- Chimera-users - RBVI Mailing Lists

Chimera comands
by Michał Kadlof 16 Nov '17

16 Nov '17

Hello, I have some troubles with finding in documentation suitable commands. How do I should write script which: - open a trajectory in saved PDB or PSF/DCD in MD movie tool. - read pseudobonds from file, and change the color of all of them at once - change origin, voxel size and rotation angle of opened volumetric data Can you help me? -- best wishes, Michał Kadlof <m.kadlof(a)cent.uw.edu.pl <mailto:m.kadlof@cent.uw.edu.pl>>

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scripting: howto add IDATM labels
by Wiktor Pronobis 15 Nov '17

15 Nov '17

Hi all, I have a python script and want to know, how do I 1. add IDATM labels to the atoms 2. add a label in the upper right/left corner 3. make image nicer 4. save image as png I use the command "from chimera import runCommand as rc" and then "rc(COMMAND)" What should COMMAND be for my questions 1. - 4.? Thanks in advance, wpron

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Re: [Chimera-users] the matrix reported in 'fit in map'
by Tom Goddard 14 Nov '17

14 Nov '17

Hi Qiang, Glad you figured this out. Chimera uses whatever map origin is specified in the map file, and this may not follow the EMAN2 convention of putting the origin at the center of the map. You can change the map origin in Chimera using Volume Viewer panel menu entry Features / Coordinates, and you could save a new map with that origin with Volume Viewer menu File / Save Map As…. Tom > On Nov 13, 2017, at 8:10 PM, 周强 wrote: > > Hi Tom, > Thank you very much for your kind reply. > I have tested the Chimera matrix in EMAN2 Transform class as you described. The rotation part is consistent between Chimera and EMAN2. The translation part is also consistent if the origin index is set to the center of the map. ( For even images, the center is at (nx/2,ny/2) where the first pixel is at (0,0). For odd sized images, the center is at ((nx-1)/2,(ny-1)/2). The same concept extends to 3-D. http://blake.bcm.edu/emanwikiEman2TransformInPython ). > > Qiang > > >> -----原始邮件----- >> 发件人: "Tom Goddard" <goddard(a)sonic.net> >> 发送时间: 2017-11-14 02:13:27 (星期二) >> 收件人: "周强" <zhouq2015(a)mail.tsinghua.edu.cn> >> 抄送: >> 主题: Re: [Chimera-users] the matrix reported in 'fit in map' >> >> Hi Qiang, >> >> The 3x4 matrix reported by Chimera has the 3x3 rotation in the first 3 columns and the translation in the last column. I do not know EMAN2 conventions. Chimera does not use or convert to Euler angles. Keep in mind that the rotation is about the origin of the map coordinates which is set by the “Origin index” value (shown with Chimera Volume Viewer menu entry Features / Coordinates). If you rotate your map about a different origin, then that becomes a non-zero translation and a rotation about the map origin. >> >> Tom >> >> >>> On Nov 10, 2017, at 8:36 PM, 周强 <zhouq2015(a)mail.tsinghua.edu.cn> wrote: >>> >>> Dear Chimera developer group, >>> I am Dr. Qiang Zhou from Tsinghua university in Beijing China. Recently I'm going to calculate relative position between two maps with 'fit in map' in chimera. The 'fit in map' feature reported a matrix of 3 x 4. Can I convert this matrix to Euler angle with transform class of EMAN2 directly? Is the matrix of chimera same to that of EMAN2? BTW, The translation column in chimera matrix maybe contains a bug. I just manually rotated a map and then fit it into the original map. The matrix reported by Chimera should contain zero translation column. However, it reported a non-zero value (about 6-7 pixel) in translation column. >>> Thank you very much. >>> Qiang >>> _______________________________________________ >>> Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu >>> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >

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Help using Chimera with SFLD - I cannot 'view in chimera'
by Anne-Frances Miller 14 Nov '17

14 Nov '17

Dear Elaine, or other Chimera Guru, I would like to start using the wonderful tools in SFLD, and watched the tutorials, however when I try to do any of the things that is supposed to send something to Chimera, it crashes. I cannot open enzyme active sites in Chimera, or HMM alignments. I have updated by chimera. I am running Mac OS X 10.10.5, and firefox 56.0.2 Anne-Frances Miller Professor of Chemistry University of Kentucky

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cap clipping plane
by René Frank 13 Nov '17

13 Nov '17

Hi, I have a problem that the cap of my clipping plane is capping only some of the electron density. See screenshot attached. Any tips on how to ensure all electron densities, including smaller structures, are capped would be gratefully received. Many thanks, René ============================= Dr R. Frank, PhD MRC Laboratory of Molecular Biology Francis Crick Avenue Cambridge CB2 0QH United Kingdom Lab: +44 1223 267487 Mobile: +44 7870 208280 ============================

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question
by 等儿会儿 13 Nov '17

13 Nov '17

dear editor： i am a noob with using Chimera. Now, i want to find and select all amino acid surrounding my ligand within a particular range（eg. 10Å）,how should i do? thanks for your help ! from a user

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the matrix reported in 'fit in map'
by 周强 13 Nov '17

