May 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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Atom Specification not working in exported PDB
by Gustaf Olsson 03 Jun '18

03 Jun '18

Hello again Chimera Users So now that I have the “movie” command working decently, it turns out that I cannot export a PDB file from my MD simulation and retain the ability to select by residue or atom number. PDB files generated by other software (PACKMOL, AMBER) works fine though when I exported a PDB file from a fram in an AMBER MD simulation using chimera, I can open the file, I can select using residue names though trying to refer to atom or molecule numbers does not work. To be clear, the exported PDB file contains multiple molecules and solvent, all ar present and the file loads though trying to run commands like show :17 ~show @536-593 Affects EVERY atom and molecule in the system when it should only affect residue 17 (by specifying residue number OR all atoms in that residue). Using the show :XXX works as intended though this affects all residues XXX and I only want to affect residue 17. Am I doing something wrong or can I solve this in a simple way? Best regards // Gustaf

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Command line syntax questions
by Divita Mathur, Contractor Code 6910, FN 01 Jun '18

01 Jun '18

Hi I am trying to write an alias and am curious if I can do the following using command line (in order to include them in the alias): 1. Separate chains that belong to the same model – can I change the model # on a single chain from an existing model? For example, I built a DNA duplex, selected one chain (sel :.A) and tried to change the model # (combine sel model 8 close true) but the new model also includes chain B. 2. Change residue number of a residue in a chain. I combined a small molecule to a DNA chain between residues 18 and 19, but after combining, the molecule’s residue number remains 1. I would like to change it to 19 or 18. 3. Following point #2, I also want to assign the new molecule the same chain ID – A. In the pdb file, the chain ID is blank for the newly inserted molecule. Thank you for your help. I also want to mention that the Chimera user discussion portal has been very helpful otherwise! Best, -- Divita Mathur Postdoctoral Research Fellow Center for Bio/Molecular Science and Engineering Naval Research Laboratory Washington DC 20375 (202) 767-0687 (Office) divita.mathur.ctr.in(a)nrl.navy.mil

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Recording a movie of an MD simulation
by Gustaf Olsson 30 May '18

30 May '18

Hello everyone First time posting, looking for some advice. I have an MD simulation that was produced with the AMBER software package and I want to record a movie (MP4) file of the simulation. I wanted to use a CMD file and not go through the GUI since this would be a step in a series of steps and I was also hoping to perform some “in movie” modifications to the structure though I quickly ran into a huge issue, the frame rate. So basically i tried something like this: movie record size 3840,2160 format png supersample 3 coordset #0 1,-1 wait 10 movie stop movie encode output /Users/guolaa/Desktop/Arbete/Konferenser/MIP2018/Presentation/myMovieFolder/mdSimulationBox.mp4 format mp4 quality highest >From this I received what looked like a single frame of “movie”. This seemed very strange to me since I assumed that this would be 500 PNG images resulting in a 20 second movie at 25 fps. It seems I’m missing something in the process since MD iterations, frames and frame-rates does not seem to match up. I’ve gone through the documentation regarding maxFramerate, movie, coordset and so forth and I can’t work out a decent strategy. I have 500 iterations (MD-frames) loaded, I want to record a smooth 10 seconds (-ish) long MP4 movie file covering the entire range of MD-iterations (first frame to last frame though not necessarily every frame in between) and I want to do this in a CMD script and not using the GUI menu system since I plan to do more things while recording at some point (manipulating representations). Thank you in advance for any input, best regards // Gustaf

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chimera clear selection
by Brian Ondek 29 May '18

29 May '18

Hi chimera help,I have been using chimera and find it extremely useful. I was finding particular protein sequences within my structures and hit clear selection under the select tab.Now whenever I try and find a seq, it wdoes not show up and "selection cleared" appears in the bottom right corner of the window. I tried to reboot and the issue persists.Interestingly I can still see amino acid and chain selections just fine.How can I undo this "clear selection" issue I inadvertently caused? Thank you in advance for your help.Brian Ondek

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Interface residues in domain-domain contacts
by IDIGO Nwamaka 29 May '18

29 May '18

Hi, I am quite new to chimera. I was wondering how I can locate interface residues in different domains within the same protein model. For example, my protein has 3 domains and I want to find out the interface residues for the different domains. Thanks! Amaka Idigo PhD Student www.ed.ac.uk/centre-genomic-medicine<http://www.ed.ac.uk/centre-genomic-medicine> Centre for Genomic & Experimental Medicine<http://www.ed.ac.uk/centre-genomic-medicine> www.ed.ac.uk University of Edinburgh Centre for Genomic & Experimental Medicine The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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