi core dump
by bala 27 Sep '07

27 Sep '07

Dear chimerians, Goodday. I installed the latest-chimera for sgi irix. Installation was completed successfully. But when i give chimera, it throws the following core.. Kindly write me how to get rid of the same. ce/BPT/RangeErr/DivZero/Ovflow trap (core dumped) thanks, Bala

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Docking of PDB data
by Alexander Solodukhin 19 Sep '07

19 Sep '07

Dear Listers, I have got the CCP4 3d map of PKC created from tilted series of 2d crystals grown on lipid monolayers. Unit cell: a=b=53A, alpha=beta=90 deg and gamma=120 deg. X-rays 3d structures of three fragments: C1b, C2 of the regulatory domain and catalytic domain are available from PDB data bank. When I try to dock PDB files or their maps created with SPIDER or SITUS programs by the use of 'fit models in maps' or 'fit maps in maps' in CHIMERA, programs place this fragments into one only place around the point that looks like a 'center of gravity' of CCP4 model. If I cut off the part of model where this point is, anyway program places these fragments into the same point out of the selected subregion. How can I fix this problem? I understand that I have to assign the same origin of coordinates for my model and fragments, but I do not know how to do this. Alexander Solodukhin, Ph.D. Department of Anesthesiology University of Virginia Health System P.O.Box 800710 Charlottesville VA 22906-0710

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Molecular surface crash
by Thomas Goddard 13 Sep '07

13 Sep '07

Hi Markus, I computed a molecular surface for the PDB file you gave me by changing the probe radius from 1.4 A to 1.399 A. I set the new probe radius using the "New Surface" category of the Preferences dialog (menu Favorites / Preferences). The "New Surface" category was added in Chimera 1.2430 (July 23, 2007) so you'll need the newest Chimera snapshot on Linux http://www.cgl.ucsf.edu/chimera/download.html#snapshots or a weekly Chimera build (very latest code) on other platforms (Mac, Windows) http://www.cgl.ucsf.edu/chimera/alpha-downloads.html New Chimera surface calculation code is still 6 months away. Tom Markus Voehler wrote: > Tom > > I have switched from my SGI to a RHEL 5 machine and see the same > behavior now on that computer as I have seen on the Mac. Some pdb files > do not seem to allow me to show the surface plot. This leaves me with no > option to display the surface for some pdb's. In the past I was just > doing this work on the SGI, which worked fine. I have tried your > suggestion about increasing the vdv radius again on the Linux box, but > it did not help either on this computer. Has there been any resolution > to the mentioned report 1295? > > I have deposited the pdb online, in case you want to reproduce the > problem on your cpu. The link is: > > [deleted] > > Any help is appreciated. > > Markus >

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When structures and density maps don't align
by Walter R.P. Novak 10 Sep '07

10 Sep '07

Hi All, Amongst my colleagues (to whom I constantly evangelize Chimera) there is often an issue opening pdb and map files together. Specifically, sometimes the maps and pdb coordinates are not superimposed (often drastically). I have been able to reproduce the issue so let me explain what works and what doesn't. What works: If you take a pdb file and an mtz into Phaser (from the ccp4 suite) then refmac for rigid body refinement and convert the output mtz to a map using mapman it works. The pdb and map superimpose perfectly. What doesn't work: If you take a pdb file (of known correct solution but not transformed to the correct coordinates) and throw it into refmac (ccp4) and do some rigid body refinement and then convert the resulting mtz into a ccp4 map, the map is perfectly good (the statistics are identical to using the phaser placed model), but when opened in Chimera they do not superimpose. Both of the methods above appear valid as far as structure determination (R and Rfree are identical, etc) and I know coot will align the model and map and I believe pymol will too, though I don't use pymol personally so I cannot vouch for that. Is the correct transformation information hidden in a file somewhere so that Chimera can align the two files automatically. Often people skip the phaser step and drop the model right into refinement and then manually aligning in Chimera becomes difficult. Best, Wally Walter R.P. Novak, Ph.D. Postdoctoral Fellow Rosenstiel Basic Medical Research Center Brandeis University 415 South St. MS 029 Waltham, MA 02454-9110 Phone: (781) 736-4944 Fax: (781) 736-2405

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Benchmark scores
by Thomas Goddard 10 Sep '07

