July 2016 - Chimera-users - RBVI Mailing Lists

Docking Crystal Structure in to Cryo EM Structure
by Senavirathne, Gayan 20 Jul '16

20 Jul '16

Hello, I am trying to dock some crystal structures (PDB: 1KX5 and 3OS1) in to a cryo EM structure EMDB:2992. How can I do this task using the UCSF chimera software and how can I know the alignment is accurate? Thank you very much Regards, Gayan Senavirathne, PhD Postdoctoral Researcher The Ohio State University Wexner Medical Center Cancer Biology and Genetics 460 West 12th Avenue, Room 1040 Columbus, OH 43210 Phone (313) 316-6658 senavirathne.1(a)osu.edu<mailto:senavirathne.1@osu.edu>

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new release of UCSF Chimera
by Elaine Meng 18 Jul '16

18 Jul '16

Hello everybody, A new production release of UCSF Chimera (version 1.11) is available: http://www.rbvi.ucsf.edu/chimera/download.html Download is free for noncommercial use. Platforms: Windows, Mac OS X, Linux. 64-bit builds are recommended for all capable platforms; this will be the last release to support 32-bit builds. New since version 1.10: Molecular Dynamics Simulation tool, more Add Ions types, residue interaction networks (RINs) from trajectories shown in Cytoscape, protein contact/distance map data export, Segment Map updated to new version of Segger, volume contour levels can be specified in RMSDs from zero or SDs from mean, "flat ribbon" publication preset, Ribbon Styles tutorial, "set showCofR" to show crosshairs at center of rotation. More details are given below; see release notes for the full list: http://www.rbvi.ucsf.edu/chimera/docs/relnotes/1.11.html General I/O, Display: * standard shortcuts for File menu (Ctrl/Cmd-q for Quit, etc.) * "wall-eye stereo pair" option in Save Image dialog * PubChem fetch uses PubChem3D instead of Pub3D * "set showCofR" command to show "+" at center of rotation * "pipes" command-line implementation of PipesAndPlanks * reduced triangles in STL output for atoms/bonds Structure Analysis and Modeling: * Molecular Dynamics Simulation tool (thanks to V Munoz Robles and JD Marechal, Universitat Autonoma de Barcelona) * many more ion types in Add Ions tool * axes can be defined normal to previously defined planes * RR Distance Maps can show distance differences for a pair of structures (means, std devs already available), export data * MD Movie calculation of trajectory RINs, display in Cytoscape * PDB2PQR updated to use new web service URL Volume Data (density maps, electrostatic potential): * new input map format: IMAGIC density * Segment Map updated to new version of Segger * "volume" command options "rmsLevel" and "sdLevel" to specify thresholds in units of RMSD from zero and SD from the mean * "vop" options to sharpen map, create new zero-valued map Enjoy! On behalf of the Chimera team, 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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using scipy with Chimera
by Xiao-Bo Li 16 Jul '16

16 Jul '16

Hi, I need to use scipy with Chimera. I like to copy over the scipy folder from my ubuntu's "/usr/lib/python2.7/dist-packages/scipy" directory. This is what I have done in the past, and it works fine. However, when i installed the .bin file for Chimera from Chimera's website (I tried versions 1.11 and 1.8.1), I find that the numpy versions there are 1.7.0b2. The numpy version on my ubuntu computer is 1.11.0. Since my ubuntu python's numpy, and Chimera's numpy are different versions, I can no longer using the scipy folder for Chimera. Can you please update Chimera's numpy version to 1.11.0? XBL

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Re: [Chimera-users] A question about colouring a resmap output file in Chimera.
by Elaine Meng 15 Jul '16

15 Jul '16

Hi Thanos, I’ve never used Resmap myself (it is a separate program from Chimera), but as I understand it, the output file contains the local resolution values calculated from the input map. You would have both that original map and the resmap output map open in Chimera, show an isosurface of the original map, and color it by the values in the resmap map. It is best to send Chimera-related questions to the list CC’d here (chimera-users(a)cgl.ucsf.edu) because often other people know more about something than I do. >From this earlier post to the list, I thought Resmap also output a Chimera script that you could run to perform the coloring: <http://www.cgl.ucsf.edu/pipermail/chimera-users/2015-October/011679.html> However, even if you didn’t run such a script you could do the coloring using the Surface Color tool or the “scolor” command in Chimera. Finally, there must be more information about how to use Resmap with Chimera, and how it calculates the values, in the Resmap manual and the Resmap paper in Nature Methods, see: <http://resmap.sourceforge.net/#manual> I hope this helps, 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 15, 2016, at 4:47 PM, T-I <ignatiou(a)gmail.com> wrote: > Hello Elaine. > My question today is: > > I have run Resmap on my em-density map (.mrc) to calculate the local resolution > > When i open both the original .mrc file and the _resmap.mrc file in chimera i don't understand how to then colour the map with the values found in the resmap calculation. > > what do i do exactly? > > also i don't understand where the resmap values are?? > many thanks > Thanos >