13 Nov '17

Dear Chimera developer group, I am Dr. Qiang Zhou from Tsinghua university in Beijing China. Recently I'm going to calculate relative position between two maps with 'fit in map' in chimera. The 'fit in map' feature reported a matrix of 3 x 4. Can I convert this matrix to Euler angle with transform class of EMAN2 directly? Is the matrix of chimera same to that of EMAN2? BTW, The translation column in chimera matrix maybe contains a bug. I just manually rotated a map and then fit it into the original map. The matrix reported by Chimera should contain zero translation column. However, it reported a non-zero value (about 6-7 pixel) in translation column. Thank you very much. Qiang

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working with PDB files from XplorNIH
by Miriam Gochin 13 Nov '17

13 Nov '17

I am wondering if it is possible in Chimera to select between different chains in a multimer that are defined by the SEGID parameter in XPLOR. This appears on columns 77-80 of the PDB file, e.g. in this homotrimer: ATOM 1 N GLN 1 -2.276 -27.488 29.307 1.00 0.00 A ... ATOM 684 N GLY 1 4.365 -26.465 20.200 1.00 0.00 C --- ATOM 1357 N GLN 1 13.798 -26.207 29.441 1.00 0.00 E ... Atom selection results in picking up 3 atoms instead of 1, since Chimera expects the chain designation after the residue name. The XPLOR output is therefore not compatible with Chimera input requirements and I am wondering if there is a workaround. Many thanks for any suggestions. --------------------------------- Miriam Gochin Touro University California miriam.gochin(a)tu.edu 707-638-5463

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help！
by 余汉文 12 Nov '17

12 Nov '17

Good afternoon! Can you give me a favor? I have a serious problem in the process of studying application cytoscape. I can't open protein structure formate file in cytoscape via RINalyzer. However UCSF Chimera does not start. SO I check the path to UCSF Chimera. The Chimera is installed at D:\Chimera. Finally, i open the dialog Cytoscape Preferences Editor to modify the path "D:\Chimera\bin". But i can't open the protein structure formate file in cytoscape via RINalyzer as same as early. I Heartfelt thank you to help me solve this problem. From the student in china

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Help with chimera / sfld compatibility
by Anne-Frances Miller 11 Nov '17

11 Nov '17

Hello experts, I have tried reloading many things and switched browsers. When I am in SFLD and want to view my aligned sequences of the subgroup identified by my enzyme, in chimera, I get the error message: Error while processing /Users/afm/Desktop/sfld-3.chimerax: '/var/folders/zg/vzx644v88xl59y001s75rw2h0000gp/T/hmmer_align_fsgWHiJp.sto' is not a Stockholm file Also Any ideas? IOError at /ajax/download_temp/hmmer_align_mZdHMnpU.sto/ [Errno 2] No such file or directory: u'/tmp/sfld/hmmer_align_mZdHMnpU.sto' Request Method: GET Request URL: http://sfld.rbvi.ucsf.edu/django/ajax/download_temp/hmmer_align_mZdHMnpU.st… Django Version: 1.6.8 Exception Type: IOError Exception Value: [Errno 2] No such file or directory: u'/tmp/sfld/hmmer_align_mZdHMnpU.sto' Exception Location: /usr/local/projects/sfld/production/www/sflddjango/apache/../../sflddjango/sfldajax/views.py in download_tempfile, line 61 Python Executable: /usr/bin/python Python Version: 2.7.5 Python Path: ['/usr/local/projects/netgen/production/lib/python/netgen/interface', '/usr/local/projects/sfld/production/lib/python/sqlparse-0.1.13-py2.7.egg', '/usr/local/projects/sfld/production/lib/python/MySQL_python-1.2.3-py2.7-linux-x86_64.egg', '/usr/local/projects/sfld/production/lib/python/django_debug_toolbar-1.2.2-py2.7.egg', '/usr/local/projects/sfld/production/lib/python/pycharm-debug.egg', '/usr/local/projects/sfld/production/lib/python/Sphinx-1.0.7-py2.7.egg', '/usr/local/projects/sfld/production/www/sflddjango/apache/../../../lib/python', '/usr/local/projects/sfld/production/www/sflddjango/apache/../..', '/usr/lib/python2.7/site-packages/PEAK_Rules-0.5a1.dev_r2713-py2.7.egg', '/usr/lib/python2.7/site-packages/Extremes-1.1.1-py2.7.egg', '/usr/lib/python2.7/site-packages/AddOns-0.7-py2.7.egg', '/usr/lib/python2.7/site-packages/DecoratorTools-1.8-py2.7.egg', '/usr/lib/python2.7/site-packages/BytecodeAssembler-0.6-py2.7.egg', '/usr/lib/python2.7/site-packages/SymbolType-1.0-py2.7.egg', '/usr/lib/python2.7/site-packages/PrivateWikis-1.0.0-py2.7.egg', '/usr/lib64/python27.zip', '/usr/lib64/python2.7', '/usr/lib64/python2.7/plat-linux2', '/usr/lib64/python2.7/lib-tk', '/usr/lib64/python2.7/lib-old', '/usr/lib64/python2.7/lib-dynload', '/usr/lib64/python2.7/site-packages', '/usr/local/lib64/python2.7/site-packages', '/usr/lib64/python2.7/site-packages/gtk-2.0', '/usr/lib/python2.7/site-packages', '/usr/local/lib/python2.7/site-packages', '/usr/local/projects/netgen/production/lib/python'] Server time: Sat, 11 Nov 2017 08:54:00 -0800 Anne-Frances Miller Professor of Chemistry University of Kentucky

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labels turned white
by Oleksiy Kovtun 09 Nov '17

