- Chimera-users - RBVI Mailing Lists

Curved helical filaments
by Tom Goddard 11 Jul '11

11 Jul '11

Hi Andy, The "vop unbend" command can straighten the density from a curved filament. The tricky part is you need a center-line path. You could define that by placing 3 markers. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#unbend Bending a straight filament map to follow a curve is not available. This is the inverse of the vop unbend operation. You can do a fake version of this by making a helical curve around the straight density map and then using vop unbend. That won't center the filament on the helical path, but it will create something similar by straightening the helix which I think will twist the density. Tom > Hi Tom- > > Not sure if there is an option for this - > > 1. can we bend an electron density map of a filament/tube by an small > angle ? > > 2. Can we generate an helix using a density map of a filament. > An example will be that of the bacterial flagella - it has the local > helical arrangement of the flagellin molecule and then thAT > ARRANGEMENT extends over several micrometers like a "sinusoidal wave" > with different helical arrangement to the filament axis. > > Best > Andy > > > Dr. Anindito Sen (Ph.D) >

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Tear-off menus in Chimera 1.5.3 for Mac OS X
by Jeff Lawton 11 Jul '11

11 Jul '11

Hi, I am running the native aqua version of Chimera 1.5.3 on Mac OS X 10.6, and it seems that the "tear off" feature of the menus is not available, though I was previously able to do that when running the X window version of Chimera. Is there a way to use the menu "tear off" feature in the native aqua version? Thanks! Jeff -- Associate Professor of Biochemistry Department of Chemistry Eastern University 1300 Eagle Road St. Davids, PA 19087 (610) 341-1545

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Re: [Chimera-users] distance between 2 residues
by Dedan Githae 11 Jul '11

11 Jul '11

how is the problem solved in chimera? i want to measure distance between 2 residues

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Invitation à se connecter sur LinkedIn
by Vincent Zoete 08 Jul '11

08 Jul '11

LinkedIn ------------ J'aimerais vous inviter à rejoindre mon réseau professionnel en ligne, sur le site LinkedIn. Vincent Vincent Zoete Associate group leader chez Swiss Institute of Bioinformatics Région de Genève, Suisse Veuillez confirmer que vous connaissez Vincent Zoete https://www.linkedin.com/e/vxh6i1-gpupen7z-1e/isd/3469346511/KWdfhuHl/ -- (c) 2011, LinkedIn Corporation

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Problem with multiple monitors and NVidia 3D Vision - any suggestions ?
by Steven Ludtke 07 Jul '11

