- Chimera-users - RBVI Mailing Lists

Chimera X color by attribute middle range value
by Zimanyi, Marcell 12 Apr '22

12 Apr '22

Hello Chimera Community, I have a .defattr file where I have assigned a value to a few residues on my protein. I'd like to set the range to be 0.2, 1, and 4 so that values with 1.0 will be the middle color. I currently don't see a way to set the middle value for the range. In Chimera, I could set the middle range value in the define attribute GUI. In Chimera X, I'm using color byattribute range 0.2,4 because the range argument will only accept two values. I see that I can bring up the color key gui, but when I change the color key I don't see a way to update the coloring on the residues themselves. Could you please help me figure out how to set attribute range with 3 values as in Chimera? Thanks, Marcell

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Align two structures
by Catherine Jenifer Rajam Rajendran 11 Apr '22

11 Apr '22

Hi, I'm trying to use the "match" command to align two protein pdb structures. Instead of specifying which chains or atoms or residues to align, Is there a way to align the whole structure from the command line? Thanks, Catherine

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Problem running Chimera on MacBook
by Levine, Judy 08 Apr '22

08 Apr '22

Hello all – I’m having trouble doing the ViewDock tutorial on my MacBook. I am able to open the ras.mol2 file in ViewDock, but when I then open the setup file the program freezes – and in fact the only way to exit the program at that point is to do a force quit. I have done it successfully several months ago and wanted to refresh my memory but now am experiencing this problem. I installed the latest version (1.16) in case that was the problem, but that didn’t help. I also considered using ChimeraX instead but was unable to figure out whether the ViewDock feature is available in that. I’m able to do the tutorial on my home desktop PC, but at work I only have the MacBook so it’s frustrating not to have Chimera working properly. Has anyone else experienced this problem? (In case it’s not obvious, I am quite the novice Chimera user. I’m using it in undergraduate biochemistry teaching, primarily to analyze results from SwissDock.) Thanks! Judy Levine ***************************************** Dr. Judy Levine Center for the Natural Sciences; Program in Biochemistry and Molecular Biology Goucher College 1021 Dulaney Valley Rd. Baltimore, MD 21204 410-337-6525; judith.levine(a)goucher.edu<mailto:judith.levine@goucher.edu> *****************************************

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Openning XYZ files with ChimeraX
by Henrique Castro 07 Apr '22

07 Apr '22

Hello, everyone, I'm trying to adapt to ChimeraX and when trying to open an XYZ file I'm receiving the message "Opener for format 'XYZ file' is not installed; see log for more info". Is it possible to work with his format as in the Classic Chimera? -- Henrique C. S. Junior

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Creating distances using the command line
by Lucic, Iva 07 Apr '22

07 Apr '22

Hello, I would like to measure distances between atoms in a structure by using the command line, and not manually by clicking on the atoms and then clicking on "create" button in the Structure Measurements tool. I would like to map many distances on the same structure (I performed a crosslinking experiments, so I would now like to map the crosslinks on the structure of my protein of interest). I tried something like distance #1 :347.A@ca - :323.A@ca and similar variations, hoping that I could get the distance between CA atoms of residues 347 and 323 of chain A (there are 12 chains in my protein) from model 1. But I couldn't find a good combination of commands to give me a distance. I would highly appreciate any advice. Otherwise, I would have to map manually over 20 crosslinks for each chain... Thank you in advance, Iva

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Re: [Chimera-users] Assembling 2 protein subunits into a heteromer
by Elaine Meng 05 Apr '22

05 Apr '22

> On Apr 4, 2022, at 11:32 PM, SANTOSH RAMA BHADRA RAO TATA <19807877(a)students.latrobe.edu.au> wrote: > > Good evening, Meng, > > I'm trying to bind to protein subunits A and B with the stoichiometry of A-A-B-A-B pentameric form how can I do that in chimera? I have both A and B PDB files single chains. > > Thanking you, > > With best wishes, > Tata Santosh Rama Bhadra Rao, > PhD Scholar, > C/O Prof Helen Irving, > La Trobe university, > Bendigo, Vic-3550, > Australia. > Email: 19807877(a)students.latrobe.edu.au; > S.Tata(a)latrobe.edu.au > Phone: 0499263974 Hello, The recommended address for Chimera questions is chimera-users(a)cgl.ucsf.edu CC'd here. Chimera doesn't predict how A and B would bind each other. Instead you have to use any other information you might have. If there is a similar structure already known in pentameric form, then you could: - open the known pentamer - open the A structure 3 times and the B structure 2 times - superimpose each of your structures on one monomer of the known pentamer, e.g. with matchmaker See matchmaker (GUI tool or command) and other methods for superimposing structures: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.html> 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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Question regarding chimerax module
by Prathvi Singh 04 Apr '22

04 Apr '22

Hello again Elaine, Is it possible to install the chimerax module in anaconda for usage in jupyter notebook? -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

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Extracting secondary structure residue info
by Prathvi Singh 03 Apr '22

