- Chimera-users - RBVI Mailing Lists

All PDB ca atom pairwise distance
by Kyle Morris 03 Nov '17

03 Nov '17

Dear chimera dev and users, Is there a way to calculate (using the GUI, commands or using a python script) the pairwise distances for every single c-alpha atom in a set of loaded PDB coordinates and spit this out to a file for further analysis? There are 142,800 atoms in the current loaded assembly. Thanks! Kyle

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rmsd graph
by SEFA ÇELİK 02 Nov '17

02 Nov '17

Dear Dr. I am using Chimera software(windows platform). I tried to get rmsd graph. And I got the result. But, graph's x-axis "*frame*" and y-axis "*rmsd*" value. I want the x axis to be the "*time*". Briefly, I want to see how the value of rmsd changes with time. Can you help with this? Could you explain in detail? Best regard Dr. Sefa Celik

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error during MPEGM enconding
by Edoardo D'Imprima 02 Nov '17

02 Nov '17

Dear Chimera team, I ma trying to record a simple movie using the following command #!/bin/csh -f # # windowsize 900 1094 movie record supersample 4 volume #0 style solid; wait volume #0 planes z,0,0; wait volume #0 planes z,0,115; wait movie stop ###bitrate 5000 movie encode output my_movie.mp4 quality highest framerate 25 mformat mp4 however I keep on getting this error message: /Applications/Chimera/Chimera.app/Contents/Resources/bin/ffmpeg -r 25.0 -i /var/folders/2h/r_flycl50hj8klh8w4t1xmw400030f/T/chimovie_Vcz6-%05d.ppm -vf crop=floor(in_w/2)*2:floor(in_h/2)*2:0:0 -y -f mp4 -pix_fmt yuv420p -qscale 1 /Users/user/Desktop/folder/my_movie.mp4 An error occurred during encoding. See Reply Log for details. Error during MPEG encoding: ----------------------------- Exit value: 1 Error message: libavutil 52. 48.100 / 52. 48.100 libavcodec 55. 39.100 / 55. 39.100 libavformat 55. 19.104 / 55. 19.104 libavdevice 55. 5.100 / 55. 5.100 libavfilter 3. 90.100 / 3. 90.100 libswscale 2. 5.101 / 2. 5.101 libswresample 0. 17.104 / 0. 17.104 libpostproc 52. 3.100 / 52. 3.100 [image2 @ 0x7fac00802000] Could find no file with path '/var/folders/2h/r_flycl50hj8klh8w4t1xmw400030f/T/chimovie_Vcz6-%05d.ppm' and index in the range 0-4 /var/folders/2h/r_flycl50hj8klh8w4t1xmw400030f/T/chimovie_Vcz6-%05d.ppm: No such file or directory Could you please let me know what am I doing wrong? I tried both on my laptop (MacBook Pro (Retina, 13-inch, Early 2015) with OS version 10.11.6 (15G1004)) and our linux terminals (Linux sbterm 3.10.0-514.16.1.el7.x86_64 GNU/Linux) It happens on both Chimera 1.12 and Chimera 1.11 Many thanks in advance, Edoardo --------------------------------------------------- Edoardo D'Imprima PhD Student Max Planck Institute of Biophysics Structural Biology Department Max-von-Laue Straße 3 60438 Frankfurt am Main Germany Tel: +49 (0) 69 6303 3015

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ChimeraX x Chimera feature comparison?
by Gustavo Seabra 02 Nov '17

02 Nov '17

Hi guys, I wonder if there is a ChimeraX x Chimera feature comparison anywhere. I’m aware of the “ChimeraX Advantages” page (http://www.rbvi.ucsf.edu/chimerax/docs/user/advantages.html) However, I’m actually looking for a comparison that can tell what features are currently on Chimera that are *not* in ChimeraX, to consider if there is any reason to keep both in the computer. Thanks, -- Gustavo Seabra Adjunct Professor Federal University in Pernambuco Recife - PE - Brazil +55-81-2126-7450 x5023 (goo.gl/ktsXSc)

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problem with showing broken peptide after residues with alternative conformation
by Wangshu Jiang 01 Nov '17

