- Chimera-users - RBVI Mailing Lists

how to create using Chimera?
by Paris Tzou 10 Nov '18

10 Nov '18

Dear Sir, I am studying PDB id: 5MCT (p53-dna) complex. There is a "BIOMT TRANSFORMATIONS" required to generate the biological unit. Would you please guide me how to do this? Thanks a lot, Paris

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Re: [Chimera-users] 1up opt
by Elaine Meng 09 Nov '18

09 Nov '18

Hi Zhengzheng The format of your PDB file is not standard because all the H atoms are all at the end instead of with their their residues. Also they are all in a different chain (chain A) than the other atoms (chain B). Whatever program wrote this file wrote it incorrectly. You can easily see all atoms, e.g. commands: ~ribbon display (or use Actions menu to do the same things) but if you use Chimera features requiring chemical knowledge (findhbond etc.) it will not work correctly if the H and the other atoms are not recognized as being in the same residue. I tried editing so that all atoms were chain B, but it did not fix the problem, which is apparently instead caused by placing all the H atoms at the end instead of with their individual residues. You could fix it be removing and re-adding hydrogens in Chimera, but then the H atom positions wouldn’t be exactly the same. Commands: delete H addh It is recommended to send questions to chimera-users(a)cgl.ucsf.edu (CC’ed here) in case I’m not available to answer. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Nov 7, 2018, at 8:02 AM, zheng l <zhengsfriend(a)hotmail.com> wrote: > > Dear Dr. Meng > > I used Chimera software for analyzing many protein crystal structures and then modified them and it has so faithfully doing job for me. However, this structure that I attached below is very difficult to modify. > > The problem is that the hydrogens in structure are hidden. Usually when I need to, for example, replaces a carbon to a nitrogen in a Phe the nitrogen will attached with a hydrogen if I set to have 3 bond for the nitrogen. But this structure is not showing hydrogens at all > > Would you please help me find a way of show all hydrogens need for modifying the protein structure? > > Thank you! > > Best regards! > >> Zhengzheng > > <1tup chain b opt 2.pdb>

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(no subject)
by rekha pydala 08 Nov '18

08 Nov '18

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FW: Chimera [viewer] for iOS in the future?
by Williams, Joanne 05 Nov '18

05 Nov '18

From: Bryan Crawford <bryanc(a)unb.ca> Date: Wednesday, October 31, 2018 at 3:53 PM To: "chimera(a)cgl.ucsf.edu" <chimera(a)cgl.ucsf.edu> Subject: Chimera [viewer] for iOS in the future? Hello, I use Chimera occasionally in my research, and extensively for teaching (biochemistry, cell biology, developmental biology). It is now the only remaining piece of software I use that requires me to bring a laptop computer to class. For everything else (PDFs, animations, Keynote presentations, etc.) I can use my iPad which connects by AirPlay to the projector, and screencast everything using Doceri. Furthermore, the touch-screen interface of the iPad seems ideally suited for many of the analyses and/or molecular renderings people use Chimera for. So I’m wondering if there are any plans to produce either a full or partial version (perhaps with only viewing capabilities) of Chimera that runs on iOS? If there is, I would be very happy to help with beta testing. If not, can I ask if you can recommend any software that runs on iOS that I might consider? Cheers -- Dr. B.D.Crawford Professor Matrix Dynamics Lab Department of Biology University of New Brunswick Fredericton, NB, Canada

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Automating H bond distance retrieval
by Samuel FreemanFox 01 Nov '18

01 Nov '18

Hi, I was wondering about the possibility of writing a setup.com file which is capable of opening a receptor.pdb and ligand.pdb file, locating the H-bonds between these two structures and then reporting back the lengths of the bonds? Currently I am able to open both files, execute addh, addcharge, and hbonds with my setup.com file. However I am unsure of how to proceed from there. Many thanks and I look forward to your response. Samuel Freeman-Fox ************************************************************************** The information contained in the EMail and any attachments is confidential and intended solely and for the attention and use of the named addressee(s). It may not be disclosed to any other person without the express authority of Porton Biopharma Ltd, or the intended recipient, or both. If you are not the intended recipient, you must not disclose, copy, distribute or retain this message or any part of it. This footnote also confirms that this EMail has been swept for computer viruses by Symantec.Cloud, but please re-sweep any attachments before opening or saving. *******************************************