03 Apr '22

Hi Elaine, I have a PDB file which only has rows starting with ATOM. When I open it in UCSF chimera, it displays all the secondary structures which the residues form. Is it possible to extract the starting & ending residues of each alpha helix (or any other secondary structure for that matter)? -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

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How to run a script in ChimeraX
by Shanti Pal Gangwar 30 Mar '22

30 Mar '22

Hi I am trying to run a script in chimeraX but it did not work. I even downloaded the example files and that also did not work. I wonder if a script can be run in ChimeraX as we do in PyMol. Any help would be appreciated. Thank you Shanti Pal

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using old cmd files in chimerax
by Hansen, Bryan (NIH/NIAID) [E] 29 Mar '22

29 Mar '22

Hi, How do I used/open old cmd scripts I have or outputs from things like resmap in chimerax? Bryan Hansen Computational Biologist / Electron Microscopist NIH/NIAID/RTB/RML/EMU Rocky Mountain Laboratories 903 S. 4th St Hamilton, MT 59840 406.363.9202 *********************************************************** The information in this e-mail and any of its attachments is confidential and may contain sensitive information.It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error, please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives. ***********************************************************

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Hello could you please help me and my editor
by Kevin Kelly 25 Mar '22

25 Mar '22

I am a visual artist from the university of Manitoba in Canada My name is Kevin Kelly I am a associate professor at the school of art . First I want to say how absolutely amazed I am at the quality and precision of this astonishing software!!!!! I am working on trying to make an animation with the images and am working with a very clever animator editor and digital designer BEN KATZ that works with CINEMA 4D. We are trying for hours to figure out how to export all the variables of visualizations of the 3D molecular models into a useable 3D model. Is there a way to export the whole model with layers? Like the surface, atoms and ribbons? And is there anyway to export the model with colors? Any suggestions would be greatly appreciated . It would be super if you could help us out! And once again WOW! All my best Kevin Kelly Sent from my iPhone

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change the protonation states
by 孙钦超 24 Mar '22

24 Mar '22

I would like to make the Glu and Asp protonated, and the Lys and Arg uncharged. While I was trying to do it by addH function with chosing the protonation sates option -> Asp, or chose His. The resulting protonation states of Glu and Arg were the same, as Glu deprotonated and Arg protonated. How could I reach the right protonatation states as I expected? Thanks Qchao

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tile function
by Hansen, Bryan (NIH/NIAID) [E] 23 Mar '22

23 Mar '22

Hi, Is there an option with the tile command in ChimeraX to get the volumes to rotate in place like it did with Chimera or maybe a different command now that I haven't found yet? Right now when I use Tile the maps rotate together round a single axis, but I liked it a lot in chimera with the tile were the maps rotated on their own axis. Thanks I'm sure it's most likely a command option that I missed in the documentation or a new command I haven't found yet. Bryan Hansen Computational Biologist / Electron Microscopist NIH/NIAID/RTB/RML/EMU Rocky Mountain Laboratories 903 S. 4th St Hamilton, MT 59840 406.363.9202 *********************************************************** The information in this e-mail and any of its attachments is confidential and may contain sensitive information.It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error, please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives. ***********************************************************

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Visualizing
by Prathvi Singh 22 Mar '22

22 Mar '22

Hi Elaine, I was wondering whether it is possible to show the axis guides at the bottom left or bottom right side of the screen just like in VMD? -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

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Mac Studio
by Greg Williams 21 Mar '22

21 Mar '22

I just bought a Mac Studio running OS 12.3. I downloaded Chimera 1.16. None of my old .py files will open. The app tells me the files are open, but there’s no content. I can Fetch new files from the pdb, and they work fine. Is this an incompatibility with the new hardware? I know you encourage people to use Chimera X, but I need the vrml export function, so 1.16 is what I have to use. Thank you. Greg Williams

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reading output files (pdbqt) from an external vina dock run back into chimera
by Joern Werner 20 Mar '22

20 Mar '22

Hello is there a way of reading a series of pdbqt files of docked ligands using vina dock externally back into chimera for inspection and analysis? It looks like Viewdock, should do this but I have a directory full of individual ligand files and I don't know how to prepare them so that Listview reads them into an ordered set i.e. ligand1 ligand2 etc. I can read individual ligands fine. Many thanks Joern

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Place Objects output to mrc
by Pranav Shah 17 Mar '22

17 Mar '22

Hi Elaine, Is it possible to convert object instances generated by the Place Objects plugin developed by the Briggs group into mrc maps? Best, Pranav -- Pranav Shah Postdoctoral Research Fellow. Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK

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question on cyclization of peptide
by JESSE JAYNES 15 Mar '22

15 Mar '22

Hi Folks, I have greatly appreciated the access to Chimera, thank you. I need to generate a pdb of a cyclized version of linear 10mer peptide. Is that possible to do in Chimera? Thank you,Jesse

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Re: [Chimera-users] Chimera Help Needed- Wring output of status line to file
by Elaine Meng 10 Mar '22