09 Nov '17

Dear community, I encountered a problem with 2D labels turning white disregards what colour presets I give. The script reads title presets from a file (2dlabel path) and then display the title with these commnads: 2dlabels change * bgColor 1,1,1,0.75; 2dlabels change title visibility show The 'title' label should appear as opaque black font as defined in the label file: Label title (x,y): (0.18,0.5) text: u'Title' shown: False font size(s): 40 font style(s): bold font typeface(s): sans serif color(s): (0, 0, 0, 1) But it appears in white. Bizarrely all other presets in the label file translate into the title appearance as they should except for the colour. I run Chimera 1.11.12 (build 41280) on Unix. Script and label file are attached. Thank you. Oleksiy Dr Oleksiy Kovtun Research Fellow Briggs group MRC Laboratory of Molecular Biology Francis Crick Avenue Cambridge CB2 0QH UK Tel: + 44 1223 267551 Email: okovtun(a)mrc-lmb.cam.ac.uk

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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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Parse error in reply log
by Dr. Samson Soon 24 Oct '17

24 Oct '17

Dear experienced chimera users, I’m constantly failing my auto docking experiments due to the problem attached. Solution to this problem is urgently required. Thank you for any kind assistance rendered. Best regards Samson

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Selecting residues in chains defined by segname
by Francesco Pietra 23 Oct '17

23 Oct '17

Hi Elaine: I am referring to Oct 28, 2005, at 9:50 AM, Eric Gillitzer wrote: and your answer: command: select :45.a-d > or > command: select :45.* > > Or, to select > residue 45 in just chains A and D: > > command: select :45.a,45.d > I have a more complex case, where chains are defined by segname, for example A1 A2 A3 A4 A5 etc while the standard PDB definition is "A" for all them. The same for standard "B", "C" etc. As I want to display a movie of ligand pathways, where the ligand moves from, say, "A1" to, say, "F3", I want in the first instance become able to select particular residues in particular chains, as defined by their segname. Could you imagine a simple way not requiring selection by atom numbers? Thanks francesco pietra .

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Chimera build instructions?
by Yuri 23 Oct '17

23 Oct '17

Are there build instructions anywhere? https://www.cgl.ucsf.edu/chimera/docs/sourcecode.html is rather discouraging, and doesn't contain a "Build" section. GNUmakefile prints "there is no default make target". Is there a script or a makefile that builds it? Thanks, Yuri

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Matrix Application
by Amanda Constantinides 23 Oct '17

23 Oct '17

I have a structure with two subunits. I am trying to show movement of the C-terminal subunit upon ligand binding by superposition with another structure from the same strain in the apo form. I want to superpose the N-terminal subunits (A), note the RMSD, then apply the resulting matrix to the superposition of both subunits of the molecule with both subunits of the other (B),then I want to superpose on the C-terminal subunits (C), and then measure the RMSD between (C) and the C-terminal subunits from (B). How can I do this in Chimera? I know how to superpose molecules and calculate the RMSD in Chimera, but I do not know how to apply the resulting matrix from (A) to (B). I tried to save the aligned structures from (A) as a PDB file to check and see if there was a matrix in the file, but an error message came up saying that I needed to save the file as $name or $number. I tried to save the file with $ in front of the name, but it didn't work. Thanks in advance, Amanda Constantinides Graduate Research Assistant Georgia State University

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Re: [Chimera-users] Chimera-users Digest, Vol 174, Issue 30
by Boaz Shaanan 22 Oct '17

22 Oct '17

Hi Elaine, That's perfect and works great. Thanks so much for your help. Regards, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaanan(a)bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 ________________________________________ From: Chimera-users [chimera-users-bounces(a)cgl.ucsf.edu] on behalf of chimera-users-request(a)cgl.ucsf.edu [chimera-users-request(a)cgl.ucsf.edu] Sent: Saturday, October 21, 2017 6:47 PM To: chimera-users(a)cgl.ucsf.edu Subject: Chimera-users Digest, Vol 174, Issue 30 Send Chimera-users mailing list submissions to chimera-users(a)cgl.ucsf.edu To subscribe or unsubscribe via the World Wide Web, visit http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users or, via email, send a message with subject or body 'help' to chimera-users-request(a)cgl.ucsf.edu You can reach the person managing the list at chimera-users-owner(a)cgl.ucsf.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Chimera-users digest..." Today's Topics: 1. Re: Distance tool: Line thickness of the number (of angstroms) in the picture (Elaine Meng) ---------------------------------------------------------------------- Message: 1 Date: Sat, 21 Oct 2017 08:47:21 -0700 From: Elaine Meng <meng(a)cgl.ucsf.edu> To: Boaz Shaanan <bshaanan(a)bgu.ac.il> Cc: "chimera-users(a)cgl.ucsf.edu" <chimera-users(a)cgl.ucsf.edu> Subject: Re: [Chimera-users] Distance tool: Line thickness of the number (of angstroms) in the picture Message-ID: <CDAC071B-A031-4704-8BD3-F016F10794CA(a)cgl.ucsf.edu> Content-Type: text/plain; charset="utf-8" Hi Boaz, The only user interface to the label font size and style is the Preferences (open from Favorites menu), category: Labels. You could change the size number and make the style bold. This is for all ?3D? atom and distance labels that move along with the structure; size/font of 2D labels that don?t move with the structure can be set individually. Looks like the Labels Preferences size menu only goes up to 36, but you can enter some bigger number? for example, I entered 50 (see screenshot attached). Smaller size changes were barely perceptible on my high-resolution screen; maybe that is what happened for you. If that doesn?t work, I?m at a loss? maybe some weird rendering problem? I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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Re: [Chimera-users] Distance tool: Line thickness of the number (of angstroms) in the picture
by Boaz Shaanan 21 Oct '17

