July 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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defining planes and axes based on existing ones
by ChuHui Fu 25 Oct '18

25 Oct '18

Hello, I am trying to define planes and axes that are orthogonal to the planes and axes that I have previously defined. I have an alpha helix, and I only managed to define one plane and two orthogonal axes around the helix. Is it possible to define the rest of the axes and planes? Thanks! -- ChuHui Fu B.S.Candidate in Chemistry Haverford College, Class of 2019 cfu(a)haverford.edu

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fixed: error saving scene with independent rotation
by Elaine Meng 31 Jul '18

31 Jul '18

Hi Yanhe, The bug you reported a few days ago has been fixed! I just confirmed that with the current daily build of Chimera, you can now save scenes with independent rotation and use them in the Animation tool and in scripts. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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Is there any tool to write some calculated attribute into a header format?
by Sergio Garay 31 Jul '18

31 Jul '18

Hi All! I would like to know: Is there any way or tool to write some calculated attribute into a header format? I want to see the same color values obtained for some a calculated attribute projected onto a sequence. I have read in the chimera list the inverse process: exporting a header from a sequence window to be read as an attribute. Thank you in advance. -- *Sergio GarayDr. en Ciencias BiológicasFacultad de Bioquimica y Cs. BiológicasUniversidad Nacional del LitoralSanta Fe - ArgentinaC.C. 242 - Ciudad Universitaria - C.P. S3000ZAAArgentinaPh. +54 (342) 4575-213Fax. +54 (342) 4575-221 *

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Fwd: Inquiry for new/re-registration license key_Arifuzzaman Sarder
by Elaine Meng 31 Jul '18

31 Jul '18

> From: Sarder Arifuzzaman <arifpharmju(a)gmail.com> > Subject: Inquiry for new/re-registration license key_Arifuzzaman Sarder > Date: July 31, 2018 at 9:08:53 AM PDT > To: chimera-announce-owner(a)cgl.ucsf.edu > > Hi > Greetings. > This is Arifuzzamman Sarder. I am an earlier user of chimera software tool. Recently I installed the updated version (v1.13). However, I could not draw any chemical structure by inputting canonical smiles or any other chemical ID in this tool. Even it can not capture any chemical structure from PDB, unlikely it is giving us only protein structure. Could you please let me know how can I revive this tool, so that I can use it for molecular docking and chemical structure as well. > Thank you very much in advance. I am looking forward for your response please. > Sincerely > Arifuzzaman, Sarder > PhD research fellow > Chung-Ang University > Mobile: 010-2654-2606 > E-mail: arifpharmju(a)gmail.com <mailto:arifpharmju@gmail.com> > Web: https://sarderarifuzzaman.wixsite.com/arif <https://sarderarifuzzaman.wixsite.com/arif> HI Arifuzzamman Sarder, (forwarding to the proper address for asking Chimera questions: chimera-users(a)cgl.ucsf.edu ) There is no reason it should not work as before. Chimera does not use a license key. For example, in Chimera 1.13, command: open pubchem:12123 (- or -) open smiles:C1CCNC1 …shows a small molecule in sticks, and command: open 2gbp … shows PDB entry 2GBP; protein ribbons with ligand (glucose) as sticks and nearby sidechains as sticks. If you mean that your Chimera 1.13 is not showing small molecules, or not showing sticks, I only have two ideas: (A) graphics/rendering problem of your computer or (B) New Molecules preferences was set to show only ribbons. To check (B), show Preferences from the Favorites menu, then change to category: New Molecules and check that the settings are what you want, and then click Save. The behavior I described is for the default, “smart initial display” true. If you had it false, and also had “show atoms” false, it would not show atoms when you open a structure. If you feel it is a bug, you can use menu: Help… Report a Bug and describe in detail what you did and what the problem is. However, if it is a graphics problem of your computer, it is not something we can fix. 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] Extracting asymmetric unit
by Tom Goddard 31 Jul '18

31 Jul '18

Hi Martin, Fit an atomic model of the asymmetric unit then use volume zone (Volume Viewer menu entry Feature / Zone) then save the map (Volume Viewer / File / Same Map As…). See the maskZone option description in the volume save command for details https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html#output <https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html#output> Tom > On Jul 31, 2018, at 7:00 AM, Martin Moncrieffe <mcm35(a)cam.ac.uk> wrote: > > Hi Tom, > > A quick question. I have a helical reconstruction (EM) and would like to extract the density for the asymmetric unit from the map. How does one do this? > > Best. > > __martin > >

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