- Chimera-users - RBVI Mailing Lists

Quantify the movement between two domains
by Ahmad Khalifa 27 May '21

27 May '21

Hi, I'm looking for a way to quantify the movement between two domains in my structure. I know I can calculate an RMSD between the same domains in different conformations. I can also generate a distance matrix between the two chains in different conformations. I tried to measure the distance between the two centers of mass of my domains, but the change doesn't really capture the magnitude of the movement, also the same domains are not identical in the two conformations in the sense that one domain is missing so many loops, which will affect the com calculation. What other ways to quantify the distance between two different domains? Thank you.

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Chimera wont start
by Gmail 26 May '21

26 May '21

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Web services down
by Eric Pettersen 25 May '21

25 May '21

Hi all, Due to computing cluster maintenance starting this evening (5/25) through tomorrow evening (5/26), the web services in Chimera and ChimeraX that use our cluster will be down. The frequently used web services are BLAST and Modeller for both programs, and for Chimera only: sequence realignment via Clustal Omega or MUSCLE; SAXS2; and 2D ligand depiction. --Eric Eric Pettersen UCSF Computer Graphics Lab

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Fwd: Chimera - remote start up issue
by Greg Couch 24 May '21

24 May '21

tl;dr -- VirtualGL worked. -------- Forwarded Message -------- Subject: Re: [Chimera-users] Chimera - remote start up issue Date: Mon, 24 May 2021 13:16:18 +0000 From: Filip Kadlec <Filip.Kadlec(a)vutbr.cz> To: Greg Couch <gregc(a)cgl.ucsf.edu> Good evening, I'm writing to you with feedback since I remembered you wanted to let know if any of the methods worked. I got to it a bit later than expected (sorry for the delay) and let me tell you it was painful indeed. However the final solution was with VirtualGL with Cygwin combination - Installed Cygwin with all tools needef for X11 forwarding, server... including the VirtualGL client. On server installed VirtualGL server. Then using XLaunch (cygwin provides) and setting the right $DISPLAY variable it is possible to run and quite smoothly operate with visualisation programs (vglconnect, vglrun). Chimera, ChimeraX and also PyMOL works just fine. Thank you for the previous help and advice, it pointed me in this direction! Have a great day. Kind regards Filip ------------------------------------------------------------------------ *Od:* Greg Couch <gregc(a)cgl.ucsf.edu> *Odesláno:* pátek 7. května 2021 20:35 *Komu:* Kadlec Filip (191426) <Filip.Kadlec(a)vutbr.cz>; chimera-users(a)cgl.ucsf.edu <chimera-users(a)cgl.ucsf.edu> *Předmět:* Re: [Chimera-users] Chimera - remote start up issue Yes, as you discovered, remotely displaying 3D graphics is problematic. Sometimes it works, usually if the graphics driver on the remote computer and the local computer are the same (same manufacturer, same operating system, i.e., same variant of Linux and version). In your case, I'd recommend installing the VirtualGL package on the CentOS 7 computer, along with a graphics card and its driver. That way the 3D graphics are done on the CentOS 7 computer and an image is sent to your computer. VirtualGL is available from the epel repository and virtualgl.org. This is also the solution for nomachine and x2go. An alternative would be to try the free cygwin.org X11 server, or a commercial X11 server, like Exceed 3D. If either of those work, please let us know. Good luck, Greg On 5/7/2021 4:28 AM, Filip Kadlec wrote: > Good afternoon! > > I haven't found a solution to this problem in one of your user > threads, internet and I haven't succeeded resolving the issue. > I have installed chimera 1.15 today and it runs well when working on > the desktop. However, it would be very convenient if I could run > chimera remotely. Chimera is installed on Centos 7, I am trying to > remotely operate this PC with Windows 10 PC using MobaXterm. When I > run chimera as /chimera --debug/: > > initializing general preferences > loading Tix > initializing graphics > create application > loading Pmw > creating main window > creating menus > creating toolbar > creating viewer > initializing OpenGL > X Error of failed request: GLXBadCurrentWindow > Major opcode of failed request: 146 (GLX) > Minor opcode of failed request: 5 (X_GLXMakeCurrent) > Serial number of failed request: 2711 > Current serial number in output stream: 2711 > > With OpenGL on Centos-7 PC /glxinfo | grep "OpenGL":/ > OpenGL vendor string: Mesa Project > OpenGL renderer string: Software Rasterizer > OpenGL version string: 1.4 (2.1 Mesa 10.5.4) > OpenGL extensions: > > Have you encountered such problem? Could the problem be with coliding > OpenGLs, or graphical transfer through mobaxterm? It would be a major > help if you could point me in the right direction. > > Thank you in advance and have a great day! > > Kind regards > Filip Kadlec > > > > _______________________________________________ > Chimera-users mailing list:Chimera-users@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>

