- Chimera-users - RBVI Mailing Lists

ORCA XYZ FILES
by Rade Jibawi Rivera 10 Mar '21

10 Mar '21

Hello, I am a student from Nova Southeastern University, and I am conducting research where I am interested in utilizing your software "Chimera" for visualization of molecular dynamics. My concern is if your software will be able to create a movie of bond interactions with multiple time frames using ORCA XYZ output files. I would greatly appreciate it if you can give in some input. I hope to hear from you. Thank you for your time and consideration. Best regards, Rade Jibawi Rivera

3 4

Regarding Chimera vina executable file
by Heshani Mudalige 10 Mar '21

10 Mar '21

Dear Elaine, Hi, hope you are doing well. I used Chimera for protein docking. But I got stuck in the last step when setting the local path. I downloaded the windows version and that installed to C drive program files and like this C:\Program Files(86)\The Scripps Research Institute But even after browse even it doesn't show any vina.exe file when setting the local path.Can you please tell me where I can find that? Or how to check whether that properly installed or not? Inside the Vina folder there are 3 files which two were applications files.But no exe file is visible I went many tutorials and heard after 2020 we need to install Auto dock vina to support Chimera. I did that as well.But still I can't properly debug this. Different you tube videos they mentioned inside Vina folder can fine vina.exe or inside bin can find vina.exe. Apperciate your help on this and your earliest reply.Thank you Kind regards Heshani

3 2

Sidechain selection in Python
by achatz 10 Mar '21

10 Mar '21

Hello, I want to select a sidechain without CA in Python. The working command line select #0:30 & without CA/C1' is recreated in Python like this: chimera.selection.OSLSelection("#0:30 & without CA/C1'") But the lexer complains about an "illegal symbol in identifier" which is the apostrophe after C1. How do I solve this issue? Thanks Stefan

2 1

Problem trying to download Chimera
by Elaine Meng 10 Mar '21

10 Mar '21

> From: Austine Gozie <austinegozieaustine(a)gmail.com> > Date: March 8, 2021 at 11:47:40 PM PST > > Good day sir/madam, > > I am trying to download the ucsf Chimera software for my ongoing project but its not responding. When i try to proceed to download icon, the next page displays "cant open page or refresh page, connection failed" I need your assistance in helping me with the download methodology or right website to enable me download the software. Thanks in anticipation for your kindest help. Hello Austine, I don't know what you mean by "proceed to download icon". In the download page, you would click on the link for the installer that you want: <https://www.rbvi.ucsf.edu/chimera/download.html> Then it shows the license, and if you agree, then click the "Accept" button at the bottom of the page to start the download. Occasionally the website is down, but as far as I can tell it is fine right now. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

3 3

Scene transition is delayed in chimera animation
by Shanti Pal Gangwar 10 Mar '21

10 Mar '21

Hi All, I am trying to make scene based animation in chimera where every scene is rotated 360 by using action Roll 360. What I observe is that the scene transitions from 1 scene to another is extremely slow and not continuous also. For some scenes it is fast as well. How can I keep this transition minimum and fixed to all scenes to make a continuous animation. Thank you very much Shanti Pal

2 1

Fwd: error code -1073741819
by Tom Goddard 09 Mar '21

09 Mar '21

Beni's problem with Chimera not starting was a graphics problem related to supersampling / super-resolution / multisampling. Not clear whether the fix was to change a graphics driver setting or the Chimera multisampling setting. Beni's email below. Tom > Begin forwarded message: > > From: Beni Sued <benisued(a)gmail.com> > Subject: Re: [Chimera-users] error code -1073741819 > Date: March 9, 2021 at 1:50:10 PM PST > To: Tom Goddard <goddard(a)sonic.net> > > > That's impressive knowledge! I was indeed using supersampling and superresolution (not sure if They are the same as multisampling but it worked) > Thanks so much! > solved > > On Tue, 9 Mar 2021 at 20:54, Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> wrote: > Hi Beni, > > The gzip message is just misleading. It is not an error and is explained here > > https://plato.cgl.ucsf.edu/pipermail/chimera-users/2015-July/011199.html <https://plato.cgl.ucsf.edu/pipermail/chimera-users/2015-July/011199.html> > > The real problem is almost surely that your graphics driver is broken since it gets to "Initializing graphics" and then dies. Updating the graphics driver was the right thing to try. > > One other remote possibility is that some Chimera preference setting is causing startup to fail -- like maybe you enabled multisampling in the past and the new graphics driver wipes out whenever you try to use it. The location of preferences is > > C:\Users\username\AppData\Roaming\.chimera\ > > (from documentation here https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/preferences.html <https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/preferences.html>). You might rename that .chimera folder so Chimera starts with factory default preferences and try to start. > > Tom > >> On Mar 7, 2021, at 1:18 PM, Beni Sued <benisued(a)gmail.com <mailto:benisued@gmail.com>> wrote: >> >> Hey there >> I've been using UCSF chimera for some time with no problems but it is having trouble starting up, this is the error message: >> >> Cannot execute 'gzip': no automatic decompression of .Z files >> >> initializing general preferences >> loading Tix >> initializing graphics >> Return code: -1073741819 >> Press return or enter to to exit >> >> precisely like this gentleman: >> https://plato.cgl.ucsf.edu/pipermail/chimera-users/2019-April/015675.html <https://plato.cgl.ucsf.edu/pipermail/chimera-users/2019-April/015675.html> >> and this >> https://www.cgl.ucsf.edu/pipermail/chimera-users/2011-December/007021.html <https://www.cgl.ucsf.edu/pipermail/chimera-users/2011-December/007021.html> >> >> my dxdiag info is attached, nothing wrong jumps to me. >> >> What I've tried: >> - uninstalling and reinstalling Chimera >> - manually installing GZIP for windows ( https://sourceforge.net/projects/gzip-for-windows/ <https://sourceforge.net/projects/gzip-for-windows/> ) >> - updating drivers (graphics drivers and chipset drivers) >> - getting the alpha version of the program >> - going to and fro compute mode in the the graphical settings >> >> I'm using Chimera 1.15 and this is my hardware >> chipset b550m >> ryzen 5600x >> RX 590 >> >> in trying to fix it I learned about ChimeraX, I'm learning to use it, but I would still like to keep chimera until i can properly stop and change my workflow >> >> thanks so much, let me know if I missed any info >> <DxDiag.txt>_______________________________________________ >> Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> >> Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users> >