21 Oct '17

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Distance tool: Line thickness of the number (of angstroms) in the picture
by Boaz Shaanan 21 Oct '17

21 Oct '17

Hi, The number that shows up after creating a distance is very thin and can hardly be seen. I couldn't find how to make it thicker (I did change the actual line thickness in the menu). I also tried in the preference menu that you pointed to a user a while ago but it didn't work for me. How can I change it? This is on the Windows 64b nightly build from 17 October. Thanks. Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaanan(a)bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 ________________________________________ From: Chimera-users [chimera-users-bounces(a)cgl.ucsf.edu] on behalf of chimera-users-request(a)cgl.ucsf.edu [chimera-users-request(a)cgl.ucsf.edu] Sent: Saturday, October 21, 2017 1:17 AM To: chimera-users(a)cgl.ucsf.edu Subject: Chimera-users Digest, Vol 174, Issue 28 Send Chimera-users mailing list submissions to chimera-users(a)cgl.ucsf.edu To subscribe or unsubscribe via the World Wide Web, visit http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users or, via email, send a message with subject or body 'help' to chimera-users-request(a)cgl.ucsf.edu You can reach the person managing the list at chimera-users-owner(a)cgl.ucsf.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Chimera-users digest..." Today's Topics: 1. Re: Trouble with Volume surface and active model not aligned (Elaine Meng) 2. Re: Selecting residues in chains defined by segname (Francesco Pietra) 3. Re: Selecting residues in chains defined by segname (Elaine Meng) 4. Re: Trouble with Volume surface and active model not aligned (Phan Trieu Truong) ---------------------------------------------------------------------- Message: 1 Date: Fri, 20 Oct 2017 13:41:34 -0700 From: Elaine Meng <meng(a)cgl.ucsf.edu> To: Phan Trieu Truong <truongp(a)uga.edu> Cc: "chimera-users(a)cgl.ucsf.edu" <chimera-users(a)cgl.ucsf.edu> Subject: Re: [Chimera-users] Trouble with Volume surface and active model not aligned Message-ID: <5596D972-35F9-4643-8CDB-6F7D4DE590FD(a)cgl.ucsf.edu> Content-Type: text/plain; charset=utf-8 Hi Phan, I?m not sure what happened either, since your images show the ?A? (active for motion) boxes in the Model Panel are checked for both the molecule and the orbitals, meaning that using the mouse should move both of them together. You could try command: reset ? to put them back together. If that doesn?t work, you may have to start over by quitting and reopening the files. However, if you didn?t uncheck the ?A? boxes or the ?Active models? boxes below the Command Line, mouse movements should always move them both together. Maybe you accidentally had one of the A(ctive) boxes unchecked and moved the other model. In that case, reset will work. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Oct 20, 2017, at 8:57 AM, Phan Trieu Truong <truongp(a)uga.edu> wrote: > > Hi, > > I have been using Chimera to visualize MO orbital on molecules from ORCA calculations. I have been able to visualize the MO orbitals as a surface volume from cube files. However, I just found out that when I try to reorient the molecule with the surface volume, they are no longer aligned. I don't know what I did to cause this. Any help is much appreciated. > > Attached is the picture of the molecules before and after I tried to reorient the molecule with the surface volume. > > Thank you, > Phan > <Before and after reorientation.jpg.png>_______________________________________________ > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users ------------------------------ Message: 2 Date: Fri, 20 Oct 2017 23:37:32 +0200 From: Francesco Pietra <chiendarret(a)gmail.com> To: Eric Pettersen <pett(a)cgl.ucsf.edu> Cc: chimera <chimera-users(a)cgl.ucsf.edu> Subject: Re: [Chimera-users] Selecting residues in chains defined by segname Message-ID: <CAEv0nmsDA8dd+hQ8H_t9uK8-LntPucKQ7UiiqVybva3XWdBgjA(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" A pity, in my view. As more and more complex proteins are being examined (thanks to faster clusters), working without segname would be practically impossible in the frame of today pdb files. For example, how visualizing the trajectory of a particular ligand in a 24-chain protein assembly? I can do that with vmd, but at the price of a less clear-cut trajectory and poorer graphics. But I understand that there may be different viewpoints. Cheers francesco On Fri, Oct 20, 2017 at 8:36 PM, Eric Pettersen <pett(a)cgl.ucsf.edu> wrote: > Realistically no. Too many other priorities. The gap will eventually get > filled in in ChimeraX, but even that will be awhile. > > ?Eric > > On Oct 19, 2017, at 1:24 PM, Francesco Pietra <chiendarret(a)gmail.com> > wrote: > > Hi Eric: > > Any plan to fill this gap? > > thanks > > francesco > > On Thu, Oct 19, 2017 at 7:59 PM, Eric Pettersen <pett(a)cgl.ucsf.edu> wrote: > >> Hi Francseco, >> Unfortunately, segment IDs are not preserved by the trajectory reader. >> >> ?Eric >> >> Eric Pettersen >> UCSF Computer Graphics Lab >> >> >> On Oct 19, 2017, at 9:53 AM, Francesco Pietra <chiendarret(a)gmail.com> >> wrote: >> >> Hi Elaine: >> While, as I wrote, the commands for segname did work fine with .psf/.pdb >> namd files, >> in contrast, with .psf/.dcd files (movie) >> >> select @/pdbSegment=C1 >> >> selects all chains of the protein assembly, including ligands. The same >> occurs with >> >> select @/pdbSegment=O2C1 >> >> where O2C1 is the segname of the molecule dioxygen associated with chain. >> >> This occurs both on my desktop and on a large-memory nextscale cluster on >> remote visualization (the latter is the actual interest) >> >> Do you know of any remedy? >> >> thanks a lot >> >> francesco >> ---------- Forwarded message ---------- >> From: Francesco Pietra <chiendarret(a)gmail.com> >> Date: Mon, Oct 16, 2017 at 7:12 PM >> Subject: Re: [Chimera-users] Selecting residues in chains defined by >> segname >> To: UCSF Chimera Mailing List <chimera-users(a)cgl.ucsf.edu> >> >> >> Hi Elaine: >> >> Great! >> >> thank you >> francesco >> >> On Mon, Oct 16, 2017 at 5:58 PM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: >> >>> Hi Francesco, >>> The symbol for intersection is ?&? ... in other words, you could use >>> >>> select :17 & @/pdbSegment=A1 >>> >>> Intersection and union symbols are explained here: >>> <http://www.rbvi.ucsf.edu/home/meng/docs/UsersGuide/midas/at >>> om_spec.html#combinations> >>> >>> I hope this helps, >>> Elaine >>> >>> > On Oct 16, 2017, at 12:29 AM, Francesco Pietra <chiendarret(a)gmail.com> >>> wrote: >>> > >>> > Hi Elaine: >>> > That works fine. However, I was unable to extend your suggestions to >>> pick up a specific residue within a specific chain. Neither "select :17 >>> @/pdbSegment=A1" nor "select @/pdbSegment=A1 :17" are valid commands >>> (obviously expected). >>> > >>> > On the other hand, with such complex situations, it is Xplor, with its >>> segname features, that helps. >>> > >>> > Should you need a pdb fine with segname, I could attach a simple one, >>> with a single chain. >>> > >>> > On Sun, Oct 15, 2017 at 8:04 PM, Elaine Meng <meng(a)cgl.ucsf.edu> >>> wrote: >>> > Hi Francesco, >>> > Although I don?t have an example file with segnames to try myself, I?m >>> told you can specify by the atom attribute pdbSegment, e.g. >>> > >>> > select @/pdbSegment=A1 >>> > color red @/pdbSegment=F3 >>> > >>> > I hope this helps, >>> > Elaine >>> > >>> > > On Oct 15, 2017, at 10:40 AM, Francesco Pietra < >>> chiendarret(a)gmail.com> wrote: >>> > > >>> > > Hi Elaine: >>> > > >>> > > I am referring to Oct 28, 2005, at 9:50 AM, Eric Gillitzer wrote: >>> > > and your answer: >>> > > >>> > > command: select :45.a-d > or > command: select :45.* > > Or, to >>> select residue 45 in just chains A and D: > > command: select :45.a,45.d >>> > > >>> > > I have a more complex case, where chains are defined by segname, >>> > > for example >>> > > >>> > > A1 A2 A3 A4 A5 etc >>> > > >>> > > while the standard PDB definition is "A" for all them. >>> > > >>> > > The same for standard "B", "C" etc. >>> > > >>> > > As I want to display a movie of ligand pathways, where the ligand >>> > > moves from, say, "A1" to, say, "F3", I want in the first instance >>> > > become able to select particular residues in particular chains, >>> > > as defined by their segname. >>> > > >>> > > Could you imagine a simple way not requiring selection by atom >>> numbers? >>> > > Thanks >>> > > francesco pietra >>> > >>> > >>> > _______________________________________________ >>> > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu >>> > Manage subscription: http://plato.cgl.ucsf.edu/mail >>> man/listinfo/chimera-users >>> >>> >> >> _______________________________________________ >> Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu >> Manage subscription: http://plato.cgl.ucsf.edu/mail >> man/listinfo/chimera-users >> >> >> > >