07 Jul '11

Hi. I just set up a 3-D vision compatible stereo monitor as a second display on my desktop. I have a Quadro 4000 video card and am running 64 bit linux (Ubuntu 11.04) with the latest 270.41.06 Nvidia driver. If I only have one monitor (the stereo capable one) attached to the machine, I can get stereo working (looks very nice), but if I have the second non-stereo capable monitor connected at the same time, it will not initialize the stereo display mode (on either display). I have it configured using Xinerama, so the 2 displays are on separate X-servers. Even when I disable Xinerama, and the second display is running on a completely independent Screen, it still won't go into stereo mode. Here are the relevant lines from the Xorg log file: [ 9016.284] (**) NVIDIA(0): Depth 24, (--) framebuffer bpp 32 [ 9016.284] (==) NVIDIA(0): RGB weight 888 [ 9016.284] (==) NVIDIA(0): Default visual is TrueColor [ 9016.284] (==) NVIDIA(0): Using gamma correction (1.0, 1.0, 1.0) [ 9016.285] (**) NVIDIA(0): Option "TwinView" "0" [ 9016.285] (**) NVIDIA(0): Option "MetaModes" "nvidia-auto-select +0+0" [ 9016.285] (**) NVIDIA(0): Option "TwinViewXineramaInfoOrder" "DFP-2" [ 9018.424] (II) NVIDIA(GPU-0): Display (DELL3007WFPHC (DFP-0)) does not support NVIDIA 3D [ 9018.424] (II) NVIDIA(GPU-0): Vision stereo. [ 9018.466] (**) NVIDIA(1): Depth 24, (--) framebuffer bpp 32 [ 9018.466] (==) NVIDIA(1): RGB weight 888 [ 9018.466] (==) NVIDIA(1): Default visual is TrueColor [ 9018.466] (==) NVIDIA(1): Using gamma correction (1.0, 1.0, 1.0) [ 9018.467] (**) NVIDIA(1): Option "Stereo" "10" [ 9018.467] (**) NVIDIA(1): Option "TwinView" "0" [ 9018.467] (**) NVIDIA(1): Option "MetaModes" "1920x1080_120 +0+0" [ 9018.467] (**) NVIDIA(1): USB IR emitter stereo requested [ 9019.116] (II) NVIDIA(GPU-1): Display (Acer HN274H (DFP-0)) supports NVIDIA 3D Vision [ 9019.116] (II) NVIDIA(GPU-1): stereo. [ 9019.117] (II) NVIDIA(1): NVIDIA GPU Quadro 4000 (GF100GL) at PCI:2:0:0 (GPU-1) [ 9019.117] (--) NVIDIA(1): Memory: 2097152 kBytes [ 9019.117] (--) NVIDIA(1): VideoBIOS: 70.00.37.00.03 [ 9021.570] (II) NVIDIA(1): USB emitter - Copyright (c) 2009 NVIDIA Corporation NVIDIA [ 9021.570] (II) NVIDIA(1): stereo controller [ 9021.598] (II) NVIDIA(1): Setting mode "1920x1080_120+0+0" So, the logfile seems to indicate that it's initialized correctly, but when chimera tries to open a Stereo window, it raises an error :^( Here are the relevant xorg.conf sections: Section "ServerLayout" Identifier "Layout0" Screen 0 "Screen0" 0 0 Screen 1 "Screen1" 2560 0 InputDevice "Keyboard0" "CoreKeyboard" InputDevice "Mouse0" "CorePointer" Option "Xinerama" "1" Option "XineramaStereoFlipping" "0" EndSection Section "Device" Identifier "Device0" Driver "nvidia" VendorName "NVIDIA Corporation" BoardName "Tesla C2070" BusID "PCI:131:0:0" EndSection Section "Device" Identifier "Device1" Driver "nvidia" VendorName "NVIDIA Corporation" BoardName "Quadro 4000" BusID "PCI:2:0:0" EndSection Section "Screen" Identifier "Screen0" Device "Device0" Monitor "Monitor0" DefaultDepth 24 Option "TwinViewXineramaInfoOrder" "DFP-2" Option "TwinView" "0" Option "metamodes" "nvidia-auto-select +0+0" SubSection "Display" Depth 24 EndSubSection EndSection Section "Screen" # Removed Option "metamodes" "nvidia-auto-select +0+0" Identifier "Screen1" Device "Device1" Monitor "Monitor1" DefaultDepth 24 Option "TwinView" "0" Option "metamodes" "1920x1080_120 +0+0" Option "Stereo" "10" SubSection "Display" Depth 24 EndSubSection EndSection Section "Extensions" Option "Composite" "Disable" EndSection Anyone else have a Stereo configuration with dual monitors working ? cheers ---------------------------------------------------------------------------- Steven Ludtke, Ph.D. Associate Professor Co-Director National Center For Macromolecular Imaging Dept of Biochemistry and Mol. Biol. Baylor College of Medicine sludtke(a)bcm.edu stevel(a)alumni.caltech.edu

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Re: [Chimera-users] Regarding adding plane surfaces....
by Elaine Meng 07 Jul '11

07 Jul '11

On Jul 6, 2011, at 11:23 PM, chinmaya joshi wrote: > Hi Elaine, > > I have three objects in the chimera image. > All these objects are in different planes. > How to add surfaces to each of these so that they can be shown to lie in diff planes? > I have attached a typical image herewith. > > Regards, > Chinmaya Hi Chinmaya, There is a tool to define planes from sets of atoms, but I don't know if you have atoms. The "objects" (your image included below) look like isosurfaces in one volume data set. If you had atoms to start with, for example if you made the volume from atoms using the command "molmap", you could go back to those atoms use them to define planes. It could be done with the "define" command or "Axes/Planes/Centroids" (under Tools... Structure Analysis). <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/define.html> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/stru…> I don't know any way to define planes for isosurface blobs directly, without atoms. However, if you can calculate the plane coordinates yourself from these blobs, you can create plane objects with those coordinates in the BILD format. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/bild.html> The last idea is that you can use the Volume Viewer tool, Features menu entry "Planes" to view only certain slices of your data at a time, but this does not draw a plane object. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volum…> Please send Chimera questions to chimera-users(a)cgl.ucsf.edu instead of directly to me. Thanks, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

