- Chimera-users - RBVI Mailing Lists

Fit map in map
by src9697 04 Oct '07

04 Oct '07

Hello, I was just searching the archieves and I understand now that my last question was alittle dumb (i.e. the x,y,z rotation angles are not helpful). In this case does the "Rotation angle" and the " Axis" define a single rotation that transforms the "Fit map" to the "with in" map. Can I draw the axis using a .bild file (i.e .arrow with start and end coords given by axis and axis point). if I want to compare several maps to one reference, is it possible to define a single axis for them all? such that i can compare them all just by the magnitude of the rotation? does this make sense? thanks in advance sean

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Fit map in map
by src9697 04 Oct '07

04 Oct '07

Hello, I was wondering if it is possible to use the output (translation matrix, axis, ect.) from the "Fit map in map" command to obtain the angles of rotation around the x, y and z axis given an arbitrary origin (i.e. the center of the map). thanks sean

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Protein RMSD
by Beale, John 03 Oct '07

03 Oct '07

Is there any feature in Chimera that will allow the calculation of the RMSD between a protein and a reference structure? Thanks! John Beale

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updating hydrogen bonds in an MD movie
by E. Merkley 03 Oct '07

03 Oct '07

Hi Chimera crew, I am using chimera to visualize an MD trajectory. I want to look at the fluctuations of hydrogen bonding patterns in a helix over the course of the trajectory. Is there a way to use Find HBonds on each frame and display the updated pseudobonds as I view the movie in Chimera? Also, may I take this occasion to point out that requiring consecutive frames to have consecutive numbers in the file names is inconvenient. For instance, my simulation is 41 ns long, and the structures are stored (in our in-house format) every 1 ps. So rather then write out 41000 .pdb files, I'll write them out every 10 or 100 ps. To use chimera to view a movie, I have to rename the files using a perl script. Incidentally, I've been using Chimera for 3 years now and love it. -Eric Merkley Graduate student Biochemistry Department University of Washington

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chimera instalation
by Paola Beassoni 03 Oct '07

03 Oct '07

Dear all, i have downloaded chimera 1.2422 for linux and i don know hoe to install it. I have OpenSUSE but i am really new in linux. I have the file "chimera-1.2422-linux.exe" but i don know how to run it. My shell doen recognizes the command "run". So, please if anyone can help me i would really appreciate it. Best Regards Paola -- Paola Beassoni - PhD Dpto. Biologia Molecular - FCEFQyN Universidad Nacional de Rio Cuarto Río Cuarto - Argentina 00-54-358-4676422 00-54-358-4676232 (Fax)

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chimera for Amber9
by Francesco Pietra 02 Oct '07

02 Oct '07

Having installed DOCK6.1/DMS (debian Linux parallel amd64) and Chimera 1.2422 (scp-linked desktop Debian Linux i386), may I ask: 1) Can I use Chimera for Amber9 in place of VMD, which I currently use? 2) Being superficially familiar with VMD, I was looking in Chimera for *.prmtop and *.inpcrd file types, as well as rst file, etc.. I suppose I was unable to turn Chimera to use with Amber9. That said, I was very much impressed by Chimera at the first touch. Thanks francesco pietra ____________________________________________________________________________________ Be a better Globetrotter. Get better travel answers from someone who knows. Yahoo! Answers - Check it out. http://answers.yahoo.com/dir/?link=list&sid=396545469

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Setting camera viewpoint
by Thomas Goddard 01 Oct '07

01 Oct '07

Hi Matt, There is no Chimera command to set the camera. But there are commands to orient and position the displayed models precisely (turn, move, scale, cofr, clip, savepos, reset). The Chimera world keeps the camera fixed and moves the models. If you want to use Euler angles there is a plugin to do that called Transform Molecule Coordinates available at: http://www.cgl.ucsf.edu/chimera/experimental/experimental.html Tom Matthew Baker wrote: > Tom, > > Is there a way of specifying a camera position and a viewing angle from > the command line in chimera. I want to make a few snapshots of a > molecule (actually, several different PDBs) with very specific view angles. > > Thanks > > Matt

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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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Chimera electrostatic potential
by Kate Hardie 07 Sep '07

07 Sep '07

Hi, I've been unable to figure out how to colour the electrostatic surface of a protein red/white/blue. I'm assuming that you have to some how assign electrostatic potential before colouring but how is this done? I'm using a Mac and I've tried to use apbs with pymol but it will not recognise my pqr file generated on the pdb2pqr server or generate it itself. Thanks, Kate

