November 2018 - Chimera-users - RBVI Mailing Lists

Fw: Open MTZ file
by Williams, Joanne 20 Aug '20

20 Aug '20

Hello! Can you help with the inquiry below? thanks, Jo ________________________________ From: Sharyn Endow, Ph.D. <sharyn.endow(a)duke.edu> Sent: Thursday, February 22, 2018 5:01 AM To: chimera(a)cgl.ucsf.edu Subject: Open MTZ file Is it possible to open an .mtz file in Chimera? ~~~~~~~~~~~~~~~~~~~~~~~~~~ Sharyn A. Endow, PhD Professor of Cell Biology, DUMC Professor of NBD, Duke-NUS PO Box 3709 450 Sands Bldg/Research Drive Durham, NC 27710 USA T 919 684-4311 F 919 681-9929 ~~~~~~~~~~~~~~~~~~~~~~~~~~~

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Chimera Settings
by Nuwan De Silva 24 Apr '19

24 Apr '19

Hi, Every time when when I open a file my background color, and presets, changes. I want to keep them same for every time. How can I set these things? For example, I wanted to have A) Presets —> Select Publication 1 B) Tools —> Structure —> Find H bonds C) Actions —> Atoms & Bonds —> Balls & Sticks Thank you, Nuwan

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about select and label a residul with another different from the color of the whole model
by 张雷 13 Apr '19

13 Apr '19

Hi the experts of Chimera, Good noon! I had selected a residul and labeled it with the commands sel #0:500 rlabel #0:500. Then, the label can be displayed on the selected residul. How could I change the color of the label and display the label in a different color different from the color of the whole model? Thank a lot! Sincerely, Lei Zhang Peking University, Beijing, China

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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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rmsd graph
by SEFA ÇELİK 31 Jan '19

31 Jan '19

Dear Dr. I am using Chimera software(windows platform). I tried to get rmsd graph(using the plotting in the MD Movie trajectory viewer). 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. *I added files to the e-mail. Can you explain what "1001 frames" mean? And how do I convert "1001 frames" to time. I want to see the RMSD change by time.* Can you help with this? Could you explain in detail? Best regard Assoc Prof. Dr. Sefa Celik

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Color subunits for map density
by BuddySphinx 12 Dec '18

12 Dec '18

Dear Chimera developers, I have a quick question about coloring. I have a filament map with multiple monomers, how can I color each monomer density with different color? I have a built model, should I do it based on the atom number or should I segment the filament? Best, Yangqi Sent from Mail for Windows 10

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needing help for separating structures
by Yu Guo 30 Nov '18

30 Nov '18

Dear Sir/Madam, I am using Chimara to display large proteins. It is very nice. 6DHO(PDB structure, see attachment) is a very recent PSII structure consisting both S2 and S3(richer) states, which are highly overlapped in the raw data. I am urgently wondering how can I separate S3 out from the S2/S3 mixture by Chimera, especially the OEY? cluster and all its ligands? Thank you very much! Best wishes

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UCSF import Error
by Cackett, Gwenny 28 Nov '18

28 Nov '18

Hi so I am running Linux Fedora 29 and since updating from Fedora 28 I have noticed my Chimera installation has stopped working - the icon does not open the program. And when I try to run from the command line I get the code below, which I gather is an issue with python importing a module: Traceback (most recent call last): File "/home/gwenny/.local/UCSF-Chimera64-1.12/share/__main__.py", line 69, in <module> value = chimeraInit.init(sys.argv) File "/home/gwenny/.local/UCSF-Chimera64-1.12/share/chimeraInit.py", line 628, in init import chimera File "/home/gwenny/.local/UCSF-Chimera64-1.12/share/chimera/__init__.py", line 2758, in <module> from SimpleSession import BEGIN_RESTORE_SESSION, END_RESTORE_SESSION File "/home/gwenny/.local/UCSF-Chimera64-1.12/share/SimpleSession/__init__.py", line 14, in <module> from save import saveSession, sessionID, noAutoRestore, autoRestorable, \ File "/home/gwenny/.local/UCSF-Chimera64-1.12/share/SimpleSession/save.py", line 13, in <module> from chimera import replyobj, selection, SessionPDBio, version File "/home/gwenny/.local/UCSF-Chimera64-1.12/share/chimera/replyobj.py", line 24, in <module> import Tkinter File "/home/gwenny/.local/UCSF-Chimera64-1.12/lib/python2.7/lib-tk/Tkinter.py", line 39, in <module> import _tkinter # If this fails your Python may not be configured for Tk ImportError: /usr/lib64/libfontconfig.so.1: undefined symbol: FT_Done_MM_Var Any help would be appreciated. Thanks and best wishes, Gwenny Cackett PhD Student RNAP Lab Institute of Structural & Molecular Biology University College London Gower Street, London, WC1E 6BT Phone: 020 7679 3899

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Chimera Interface to Modeller
by Alisson Oliveira 28 Nov '18

28 Nov '18

Good night, I would like to construct a human DDX3 homology model in its closed conformation. However, I can not perform a proper alignment. I target the sequence Uniprot ID: O00571 and as models the PDB structures: 2I4I and 2DB3. However, the generated models present unsatisfactory results in terms of their quality. Attached is the image of the alignment. Can you help me??? [cid:3ddc1e68-24f3-40bf-8654-0fea58f849dc] [cid:e60c81ce-40de-4d0e-8e3a-a071a3aca2d0] Att. Alisson Felipe de Oliveira Farmacêutico CRF/RS: 18468 Mestrando em Ciências Farmacêuticas - UNIPAMPA

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Chimera-users November 2018