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Trouble with Volume surface and active model not aligned
by Phan Trieu Truong 20 Oct '17

20 Oct '17

Hi, I have been using Chimera to visualize MO orbital on molecules from ORCA calculations. I have been able to visualize the MO orbitals as a surface volume from cube files. However, I just found out that when I try to reorient the molecule with the surface volume, they are no longer aligned. I don't know what I did to cause this. Any help is much appreciated. Attached is the picture of the molecules before and after I tried to reorient the molecule with the surface volume. Thank you, Phan

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Map to CCP4 Style Mask
by Martin Lawrence 20 Oct '17

20 Oct '17

Hi All, Is there a quick and easy way in Chimera to impose a density level cutoff and write out a ccp4 style mask file? Thanks, Martin Martin Lawrence Department of Chemistry and Biochemistry Montana State University Bozeman, MT 59717 USA

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Coloring higher ordered structures
by Frances Shepherd 19 Oct '17

19 Oct '17

Hello, I’m working with a rotavirus capsid structure and I’d like to highlight individual residues on it if possible. I’m using PDB #3IYU which I split into individual chains, and used the multiscale model function to create the capsid structure. I’m able to color different surfaces, but it applies the color to each spot where the chain is on the entire capsid, rather than just one subunit. I’d like to recreate the kind of figure from a paper by Zeller et al (2012), attached below. Additionally, is it possible to color individual residues on a capsid structure? Thanks in advance! -Frances Shepherd