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Re: [Chimera-users] problem while readin .phi file
by Thomas Goddard 06 Sep '07

06 Sep '07

Hi Ula, I do not use DelPhi so I don't know what the "maximum number of radius records" means. But I don't think Amber can produce a DelPhi format electrostatics file, and your *.phi file probably does not open in Chimera because it is not the expected DelPhi format. An alternative to DelPhi for computing electrostatics is APBS. It is free and not too hard to use and Chimera will display its output. Tom Urszula Uciechowska wrote: > Hi Tom, > > I was trying to use DelPhi program but i am getting the error: > > maximum # of radius records exceeded > increase nrmax > FORTRAN STOP Do you know maybe how to get rid of it? > so i used amber to get phi file. > > Ula

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benchmark scores
by Waterman, DG (David) 06 Sep '07

06 Sep '07

Hi, My info: Graphics - NVIDIA Quadro NVS 285 Processors - 2 Intel Pentium 4 Clock (MHz) - 3400 OS Type - Windows Surface - 261 Mesh - 116 Contour - 144 Solid - 110 Recolor - 95 Notes - Test Date - 04 sept 2007 Chimera Version - 2422 Machine - Dell Precision WorkStation 380 Graphics Memory (Mb) - 64 Main Memory (Mb) - 1024 OS Version - XP Professional, 5.1.2600 Service Pack 2 Build 2600 Driver Version - 7.1.8.4 Host name Dr. Dave's computer The machine isn't that bad, I guess it is let down by a poor graphics card. Cheers, D David Waterman Post-Doctoral Research Associate Macromolecular Crystallography +44(0)1235 778722 Diamond Light Source Ltd. Diamond House Harwell Science and Innovation Campus Didcot Oxfordshire OX11 0DE United Kingdom <DIV><FONT size="1" color="gray">This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom </FONT></DIV>

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soliciting chain-trace opinions
by Eric Pettersen 05 Sep '07

05 Sep '07

Hi all, Right now, if you do the "chain trace" action (or type "chain @ca") Chimera shows carbon alphas and any inter-residue connectivity of those residues, including disulfide linkages. I'd like to know if users generally like this behavior or would instead prefer a "strict" backbone-only trace, so I can determine whether to change the behavior, offer both alternatives, or leave things alone. This is only really relevant to the "trace" depiction since although the "full" and "minimal" backbone depictions also show disulfides, that can be turned off by turning off auto-chaining via the Model Panel, Selection Inspector, or "setattr" command*. So what do people think? --Eric Eric Pettersen UCSF Computer Graphics Lab pett(a)cgl.ucsf.edu http://www.cgl.ucsf.edu * in the setattr command you would be setting "autochain" to false.

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selection of some chain but not some particular residue
by Dhiraj Srivastava 05 Sep '07

05 Sep '07

Hi All I am new to Chimera and i have hard time finding commands like how to select some chain and exclude 1 or 2 residue in that chain? also i have a protein with 2 chain. how can i make different model for different chain or different portion of same chain so i can perform some action like clipping on these model independentaly? can any one please help me for these problems? Thank you -- Dhiraj K. Srivastava Department of Chemistry University of Missouri-Columbia MO, 65211 Ph. no. 001-573-639-0153

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(no subject)
by Wang, Xuelin 05 Sep '07

05 Sep '07

Dear Chimera's users: I have a problem to make an Amber MD movie using Chimera. I am sure I used the right Amber top file and mdcrd file, since I can use VMD to display them. In my trajectory file, I already striped water and counter-ions. Only box information was left with trajectory. However, when I display trajectory, all trajectories were out of shape. I saw the similar thing when I used VMD to display the trajectory without including PBC option. I doubt that there is something wrong with box information. But I don't know how to fix it. Any ideas? Thanks Xuelin

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problem while readin .phi file
by Urszula Uciechowska 05 Sep '07

05 Sep '07

Dear chimera users, I am trying to open my .phi file in chimera, but i am getting this message on the reply log: pbsa.phi: Record size at end of record 538976288 != size at head of record 20 it is becouse my file is too big? Thanks in advance! Ula -- MSc.PhD Student Medicinal Chemistry Group University of Halle-Wittenberg

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Vista compatibility
by Forbes J. Burkowski 30 Aug '07

30 Aug '07

Hi: Does anyone have any information about Chimera running on the Vista OS (specifically the 64-bit version)? Thanks in advance. Forbes Burkowski

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