- Chimera-users - RBVI Mailing Lists

Command for measuring distance between centroids and to show dotted lines depicting the measurement
by Shubham Devesh Ramgoolam 21 Apr '22

21 Apr '22

Hi, I hope you are doing well. Is there a command in chimera that allows us to measure the distance between centroids and also to show dotted lines depicting the measurement? I used the command distance but no lines were shown for centroids. I am considering of using the coordinates of the centroids to place dummy atoms and then, use distance. However, I do not know if there is a command for placing dummy atoms in specified positions. Regards, Shubham Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows

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Upcoming deprecation of Chimera webservices
by Zach Pearson 21 Apr '22

21 Apr '22

Hello Chimera users, In the next 12 to 18 months, some Chimera tools that depend on web services may stop working: BLAST protein (which is also used by Multidomain Assembler), Modeller comparative and loop modeling, multiple sequence alignment with Clustal Omega and MUSCLE, Small-Angle X-Ray Profile, and 2D Chemical Diagram (used by Structure Diagram and ViewDock). The reason is that some necessary upgrades to our internal systems may break these web services. However, ChimeraX uses a different type of web service that will continue to work, and we have already integrated the following into ChimeraX: BLAST protein, Modeller comparative and loop modelling. In progress: multiple sequence alignment with Clustal Omega and MUSCLE. We wanted to make sure that our users would be prepared for the need to switch to ChimeraX for these features. If you have comments on how to prioritize integrating the remaining services (Small-Angle X-Ray Profile, 2D Chemical Diagram) with ChimeraX, please let us know. Thank you!

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Loop through hundreds of files and find HBonds
by Samuel Kyobe 19 Apr '22

19 Apr '22

Dear Chimera (and ChimeraX) team I have run a large docking experiment using several ligands to determine the best binders for further analysis in Molecular Dynamics studies and possible wetlab evaluation. I need to find some python example or code snippet capable of looping over hundreds of files and find several .pdb poses from a docking run and find Hydrogen bonds in each one using one receptor. In the process of finding the H bonds, I would like to add Hydrogens, and the protonation state is unspecified. Then at FindHBond, I want to find intermodal Hbonds and write the results to a file. Thanks Samuel Dr. Samuel Kyobe Department of Medical Microbiology, 3rd floor, Pathology/Microbiology BLDG, School of Biomedical Sciences College of Health Sciences, Makerere University. Box 7072, Kampala, Uganda. Mob: +256775468605 Skype: samuelkyobe

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Chimera(X) in Centos stream 9
by Antonio Díaz Quintana 19 Apr '22

19 Apr '22

Dear all, I am unable to install Chimerax and Chimera—yes I still use the old one because its great tools—using the rpm package in Centos Stream 9, because lack of LibOSMesa package in this distribution. I tried using dnf, but a mesa-libGL library (21.3.4...) is already installed Similarly, it seems my OS distribution does not contain python Tk, nor I can get suitable python with Tk-devel from repository, so I get the following message. Could I get any help? Meanwhile I got it on my old Win10, 11 years-old laptop. Both programs work well there. Best, Antonio -- Dr. Antonio J. Díaz Quintana Instituto de Investigaciones Químicas Universidad de Sevilla - CSIC Avda. Americo Vespucio 49 41092 Sevilla Spain Phone: +34 954 48 9631

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Command for selecting aromatic ring
by Shubham Devesh Ramgoolam 18 Apr '22

18 Apr '22

Hello, I hope you are doing well. Is there a command on chimera that will allow me to select for the atoms in aromatic rings? I found a workaround by defining the atoms involved in the aromatic rings and then making my selection. However, I would like to use a command (or perhaps combination of commands) from chimera to select the aromatic atoms. Regards, Shubham Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows

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Revised Need Help
by Ali Raza Azeemi 15 Apr '22

15 Apr '22

Hi, hope you are doing well? dear, we have a question about making an animation/movie in chimera. I want to add molecular dynamics(MD) movie to the animation timeline, so I am facing difficulty to add on it. Kindly tell me if an option is available for this?. I will be very thankful to you. Thank you -- *Ali Raza Siddiqui* *Jr. Research Fellow* *Computer-Aided Drug Design (CAAD) unit. P-133, PCMD* H.E.J. Research Institute of Chemistry International Center for Chemical & Biological Sciences University of Karachi, 75270 Karachi- Pakistan.

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Question regarding bond angle
by Prathvi Singh 14 Apr '22

14 Apr '22

Hi again Elaine, Is there a way in chimera or chimeraX to change the angle between three atoms A,B,C where atoms A & B are covalently bonded to each other but neither A nor B is bonded to C ? -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

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Need Help
by Ali Raza Azeemi 14 Apr '22

14 Apr '22

Hi, hope you are doing well? dear, we have a question about making an animation/movie. I want to add molecular dynamics(MD) movie to the animation timeline, so I am facing difficulty to add on it. Kindly tell me if an option is available for this?. I will be very thankful to you. Thank you -- *Ali Raza Siddiqui* *Jr. Research Fellow* *Computer-Aided Drug Design (CAAD) unit. P-133, PCMD* H.E.J. Research Institute of Chemistry International Center for Chemical & Biological Sciences University of Karachi, 75270 Karachi- Pakistan.

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Loop through pbd files (ligand poses) and find hydrogen bonds against one template receptor
by Samuel Kyobe 13 Apr '22

13 Apr '22

Dear Chimera (and ChimeraX) team I have run a large docking experiment using several ligands to determine the best binders for further analysis in Molecular Dynamics studies and possible wetlab evaluation. I need to find some python example or code snippet capable of looping over hundreds of files and find several .pdb poses from a docking run and find Hydrogen bonds in each one using one receptor. In the process of finding the H bonds, I would like to add Hydrogens, and the protonation state is unspecified. Then at FindHBond, I want to find intermodal Hbonds and write the results to a file. Thanks Samuel Dr. Samuel Kyobe Department of Medical Microbiology, 3rd floor, Pathology/Microbiology BLDG, School of Biomedical Sciences College of Health Sciences, Makerere University. Box 7072, Kampala, Uganda. Mob: +256775468605 Skype: samuelkyobe

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Chimera X color by attribute middle range value
by Zimanyi, Marcell 13 Apr '22

13 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 09 Apr '22

09 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 08 Apr '22

08 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 05 Apr '22

05 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 25 Mar '22

25 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 23 Mar '22

23 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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