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POV Ray export
by Greg Williams 19 Oct '17

19 Oct '17

I have done an Export Scene command to generate a POV Ray file for external rendering (Chimera 1.11.2 and Mac OS 10.12.6) using the default Chimera settings. If I open the file in POV Ray 3.70, the Render command gives the following error message: Possible Parse Error: Cannot find file 'transforms.inc', even after trying to append file type extension. "/Users/Greg/Dropbox/POV Ray/POV Prac 2.pov" line 7 Parse Error: Cannot open include file transforms.inc. Any suggestions for fixing the file? Thanks, Greg Williams

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Wall eye stereo has no depth in orthographic projection
by Boris Steipe 19 Oct '17

19 Oct '17

Hello - When viewing a molecule in wall-eye stereo and orthographic projection, the scene is "flat", i.e. the L and R images are identical. Perspective projection works as expected. Is there a workaround? Chimera 1.12 (41617) Mac OS X 10.11.16, NVIDIA GeForce GT 750M Thanks! Boris

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2d projection of 3d model
by D.A. Semchonok 18 Oct '17

18 Oct '17

Dear colleagues, I would like to make 2d projection of my 3d model and save it as an image. How can I do that? Thank you! Sincerely, Dmitry

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Need help performing a high throughput screen using Chimera
by NOOR GREWAL 18 Oct '17

18 Oct '17

Hello, I am an undergraduate student at UC Berkeley. I want to use UCSF Chimera as a part of my research project. How can I run multiple (~20,000 ligands) ligand-docking experiments in parallel using Chimera? I have a Mac OSX Sierra and I am trying to use the command line/terminal for this. I am unable to find documentation and tutorials that can help me. I am very new to this. Could you please guide me on how to best navigate this process? Thanks. Best, Noor

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MD Trajectory Error
by Bryan Dunyak 13 Oct '17

13 Oct '17

I'm trying to run a molecular dynamics simulation in Chimera 1.12rc on a small molecule. On the first run, it worked perfectly. On subsequent runs, when it begins the MD simulation it errors with the following message in the reply log: "The existing trajectory output files are not compatible with the current molecular system, and therefore cannot be appended to with additional MD steps. You need to either remove/rename the existing files, or specify different file names for output." I've tried to find the trajectory output files in /tmp, I've tried reinstalling Chimera, I've looked in other directories without any luck. What should I be doing at this step? Where can I find these files? Thanks! Bryan

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Genetare animation from several .cube files
by Henrique C. S. Junior 12 Oct '17

12 Oct '17

Dear list, I'm getting results from an RT-TDDFT calculation that generates several (> 450) .cube files and I'd like to know if we have a nice way to generate an animation. I know that Chimera can generate beautiful images, but can I load each .cube as a frame and animate the result? Thank you so much for any help -- *Henrique C. S. Junior* Industrial Chemist - UFRRJ M. Sc. Inorganic Chemistry - UFRRJ Data Processing Center - PMP Visite o Mundo Químico <http://mundoquimico.com.br>

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Fwd: Re: Chimera Users
by Greg Couch 12 Oct '17

12 Oct '17

Forgot to cc the list. -------- Forwarded Message -------- Subject: Re: [Chimera-users] Chimera Users Date: Wed, 11 Oct 2017 23:44:53 +0000 From: gregc(a)cgl.ucsf.edu To: Abhiram Chintangal <achintangal(a)berkeley.edu> AFAIK, Chimera works well with the current NVIDIA drivers. However, it often doesn't work remotely unless you have the same driver on both systems. Is that your use case? Please send me the output of the glxinfo command. glxinfo is in the gxl-utils package. With that information, I might be able to tell what's going on. -- Greg October 11, 2017 3:27 PM, "Abhiram Chintangal" <achintangal(a)berkeley.edu <mailto:%22Abhiram%20Chintangal%22%20%3Cachintangal@berkeley.edu%3E>> wrote: Hello, I am trying to run Chimera on Linux system and I keep running into OpenGL errors after launching it. Here is what I see on my end: X Error of failed request: BadValue (integer parameter out of range for operation) Major opcode of failed request: 155 (GLX) Minor opcode of failed request: 3 (X_GLXCreateContext) Value in failed request: 0x0 Serial number of failed request: 722 Current serial number in output stream: 723 The system where I am trying to run this has a nivdia 750ti and is running Centos7. I have installed nvidia-drivers using binaries downloaded from nvidia.com <http://nvidia.com> Looking forward to his response, Thanks! -- Abhiram Chintangal QB3 Nogales Lab Bioinformatics Specialist @ Howard Hughes Medical Institute University of California Berkeley 708D Stanley Hall, Berkeley, CA 94720

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Chimera Users
by Abhiram Chintangal 11 Oct '17

11 Oct '17

Hello, I am trying to run Chimera on Linux system and I keep running into OpenGL errors after launching it. Here is what I see on my end: X Error of failed request: BadValue (integer parameter out of range for operation) Major opcode of failed request: 155 (GLX) Minor opcode of failed request: 3 (X_GLXCreateContext) Value in failed request: 0x0 Serial number of failed request: 722 Current serial number in output stream: 723 The system where I am trying to run this has a nivdia 750ti and is running Centos7. I have installed nvidia-drivers using binaries downloaded from nvidia.com Looking forward to his response, Thanks! -- Abhiram Chintangal QB3 Nogales Lab Bioinformatics Specialist @ Howard Hughes Medical Institute University of California Berkeley 708D Stanley Hall, Berkeley, CA 94720