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Troubleshooting Residue Errors
by Mike Bergman 15 Jul '16

15 Jul '16

Good Morning. I am trying to Dock Prep the kappa1 dimer (PDB ID: 2Q20) in order to run Molecular Dynamics simulation. I keep getting an error that I'm not sure how to solve. I cleared the reply log and tried again so I could attach the reply log to this email. I have not modified the structure at all prior to the dock prep. When I looked at the residues, they seemed fine to me, but maybe you can help me figure out what's wrong. Any help would be appreciated. Thank you very much. Sincerely, Mikey Bergman

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Cannot load trajectory in chimers executed through cytoscape
by Natesh Singh 15 Jul '16

15 Jul '16

Dear Sir/Madam, I am not able to load the MD trajectory, either in PDB or XTC in the chimera that was executed from cytoscape. When I define the path for the files, it says 'reading pdb...' but the trajectory never gets loaded into the screen. and this is happening in both linux and windows. Kindly guide me on this that how can I run the trajectory in chimera from cytoscape to analyze the residue interaction network. Best regards, Natesh

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Re: [Chimera-users] error: more than 63 chains; cannot uniquely identify with single characters
by Elaine Meng 15 Jul '16

15 Jul '16

On Jul 15, 2016, at 7:39 AM, Wu, Weimin (NIH/NIAMS) [E] <weimin.wu(a)nih.gov> wrote: > Dear Elaine, > I have a pdb structure with four chains A, B, C, D. and an icoshedral cryo-EM density map. I fit the pdb into the map, and generate 60 copies. I try to merge all these 60 pdbs into a combination, but without renumbering the residues (choose "retain the name" option). I did this operation before without any error, but now it came with the error "more than 63 chains; cannot uniquely identify with single characters". > > If choose renumber the residues, then the merged is not easy to understand, not easy for comparison either. > > Is there any other way to do it? Thank you, > Weimin On Jul 15, 2016, at 8:43 AM, Wu, Weimin (NIH/NIAMS) [E] <weimin.wu(a)nih.gov> wrote: > Or easy to understand, can we add model number into the pdb as done in biological assembly pdb structure 1qgt.pdb1? Hi Weimin, I’m not sure how you made the copies, but if they are atomic structures I think this will work: Similar to what you said in your second message, instead of merging into a single model, simply keep all the models separate. You can still save to a single “multi-model” PDB file with the main menu: File… Save PDB (or just save the Chimera session for later). Then the copies will still all have chain IDs A,B,C,D which may be easier to work with anyway. I tried this with 1pov (which has chains 0,1,3) and with “sym” made the whole assembly with 59 more copies for 60 total. I looked in the model panel and they were models #0 (original) and #1.1-59 (copies). I saved as single PDB file and read it back in, and again had those same 60 models, each with the original chain IDs 0,1,3. It is recommended you send questions to chimera-users(a)cgl.ucsf.edu (CC’d here) instead of just me because I am not the expert on everything. :-) I hope this helps, 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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Distances measurement for NMR ensemble
by James Starlight 15 Jul '16

15 Jul '16

Dear Chimera Users! I wonder to ask whether it possible to calculate distances between two selected atoms by means of the Chimera's Distance measurement tool providing as input NMR-ensemble consisted of 20 snapshots (without any additional files like topology!) or alternatively small md trajectory, obtaining also some elementrary statistics (E.g RMSD etc) Thanks! James

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RMSD of protein-protein interphaces
by James Starlight 12 Jul '16

12 Jul '16

Dear Chimera users! Having several docking poses of 2 proteins I need to estimate RMSD difference between their interphaces (e.g like what I have seen in Capri) Is it possible to do it via some Chimera's plugin e.g in combination with the contact-maps plugin? Thanks! Gleb

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Structural matching of Side-chain selection
by James Starlight 12 Jul '16

12 Jul '16

Dear Chimera users! I need to estimate how the side-chains dynamics are differs in MD compared to X-ray structure. Assuming that I have 2 structures one from md and another from X-ray and I select Sidechains from the both as obj1 and obj02 is it reasonable just to match them using MatchMAker? Thanks! James

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