01 Nov '17

Dear Chimera Support, I am using Chimera to performing structural analysis for a manuscript. I have been struggling to show the protein structure with PDB entry 3LR2, the peptide bond between residue with alternative conformations and the next residue was shown broken, both in backbone and in ribbon presentation. I am not sure what went wrong here, I compared the PDB text file to other PDB entries with alternative conformations and I did not find obvious differences. It would be nice to show all the rotamers in the PDB instead of manually deleting by coot just from ‘eyeballing'. Could you please help me to solve this issue? Any suggestion is deeply appreciated! I attached an image illustrating the problem I described. I hope to hear from you soon! Best Regards, Wangshu Jiang PhD student Dept Cell and Molecular Biology BMC Box 596 Husargatan 3 751 24 Uppsala Sweden [cid:0D42E809-5937-4AC1-83FB-07A00C355333] Wangshu Jiang PhD student Dept Cell and Molecular Biology BMC Box 596 Husargatan 3 751 24 Uppsala Sweden

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Linux focus on toolbar click
by Daniel P Farrell 30 Oct '17

30 Oct '17

Hello, I'm not sure if this is a distro thing, but I'm on linux mint and when I click on something in the toolbar the first time, the window appears on top of the main chimera window. However, if the window is already open, now the window no longer is brought to the front, and instead lights up on the linux application toolbar. Would it be possible/easy to change this so that when I click on the toolbar and the window is already open for it to be brought to the front? It seems to already work this way on mac. NAME="Linux Mint" VERSION="18.1 (Serena)" ID=linuxmint Cheers, Dan

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download Chimera to new computer
by Kjaergaard, Christian Hauge 27 Oct '17

27 Oct '17

To whom it may concern, My name is Christian Kjaergaard and I'm a Scientist at FibroGen. We bought a perpetual license to use Chimera in 2014. However, Lee Wright, who has been the sole user, recently left the company. Therefore we would like to install Chimera on a different computer if possible. Do we need to obtain a new license key or what are the steps to accomplish this? Best Regards, Christian

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Resmap local resolution video
by D.A. Semchonok 26 Oct '17

26 Oct '17

Dear colleagues, How to record video: chimera-resmap animation that resmap creates for the local resolution. Sincerely, Dmitry

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Chimera 1.12 release
by Elaine Meng 25 Oct '17

25 Oct '17

A new production release of UCSF Chimera (version 1.12) is available: http://www.rbvi.ucsf.edu/chimera/download.html Download is free for noncommercial use. Platforms: Windows, Mac OS X, Linux. New since version 1.11 (see release notes for the full list): http://www.rbvi.ucsf.edu/chimera/docs/relnotes/1.12.html General I/O, Display: * Updated URLs for fetching PDB, mmCIF, EDS * improved initial display of EDS difference map (shows both positive and negative isosurfaces) * "click-to-center" mouse mode (default Ctrl-right button) uses surface vertex instead of entire surface * "clip" and "thickness" commands prevent placing the back plane in front of the front plane Structure Analysis and Modeling: * AmberTools updated to version 17 * Add Charge uses precalculated charges for NAD and NDP * Morph Conformations "core fraction" exposed for more control over hinge detection * "hbonds" command option to show as dashed or dotted lines Bugfixes * Mol2 output includes metal-coordination bonds * Dock Prep consistent handling of alternate locations in adjacent residues Note: most new development focuses on ChimeraX, also available: http://www.rbvi.ucsf.edu/chimerax/ Enjoy! On behalf of the Chimera team, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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How to write pdb file by script?
by 陈品 24 Oct '17

24 Oct '17

Dear developers, I use CHIMERA to add charge into protein file from PDB format to mol2 format, i found that the script: $ cat prep_protein.py import chimera from DockPrep import prep models = chimera.openModels.list(modelTypes=[chimera.Molecule]) prep(models) from WriteMol2 import writeMol2 writeMol2(models, "10gs_protein_charged.pdb") $ ~/.local/UCSF-Chimera64-1.12rc/bin/chimera --nogui 10gs_protein.pdb prep_protein.py This script works well, but how to write PDB format file. I can not find WriteDPB function. How Can i write the data to PDB format? Kind Regards. Pin. -------------------------------------------------------------------------------- 本邮件及其附件含有发送给特定个人和用于特定目的的保密信息。如果您不是预期的收件人，请立即删除本邮件并通知发件人。严禁任何非预期的收件人使用、传播、分发或复制本邮件或其附件。 This email and its attachments may contain confidential information intended for a specific individual and purpose. If you are not the intended recipient, you should delete this email and notify the sender immediately. Any use, dissemination, distribution, or copying of this email or its attachments by persons other than the intended recipient(s), is strictly prohibited.

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