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Automate Segmetation
by Soumya Govinda Remesh 10 Oct '17

10 Oct '17

Hello Chimera Developers, There is this repeated procedure that I have to do to get a Segmented map from my soft x-ray tomography maps. Here is what I want do: 1. open *mrc put the map to Level 0.011 2. *vop gaussian #0 sd 0.005* put Gaussian to 0.011 3. Go to: Tools --> Volume Data --> Segment Map Segment the gaussian map Smoothing step: 1 Step size: 500 voxels Keep only regions at lease: 100 voxels Save segments as an .mrc file Go to: File (Segment Map) --> Save all regions to .mrc Set Segment map to 0.011 4. Type: *vop subtract #3 #0* #3 Corresponds with ID# of the segmented .mrc file #0 Corresponds with ID# of the original file 5. *sop split #0 * #0 Corresponds with ID# of the original file - Splits surface into disconnected parts The steps in *bold *are in command line. Is there anyway to have everything in a script format? Setting the levels, opening segmentation and setting values to specific Voxel values every time is quite time consuming. I would appreciate your help. Thanks Best, Soumya Govinda Remesh, Ph.D. Postdoctoral Fellow at Advanced Light Source SIBYLS group: http://sibyls.als.lbl.gov/ Lawrence Berkeley National Laboratory 1 Cyclotron Road MS 6R2100 Berkeley, CA 94720 (phone) 510-495-8179 (cell) 804-402-8730 sgremesh(a)lbl.gov

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B-value coloring
by ARMIN HODAEI 10 Oct '17

10 Oct '17

Dear Chimera users, I would like to change the b-values of a Protein and color the residues in the ranking that I want. I have a sequence of residues from the most functionally important sites to less functionally important. I wanna define them to look red and blue respectively due to the new ranking. Sincerely, -- Armin Hodaei Department of Physics, Faculty of Arts and Sciences Koc University, Istanbul

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crop a map via commandline
by Edoardo D'Imprima 09 Oct '17

09 Oct '17

Dear Chimera users, is there an equivalent of Volume viewer/Features/Region bounds from the GUI to precisely crop several maps via command line? I tried a combination of volume region and vop zone subregion but it doesn’t really do what I would like to obtain. 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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Chimera for MOFs
by Minoofar, Payam N 06 Oct '17

06 Oct '17

Greetings and Salutations, I recently started using Chimera to view .cif files for metal organic framework (MOF) unit cells, and I get the impression that Chimera is not quite rendering them correctly. I thought I'd ask the community if visualizing MOFs is a priority for Chimera before I start whinging. (No, I'm not British.) If it is a priority, to whom can I mail the cif files in order to determine whether the problem lies with Chimera or with the file? Many thanks, Payam ------------------------------------------- Payam Minoofar, Ph. D. | Research Scientist | Teledyne Scientific & Imaging | 1049 Camino Dos Rios | Thousand Oaks, CA 91360 | 805.373.4514 voice | 805.373.4105 fax | Payam.minoofar(a)teledyne.com<mailto:Payam.minoofar@teledyne.com> | -------------------------------------------

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help please!
by Nathan Goldfarb 05 Oct '17

05 Oct '17

Hello: I am trying to prep my ligand which is a tripeptide ending with a boronic acid. Chimera will not let me assign charges to it. It does not like the boron and says there is no Sybyl equivalent in the error message. Do you know how to get around this problem? Thanks! -- Nathan E. Goldfarb, M.S., Ph.D. Assistant Professor of Biochemistry 904-716-7339 [image: LinkedIn] <http://www.linkedin.com/in/nathangoldfarb>

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Re: [Chimera-users] High Sierra fix
by VAZQUEZ SENTIS MARCO EUGENIO 05 Oct '17

05 Oct '17

Hey there, Thanks for the information. However, the representation of atoms is still wrong in with High Sierra. I’m attaching an image of what I see. Have you received reports like this?. Is there any fix for that? thanks!! [cid:C21A9AF2-1CF2-4300-9F85-A65D871E91E9@mundo-R.com]

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Chimera help for tomography data!
by Swetha Vijayakrishnan 05 Oct '17

05 Oct '17

Dear All, I am new to using chimera for EM tomography data. Essentially I am trying to create a movie with tomography and subtomogram data within a single movie. However, i am having trouble making and rendering the movie. I can open the tomogram tilt series (created in IMOD) and manually move it along using the planes option along the axis of interest. However i was trying to see if the Volume series option helps play it automatically but it doesn’t seem to do so. Is this the right way to do it? Any help on how i can play through the tomogram through the various planes back and forth and how i can create a movie will be greatly appreciated. Thanks and best wishes, Swetha Dr Swetha Vijayakrishnan MRC-University of Glasgow Centre for Virus Research (CVR) University of Glasgow, Sir Michael Stoker Building, 464 Bearsden Road, Garscube campus Glasgow G61 1QH UK Email: Swetha.Vijayakrishnan(a)glasgow.ac.uk<mailto:Swetha.Vijayakrishnan@glasgow.ac.uk> Phone: +44 (0) 141 330 4025 http://www.gla.ac.uk/colleges/mvls/supportforresearch/nerd/