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Batch Processing of Molecular Attributes
by Benjamin Feinsilver 01 Nov '18

01 Nov '18

Hello, Is it possible to pass a CSV file to Chimera containing a list of SMILEs, then output their molecular attributes in a new CSV file? For example, volume, surface area, the number of surface points with positive electrostatic potential, and the energy of the molecule's current 3D conformation. If so, would you please let me know how I would accomplish this? Thanks, Ben

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Chimera use
by Hui Min 31 Oct '18

31 Oct '18

Hi there, Sorry to disturb you. I have a question of how to use the Chimera software. If I've already got a .pdb file and use SMART to predict the domains, how can I mark the 3D structure with user defined color？ Thank you in advance for your help -- *Hui Min* Postdoctoral Scholar Research, Department of Internal Medicine, College of Medicine, University of South Florida, Tampa, FL 33612 minh8(a)health.usf.edu

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How can I load a list of residues of protein?
by Paris Tzou 30 Oct '18

30 Oct '18

Dear all, I want to load a file containing a lit of residues of protein which is already shown in Chimera. I don't want to manually select the residues under investigation through "Favorite -- Sequence". Is there a way of doing this ? I know I can do it using command line like:select #0:15-17.C,263-265, 300-310.A. Instead, I can have a text file with content like: 15,C 16,C 17,C 263,A 264,A 265,A Thank you very much. Paris Tzou

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Split map from command line
by armoelle 29 Oct '18

29 Oct '18

Dear Chimera Team, I am trying to call the split map command directly from a script but somehow I don’t seem to be able to get it to run - maybe you can help me? I am calling scolorzone (which works perfectly) and then ( as suggested in the mailing list) use the accelerator command ac sm to split the map. However, generally nothing happens - sometimes though (I don’t know what triggers it - and I am not doing anything different) it runs perfectly fine. I am a bit puzzled as the same is the case no matter if I run form command line or I use the keyboard shortcuts gui. Many thanks for your help! cheers Arne ________________________________ Dr. Arne Moeller Independent Research Group Leader Department of Structural Biology Max-Planck-Institute of Biophysics Affiliated Researcher DANDRITE, Aarhus University, DK www.moeller-lab.com www.biophys.mpg.de/en/moeller.html Arne.Moeller(a)biophys.mpg.de 0049 69 63033057 Max-von-Laue-Strasse 3 D-60438 Frankfurt am Main Office L.1.015

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CUDA on Mac OSX 10.14 Mojave
by David Bhella 26 Oct '18

26 Oct '18

Dear All I just learned (after updating) that nVidia CUDA support is not in place for the latest Mac OS X release. I have a 2010 Mac Pro with a Quadro 4000 card in - which is still fine as a desktop. Chimera throws an error now - complaining about the graphics settings being incorrect: "Display misconfiguration. Please increase the color quality (24 bit color or greater), update your display (graphics) driver, and/or upgrade your graphics card. Also see chimera installation instructions." Presumably because the graphics driver is not working correctly. Has anyone succeeded in resolving this? Or do I need to roll back to 10.13? A quick scan of the Mac/nVidia Forums suggests that CUDA support may not be forthcoming anytime soon, but I thought I would check if anyone has resolved this before going through the hassle of downgrading. Thanks, D Dr David Bhella Director - Scottish Centre for Macromolecular Imaging MRC-University of Glasgow Centre for Virus Research Sir Michael Stoker Building Garscube Campus 464 Bearsden Road Glasgow G61 1QH Scotland (UK) Telephone: 0141-330-3685 Skype: d.bhella

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