- Chimera-users - RBVI Mailing Lists

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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chimera on AMD workstation-> followup
by Vinay Kumar 30 Aug '07

30 Aug '07

Hello Tom and other list members, Your suggestion proved right. Chimera is installed and working well. Thankyou. Vinay On 8/10/07, Thomas Goddard <goddard(a)cgl.ucsf.edu> wrote: > > Hi Vinay, > > The chimera-1.2422-linux_x86_64.exe distribution is for 64-bit > versions of Linux. If you are using a 32-bit linux (even with a 64-bit > processor) then you need chimera-1.2422-linux.exe instead. > > If that is not the problem, could you be more specific about what > goes wrong when you try to install? What is the error message? > > Tom >

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(no subject)
by guiqing＠mailer.sb.fsu.edu 27 Aug '07

27 Aug '07

If I manually move and rotate the object in Chimera, how could I know the exact displacements along x, y, z and the rotation angle? Anyone has any suggestion? Thank you! Guiqing ----------------------------------------------------------------

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input file to make movie
by shivesh kumar 27 Aug '07

27 Aug '07

Dear all I am using chimera very first time.I want to know how to make the input files from .pdb file to make a movie.Thanx in advance for the suggestions. Shivesh Kumar

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Installing Chimera
by John Beale 27 Aug '07

27 Aug '07

I have a LINUX computer on which I have been running Chimera for a couple of years. On this system installing Chimera was very straightforward- just click on the executable. I just took delivery on a new Linux system and I have been trying to install Chimera. I downloaded the file from your site (an *.exe file). When I click on the executable my system tells me that the file had been downloaded as an MS/DOS file and I should open the file some other way. The executable would not run. I have no idea what to do with this. Can you suggest a solution? It is strange because it was so easy to install on my previous system. (I am using RedHat Enterprise LINUX). Thank You! John Beale jbeale(a)stlcop.edu

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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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