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Create oxime functional group
by Wikel, Jim 04 Oct '17

04 Oct '17

Hello, I recently had difficulties with creating a particular structure in Chimera. The SMILES is depicted below. The problem is I have not been able to represent the oxime portion of the molecule. I have tried to reset atomtypes, redrawing the structure, adding and deleting the atoms, passing it through other drawing programs, reformatting the file to other formats, but to no resolution. Chimera insists on adding a hydrogen to the oxime nitrogen prior to minimization. I am puzzled and suspect I may be doing fundamentally wrong. Any advice would be helpful. CC1CC(C)CN(C1)S(=O)(=O)C1=CC=C2C(=C1)C(=NO)C1=CC(=CC=C1C2=NO)S(=O)(=O)N1CC(C)CC(C)C1? Thanks you. jim

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unit for the diameter of the erase sphere
by Dieter Blaas 02 Oct '17

02 Oct '17

Hi, what is the unit of the diameter of the erase sphere Angstrom or pixels? Thank you very much, regards, Dieter ------------------------------------------------------------------------ Dieter Blaas, Max F. Perutz Laboratories Medical University of Vienna, Inst. Med. Biochem., Vienna Biocenter (VBC), Dr. Bohr Gasse 9/3, A-1030 Vienna, Austria, Tel: 0043 1 4277 61630, Fax: 0043 1 4277 9616, e-mail: dieter.blaas(a)meduniwien.ac.at ------------------------------------------------------------------------

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Re: [Chimera-users] Query (how to find H-bonds)
by Gurudeeban Selvaraj 01 Oct '17

01 Oct '17

Dear Dr. Elaine Thanks! But I want to see protein and ligand (peptide) structure. I could not see ligand, the display shows only protein structure. The file I enclosed is docked result. Instead of ligand there is a dotted line in between the protein.....I could not see this before. The attachment file has (2 to 195 protein) and (1-7 peptide). I can see the individual structure in separate file but I could not see in same pdb file (docked result). The tutorial is not helping to fix the issue Please make me clear! ------------------ Sincerely Dr. Gurudeeban Selvaraj, Ph.D. Postdoctoral Researcher Center for Food Science and Technology School of Chemical Engineering and Environment Henan University of Technology, Zhengzhou, China Mobile: +86 1883 800 2927; +91 84890 55578 ORCID:http://orcid.org/0000-0002-7223-3853 Residence: Room No. 503, Foreign Teacher's Apartment, University Garden, Lianhua Street No. 50, Hi-Tech development Zone, Zhengzhou, 450001, China ------------------ Original ------------------ From: "meng";<meng(a)cgl.ucsf.edu>; Send time: Sunday, Oct 1, 2017 1:28 AM To: "Gurudeeban Selvaraj"<gurudeeb99(a)qq.com>; Cc: "UCSF Chimera Mailing List"<chimera-users(a)cgl.ucsf.edu>; Subject: Re: [Chimera-users] Query (how to find H-bonds) Dear Dr. Selvaraj, Probably you just need to display the atoms, command “display” or menu: Actions… Atoms/Bonds… show. This is just a general part of using Chimera. I recommend going through the “Getting Started” tutorial to become more familiar with the program: <http://www.rbvi.ucsf.edu/Outreach/Tutorials/GettingStarted.html> Good luck, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Sep 30, 2017, at 4:57 AM, Gurudeeban Selvaraj <gurudeeb99(a)qq.com> wrote: > > Dear Dr.Elaine, > > Thanks for the information. It is working now but some of them I could not see hydrogen bonds (Intra). Now I could not see the ligand structure of the docked result in Chimera. > > I have enclosed file and snap shot of my issue. Let me know, what will do? > > <3_8_sol_3.ref.pdb><image.jpg>

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Re: [Chimera-users] Query (how to find H-bonds)
by Gurudeeban Selvaraj 30 Sep '17

30 Sep '17

Dear Dr.Elaine, Thanks for the information. It is working now but some of them I could not see hydrogen bonds (Intra). Now I could not see the ligand structure of the docked result in Chimera. I have enclosed file and snap shot of my issue. Let me know, what will do? ------------------ Sincerely Dr. Gurudeeban Selvaraj, Ph.D. Postdoctoral Researcher Center for Food Science and Technology School of Chemical Engineering and Environment Henan University of Technology, Zhengzhou, China Mobile: +86 1883 800 2927; +91 84890 55578 ORCID:http://orcid.org/0000-0002-7223-3853 Residence: Room No. 503, Foreign Teacher's Apartment, University Garden, Lianhua Street No. 50, Hi-Tech development Zone, Zhengzhou, 450001, China ------------------ Original ------------------ From: "Elaine Meng";<meng(a)cgl.ucsf.edu>; Send time: Friday, Sep 29, 2017 5:06 AM To: "Gurudeeban Selvaraj"<gurudeeb99(a)qq.com>; Cc: "UCSF Chimera Mailing List"<chimera-users(a)cgl.ucsf.edu>; Subject: Re: [Chimera-users] Query (how to find H-bonds) > On Sep 28, 2017, at 1:54 PM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > > Many orange lines are drawn on the structure to show the H-bonds. One minor correction: for you, the lines will be whatever color is shown in the square color well near the top of the H-bond dialog… the default is a bright blue color similar to cyan. Elaine

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