November 2017 - 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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Chimera-users November 2017