October 2017 - Chimera-users - RBVI Mailing Lists

Hidden water molecules
by Michael Sharkey 11 Apr '19

11 Apr '19

Hi I'm trying to visualise water molecules associated with the crystal structure of an enzyme (specifically PDB ID: 1C1D). They're listed when I open the pdb as a text file using WordPad, but I can't for the life of me get them to appear on the screen when I try to visualise the structure in Chimera (v. 1.10.2). What am I missing? Thanks in advance Mike --

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Constrainted fitting
by Christoph Wigge 22 Mar '19

22 Mar '19

Dear all, I would like to fit two protein monomers that form a dimer into an em density map. I know from previous mutagenesis studies that the binding takes place with two tryptophan residues and the counterpart binding pocket. How can I set this interaction as fixed so that chimera fits the rest of the molecule according to the density map without continuously changing this part of the essential protein protein interaction? I would like to fit that interaction manually and then exclude it from the automatic procedure. Thank you very much in advance. Bests Christoph Wigge

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Error in Windows saving a session
by Joel Mackay 21 Apr '18

21 Apr '18

Hi all Have other people seen (and solved!) this error before (below)? I'm having it crop up pretty much all the time now when I try to save a session (on my Win7 machine - running Chimera 1.11.2. Thanks Joel WindowsError Exception in Tk callback Function: <function command at 0x00000000155434A8> (type: <type 'function'>) Module: <module 'chimera.baseDialog' from 'C:\Program Files\Chimera 1.11.2\share\chimera\baseDialog.pyc'> (line: 447) Args: () Traceback (innermost last): File "C:\Program Files\Chimera 1.11.2\bin\lib\site-packages\Pmw\Pmw_1_3_3\lib\PmwBase.py", line 1747, in __call__ return apply(self.func, args) File "C:\Program Files\Chimera 1.11.2\share\chimera\baseDialog.py", line 449, in command getattr(s, buttonFuncName(txt))() File "C:\Program Files\Chimera 1.11.2\share\OpenSave\__init__.py", line 264, in Save getattr(self, self.keepEquiv())() File "C:\Program Files\Chimera 1.11.2\share\chimera\baseDialog.py", line 704, in OK self.Apply() File "C:\Program Files\Chimera 1.11.2\share\OpenSave\__init__.py", line 183, in Apply self.command(1, self) File "C:\Program Files\Chimera 1.11.2\share\SimpleSession\gui.py", line 41, in _saveCB saveSession(paths[0], **kw) File "C:\Program Files\Chimera 1.11.2\share\SimpleSession\save.py", line 135, in saveSession os.rename(tsave, filename) WindowsError: [Error 32] The process cannot access the file because it is being used by another process WindowsError: [Error 32] The process cannot access the file because it is being used by another process File "C:\Program Files\Chimera 1.11.2\share\SimpleSession\save.py", line 135, in saveSession os.rename(tsave, filename) See reply log for Python traceback. ------------------------------------------------------------------------------------------------------------------------------ Professor Joel Mackay | NHMRC Senior Research Fellow Chair, Biochemistry, Cellular and Molecular Biology Cluster School of Life and Environmental Sciences THE UNIVERSITY OF SYDNEY A: School of Life and Environmental Sciences | Rm 674, Building G08 | Butlin Ave The University of Sydney | NSW | 2006 | Australia T: +61 2 9351 3906 | F: +61 2 9351 5858 | S: joelmackay E: joel.mackay(a)sydney.edu.au | W: www.mmb.usyd.edu.au/mackay/

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Axes/Planes/Centroids for the OPM membrane visualization
by James Starlight 22 Nov '17

22 Nov '17

Dear Chimera Users, I have a question regarding Axes/Planes/Centroids for the visualization of the membrane plane predicted by OPM. Firstly, I have uploaded my structure with DUM atoms. Than, I selected the DUM atoms in both layers and try to show the membrane plane via defining of a plane for it. As the result, a cylindrical surface oriented perpendicular to the imaginative membrane has been emerged. What should I change in options to obtain it aligned along the membrane normal in a correct way? Is it possible to make more flexible selection of the DUM atoms only in the selected layer? Thank you for the help! Gleb

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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

2 3

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

1 0

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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Chimera-users October 2017