10 Mar '22

Hello, CCing chimera-users(a)cgl.ucsf.edu (recommended address for questions to ensure it doesn't fall through the cracks... and also because often other people know the answer when I do not)... <https://www.rbvi.ucsf.edu/chimera/docs/feedback.html> I guess you are talking about method "b" in that post? I believe the values would also go to the Reply Log in addition to the status line. You can save the Reply Log contents using a bit of python. That is beyond my expertise personally, but fortunately is described at the bottom of this page on basic scripting: <https://www.rbvi.ucsf.edu/chimera/current/docs/ProgrammersGuide/basicPrimer…> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Mar 10, 2022, at 5:46 PM, Morais Brown <moraisbrown(a)outlook.com> wrote: > > Hello, > > I followed your advice here: http://plato.cgl.ucsf.edu/pipermail/chimera-users/2012-January/007160.htmla… created a script that get the rmsd values of my residues of interest using a reference structure. How do I record these RMSD values to a file so that I can plot them? I only see them fluctuating in the status line when I play my trajectory. > > Best, > Morais

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Help for USCF chimera
by cindy g 10 Mar '22

10 Mar '22

Good morning, By Uscf chimera I have a complex with an antibody and an antigen. After determining the predicted paratopes and highlighting only their side chains, I would like to identify the side chains of the amino acids of the antigen which are in a zone <5A from the side chains of the predicted paratopes. I don't know how to do it with command lines or anything. Thank you in advance for your help Cordially

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Fwd: Download UCSF Chimera question
by Elaine Meng 10 Mar '22

10 Mar '22

> From: "zhacj(a)163.com" <zhacj(a)163.com> > Subject: Download UCSF Chimera question > Date: March 8, 2022 at 7:03:22 PM PST > To: meng <meng(a)cgl.ucsf.edu> > > Hello, > Dr. Elaine Meng, > This is West China Sceond hospital in Chengdu, China, we need to use Chimera to our scientific research，but now we encounter a difficulty to need your help: > > After we download Chimera from https://www.cgl.ucsf.edu/chimera/download.html <https://www.cgl.ucsf.edu/chimera/download.html>， we cant install and run this software, we Not sure if this downloaded installation package is available, could you please tell me Where to download the correct installation package, or could you please send the correct installation package to me, thats very thank you! > And our system environment is Linux, connda, CentOS. > Looking forward your reply, Thanks again. > Charles Zha > Project Director > zhacj(a)163.com <mailto:zhacj@163.com> > Tel: +86-28-84457808 Mob:+86-13008108764 Hello, All of the download packages and download instructions are already on that page -- make sure you get the one for Linux. I don't know what you mean by "can't install" -- you would need to say more about exactly what steps you tried and what happened. <https://www.rbvi.ucsf.edu/chimera/download.html <https://www.rbvi.ucsf.edu/chimera/download.html>> Forewarding to the chimera-users(a)cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu> address , in case anybody else has helpful comments. Also you have more details to provide about your problem, please send your question to that address. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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Information Regarding Accessibility of Chimera
by Scott Heck 09 Mar '22

09 Mar '22

Good morning, I am a member of the IT staff for the Biotechnology department at NCSU, and we are wanting to install and use Chimera for one of our instructors to use in their classes. Prior to student use, I will need to have the software approved by the university, and they require proof of the software being accessible to all students. They specifically ask this in the form of VPAT, WCAG 2.0 Standards or other accessibility documentation. Any assistance you can provide would be greatly appreciated. Best regards, Scott -- *Scott Heck | Pronouns: **They/Them <https://www.mypronouns.org/>* IT Implementation Specialist 1 P: 919.513.1021 Office Hours: M-Th 6am-5pm CALS IT Service Portal <https://ncsu.service-now.com/calsit/> NC State University Campus Box 7572 330 Patterson Hall Raleigh, NC 27695

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Changing distance between two atoms
by Prathvi Singh 04 Mar '22

04 Mar '22

Hi Elaine, I have a PDB file which has two serine residues: SER10.A and SER20.A. The distance between their sidechain O-atoms (OG atoms) is 8.925Å. I want to bring the sidechain O-atom of SER10.A closer to the sidechain O-atom of SER20.A along an imaginary line which passes through the coordinates of these two atoms such that the distance between them gets reduced to 4Å. If I am thinking right, this would also require shifting the rest of the atoms of SER10.A towards SER 20.A in a similar manner. Is it possible to achieve this in chimera? I am attaching a screenshot just for reference. Thanks anyways and regards -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

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change aminoacid in sequence alignment
by Jacqueline Vitali 26 Feb '22

26 Feb '22

I have a "residue" KCX (PDB records are Hetatm). In the sequence alignment it comes as X. Is there a way to change it to K without making a PDB file and changing it to K there? Thank you,. Jackie Vitali Cleveland State University

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Average distance between two non-bonded atoms
by Francesco Pietra 24 Feb '22

24 Feb '22

Hi all Is it any command to measure the average distance between two non bonded atoms all over a molecular dynamics trajectory? Ideally linked to examining the trajectory with Tools ... MD/Ensemble Analysis ... MDmovie (I am using psf/dcd) I.e., doing the average of the distance from all frames. Thanks francesco pietra

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