1 0

error code -1073741819
by Beni Sued 09 Mar '21

09 Mar '21

Hey there I've been using UCSF chimera for some time with no problems but it is having trouble starting up, this is the error message: *Cannot execute 'gzip': no automatic decompression of .Z filesinitializing general preferencesloading Tixinitializing graphicsReturn code: -1073741819Press return or enter to to exit* precisely like this gentleman: https://plato.cgl.ucsf.edu/pipermail/chimera-users/2019-April/015675.html and this https://www.cgl.ucsf.edu/pipermail/chimera-users/2011-December/007021.html my dxdiag info is attached, nothing wrong jumps to me. What I've tried: - uninstalling and reinstalling Chimera - manually installing GZIP for windows ( https://sourceforge.net/projects/gzip-for-windows/ ) - updating drivers (graphics drivers and chipset drivers) - getting the alpha version of the program - going to and fro compute mode in the the graphical settings I'm using Chimera 1.15 and this is my hardware chipset b550m ryzen 5600x RX 590 in trying to fix it I learned about ChimeraX, I'm learning to use it, but I would still like to keep chimera until i can properly stop and change my workflow thanks so much, let me know if I missed any info

2 1

renseignements
by Camelia Hamadouche 09 Mar '21

09 Mar '21

je n'arrive pas a télecharger votre logiciel meme si je clique sur accepter on me dirige vers une fenetre disant quelle partie vous ne voulez pas accepter? alors que j'ai bien cliqué sur accepter

2 1

each rotation of the molecule in chimera will unexpectedly add an extra "c" at command line
by xiaoyu liu 03 Mar '21

03 Mar '21

Hello, I'm Xiaoyu Liu, a chimera user. Thank you for developing and sharing this powerful software. I have a problem now and bothered me for a while when using chimera. I'm wondering if you know how to solve it. I downloaded chimera-1.15-mac64.dmg <https://www.cgl.ucsf.edu/chimera/cgi-bin/secure/chimera-get.py?file=mac64/c…> from "https://www.cgl.ucsf.edu/chimera/download.html" for my Mac OS Catalina(10.15.5). When I rotate the molecule with left mouse button, an extra character "c" will be automatically added in command line. Each rotation will result in adding one "c". Here I have some screen shot to show more clearly. [image: image.png] [image: image.png] [image: image.png] I tried to restart my computer. It is helpful within the first 10 minutes after the restart, but later it has the problem again. Please let me know if you know how to solve it. Many thanks! Best, Xiaoyu

2 1

problem with pdb file saved from chimera-autodock vina analysis
by Amol Ghodke 03 Mar '21

03 Mar '21

Hi, First of all thank you so much for making such a wonderful tool and sharing it freely with scientific community. I have been using chimera for sometime now and performed docking analysis using autodock vina. I recently come across a problem. After exporting pdb file with desired docking pose, I tried to run protein ligand interaction analysis on PLIP<https://plip-tool.biotec.tu-dresden.de/plip-web/plip/index> server. But ligand in my file does not get recognised for analysis. I opened pdb file in a text editor and upon looking care fully I see chimera saves receptor and ligand as separate model like this ATOM 7453 HD2 PRO A 462 15.986 11.983 20.450 1.00 0.00 H ATOM 7454 HD3 PRO A 462 16.532 10.334 20.885 1.00 0.00 H ENDMDL MODEL 2 HETATM 1 S1 CGT A 1 9.051 5.106 43.099 1.00 0.00 S HETATM 2 C6 CGT A 1 8.150 3.680 42.370 1.00 0.00 C After comparing it with the pdb file from pbd database I removed “ENDMDL” and “MODEL 2” and re-ran the PLIP analysis. This time it works but PLIP also mentions that – [cid:image001.png@01D7103D.5D0AB030] Analysis went well but the .pse file that I get from PLIP server does not allow me to show ligand in stick format in Pymol software. I suspect this is due to the original pdb file format. I also noticed that pdb file when opened in pymol shows ligand and receptor as different states which is not correct (if I am right). I have attached both original pdb file that I saved from Chimera-autodock vina and pse file from PLIP analysis. May I request to help me resolve this issue? Please let me know if you need any further information or clarification. Thanks for your time and support Amol --------------------------------------------------------------------------------------------------------------------------------------------------------- Dr Amol Bharat Ghodke | Post-Doctoral Research Fellow Queensland Alliance for Agriculture and Food Innovation Level 3, Queensland Bioscience Precinct [#80] Room 3.318, 306 Carmody Rd, St Lucia The University of Queensland St Lucia, Brisbane Qld 4072, AU E. a.ghodke(a)uq.edu.au<mailto:a.ghodke@uq.edu.au>

2 1