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Chimera function
by Flora Ieong 07 Jul '11

07 Jul '11

To whom it may concern, I am a chimera user and am currently doing a glycan research using Chimera 1.5.3. I wonder if chimera has a function to add glycans to a protein. Thank You. Sincerely, Pek Ieong

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movie script
by Jean-Francois Menetret 06 Jul '11

06 Jul '11

Hello, I am trying to make a movie to illustrate a conformational change between two PDBs; I would like to turn the objects while switching from one to the other. Could you give me some pointers ? Thank you J-F

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Re: [Chimera-users] Drug-Metal Complexation Modeling
by Mickey Branham 06 Jul '11

06 Jul '11

Thanks Elaine, I did check out the CCL website; a great resource. Mickey >>> Elaine Meng 07/05/11 6:25 PM >>> Hi Mickey, I don't have experience in this area, but you might try asking on the Computational Chemistry List (www.ccl.net) as to what programs might be suitable for predicting the structure of your complex. One way is to use their web form http://www.ccl.net/cgi-bin/ccl/send_ccl_message Best, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Jul 2, 2011, at 1:46 AM, Mickey Branham wrote: > Thanks Elaine, > Yes, your comments were helpful. I did a bit of window shopping with Chimera (very impressive) but I think for this project it may not be the right set of tools. Briefly, what we're trying to do is to produce stable complexes of the dipeptide carnosine with a heavy metal (i.e. ruthenium III) by high energy ball milling. > > So far this approach has been effective in producing nanosized particles which do contain [carn-Ru] complexes (ca. XRD, DSC/TGA, and FTIR) but their structure and molecularity appear to be polydispersed. > > We are trying to predict the most stable complex stoichiometry so that we can optimize milling parameters (e.g. temp, inert gas, speed and time) known to influence complex formation rate. Once we are able to reproducibly form the [carn-Ru] complex our plan is to characterize its anti-viral or anti-tumor activty. > > Don't know if this seems interesting but any comments from you would be appreciated. > > Thanks again for your response. > > Cheers > Mickey Please find our Email Disclaimer here: http://www.ukzn.ac.za/disclaimer/

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Not Responding
by Chad Junkermeier 05 Jul '11

05 Jul '11

Hello, I have been having strange behavior lately with opening coordinate files. I am using xyz format files with up to 500 atoms. When I tell Chimera to open one of these files the computer sits for a moment and then starts reporting that Chimera is "Not Responding." I have tried this on three different Mac computers, one using OS X 10.6.7 (iMac Core i7, 8 GB Ram, ATI Radeon HD 4850) with all of the latest updates, one using OS X 10.6.7 (iMac Core 2 Duo, 4 GB Ram, NVIDIA GeForce 9400), and one 3 or 4 year old Macbook that has (4GB RAM, and I don't know anything else). On each of these machines I have tried using a variety of different versions of your code, and I continually find that I have the same problem. I also just installed Chimera on a Windows XP machine and it has similar issues. The xyz files are the product of relaxing a graphene sheet in Quantum Espresso, and then copying and pasting the final configuration out of the QE output file into a xyz file. Here are a few of the things that puzzle me. First, if I place the input configuration of atoms into a xyz file, Chimera will read in the structures without any problems. The output xyz files work in VMD and in iMol. I thought that it might be an issue with the xyz data structure and transformed it to PBD and it still wouldn't load. I also wondered if it was an issue of too many decimal points (higher precision than the input file), but after reducing the number of decimal points of each coordinate on all of the atoms, it still wouldn't work. I have looked through some of the output files and there doesn't appear to be any weirdness in any of the files. Further complicating this issue is that sometimes, after if I let it sit for a while, the program magically starts working. Again, I have no problem opening other files. Does anyone have any ideas on what to do to fix this problem? Chad

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