September 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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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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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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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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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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Query
by Gurudeeban Selvaraj 28 Sep '17

28 Sep '17

Dear Support Team, Thanks for the academic free of Chimera. I have a doubt, how can I visualize H-bonding interactions of docked structure of protein-protein interaction. I used FireDock for docking studies. While running on FindHbond on structure/binding tool it says no H-bonds, but i click both shows something.....How can i see protein-protein interacting HBond and label it? For the reference, I enclosed two files. Thanks in advance! ------------------ 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

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High Sierra fix
by Eric Pettersen 28 Sep '17

28 Sep '17

We have fixed the problem where interfaces that also showed 3D graphics (Rapid Access/main window; side view) weren’t working correctly on Mac OS X 10.13 (High Sierra). The fix is in the current daily build and the very latest version of the 1.12 release candidate. If you get either of those then it will be safe to upgrade to High Sierra, at least as far as Chimera is concerned. ;-) —Eric Eric Pettersen UCSF Computer Graphics Lab

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Chimera-users September 2017