10 Sep '07

Hi Gabor, Your Quadro FX 1500 benchmark scores are about the same as the fastest system we have seen. I'll add them to our benchmark web page today. http://www.cgl.ucsf.edu/chimera/benchmarks.html Thanks for sending the numbers. Tom Gabor Papai wrote: > Hi! > > The benchmark scores of my PC are: > > CPU Information > Processor (CPU): Intel(R) Core(TM)2 CPU 6600 @ 2.40GHz > Speed: 2 401,96 MHz > Memory Information > Total memory (RAM): 2,0 GB > Total Swap: 4,0 GB > > OS Information > OS: Linux 2.6.20-1.2952.fc6 i686 > System: Fedora Core release 6 (Zod) > > Display Info > Vendor: nVidia Corporation > Model: Quadro FX 1500 > Memory: 256 MB > > Benchmark scores > surface 839 mesh 809 contour 179 solid 435 recolor 161 > > Test was done: 07 Sept. 2007 > Chimera 2422 > > I don't know whether these scores are good or not, I'm not familiar with > them. > Bye, > Gabor >

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seelction around map
by Dhiraj Srivastava 07 Sep '07

07 Sep '07

Hi all Is there any way that we can select atoms or residues within some distance of a ccp4 map in chimera? i know tha we can select map within some distance of any selected atoms but can we do opposite and if yes then how? thank you Dhiraj -- Dhiraj K. Srivastava Department of Chemistry University of Missouri-Columbia MO, 65211 Ph. no. 001-573-639-0153

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MRC map values -128 to 127
by Tom Goddard 07 Sep '07

07 Sep '07

> Hi, > > I have some mrc files on a 64 bit linux machine (linux version > 2.6.9-42.0.8.ELsmp, x86_64) and the chimera on that machine displays the > volume data fine with a range from 3 to 255 and a histogram centered > around 120 and the 3D structure shows up very well with a threshold of > 108. But after I transfer these data to a mac os x 10.4.10 and use the > chimera on the mac, the data range becomes -128-127 with the histogram > splitted into two halves close to each end of the data range. What's > worse, I can not get a good threshold to show my 3D structure. Can you > please tell me what is possibly wrong and how to fix this? > > Thank you very much. > > Zhiheng Hi Zhiheng, The trouble with displaying your MRC files with Chimera is that the files contain unsigned 8-bit data values (0-255 range) and that format is not supported by the MRC standard. Only signed 8-bit data values (-128 to 127) is supported by MRC. So why does it work on your 64-bit linux Chimera and not the Mac Chimera? I believe that is because your Linux Chimera is an old version of Chimera. About one year ago (September 19, 2006, Chimera version 1.2290) I changed Chimera to follow the MRC standard and use signed 8-bit whereas earlier versions incorrectly assumed unsigned 8-bit values. Your Mac version of Chimera is probably newer and your Linux version older. The MRC file header gives no indication that the values should be unsigned 8-bit as that value type is not supported. But some software programs ignore that, use unsigned 8-bit values and set the MRC header field to indicate signed 8-bit. They rely on software to ignore the MRC standard. I added a way to work around this problem in newer versions of Chimera (Nov 29, 2006, version 1.2315). You open then MRC map then use the keyboard shortcut "u8" to reinterpret it as unsigned 8-bit. Then you will need to save the map with the volume dialog menu entry File / Save map as... if you want to avoid using u8 every time you open the map. Saving a map which is unsigned 8-bit will automatically use the signed 16-bit MRC mode. You probably should not overwrite your original file but instead make a new file. To use this u8 shortcut you first have to turn on shortcuts with Chimera menu entry Tools / General Controls / Accelerators On. Then you can type u8 in the main Chimera window. It operates on the map currently shown in the volume dialog so you can switch maps and apply it to other maps as well. You may also be interested in shortcut "Im" which inverts the map, mapping the range value v to (255-v). Tom

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Display axes for global frame of reference?
by Andrew D. Fant 07 Sep '07

07 Sep '07

Hello All, I'm considering using Chimera as my general purpose modeling graphics front-end and have run into a snag. I have a protein that I need to globally translate and rotate to move several residues to be oriented along the x, y, and z axes. In InsightII, there is an option to display the global coordinate system in the main graphics window, so that it's easy to manipulate a structure to a given orientation. Is there a way to display the global axes like that in Chimera, and is it possible to write out the transformed coordinates of a PDB file without a lot of difficulty? Thanks, Andy

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