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What do you do for comparative modeling if the pdb is so new it's not in UniProt?
by Ralph Loring 24 May '21

24 May '21

Hi, I'm very new to Chimera and have been working through the tutorials, including the Comparative Modeling Tutorial. However I'm stumped. I'm interested in modeling chimeric proteins that involve the following pdbs: PDB 7KOO, 7KOX and 7KOQ and I can't get the sequence in my chimera to align with the template structure in the pdbs. The problem is that the template pdbs only came out in April and are not yet included in UniProt. They are deposited in RSCB and EMDB, but these don't appear to be alignment options in Chimera. Do I need to appeal to UniProt, or is there an alternative way to make the association between the sequence and the structure? Any additional tutorials on using MAV would be helpful as there seem to be a lot of editing features that are not explored in your tutorial. Thanks for your help, Ralph Loring Associate Professor of Pharmacology Department of Pharmaceutical Sciences Northeastern University 360 Huntington Avenue Boston, MA 02115 USA 617-373-3216 office 617-373-8886 fax r.loring(a)northeastern.edu

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excluded bilayer in chimera
by Yanhe Zhao 22 May '21

22 May '21

To whom may concern, This is Yanhe Zhao, from UT Southwestern Medical Center. I was curious that how can I exclude the lipid bilayer to show the transmembrane protein electron density when "zone" could not be used as I have no sequence and pdb information. Thanks a lot in advance for any input. Best regards, Yanhe

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Measuring rotation
by JAVAD KARIMBAYLI 18 May '21

18 May '21

Greetings dear sir/madam I was trying to measure the rotation of my protein before vs after activation using the "measure rotation #0 #1" command, which worked smoothly. Then I wanted to check the rotation of specific residues. However, when I tried to specify residues, for example, residue 45 of model0 vs model1, the code didn't work. I have gone through Chimera documentation but didn't really find how to solve the issue. So, I kindly ask for your suggestions about how I may get residue-specific rotations. Thank you in advance Javad Karimbayli

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Covalent bond making and docking
by Zhang, Bixia 14 May '21

14 May '21

Good evening, I was trying to make a man made side chain, which is serine plus uracil. I used the command "bond sel" to connect the oxygen and nitrogen. Then I was trying to do docking to see if this mutation changed the binding affinity. However, after I ran dock prep, the uracil was got rid of because of "poor connection". I am wondering if this arbitrary bond is feasible in chimera and can I do docking with this artificial model? Thank you, Bixia

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Question about error: "the exit code was: -1073731819"
by Sergio Garay 13 May '21

13 May '21

Dear Chimera Users My name is Sergio Garay, I have installed chimera-1.15-win64.exe on Windows 10pro 64bit. But when the program starts to run, the system gives me the following error message and the program closes: chimera exited abnormally; the exit code was: -1073731819. use the -- debug command line option for the full error message I tried installing the two previous versions of the program, with the same result. My PC has a Radeon RX 580 series videocard, and the system uses a WDDM 2.7 video controller. Could you give me any advice on how to fix this problem? Sincerely -- *Prof. Dr. Sergio Garay* *Càtedra de Práctica Profesional de Bioquímica* *Cátedra de Bioinformática* *Facultad de Bioquimica y Cs. BiológicasUniversidad Nacional del LitoralSanta Fe - ArgentinaC.C. 242 - Ciudad Universitaria - C.P. S3000ZAAArgentinaPh. +54 (342) 4575-213Fax. +54 (342) 4575-221 *

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Enquiry regarding application
by Prem Rajak 13 May '21

13 May '21

Dear Sir/madam, I have a query regarding the use of UCSF Chimera for molecular docking studies. I am a faculty at an University and would like to analyse my molecular docking research studies using UCSF Chimera. Moreover, I would like to publish the images thus analysed in national/international standard journals. Publications may be multiauthored. Therefore, please let me know whether I can use the software free of cost or I have to purchase the licence. Looking forward to your reply. Thanks and regards, Dr. Prem Rajak Kazi Nazrul University West Bengal, India

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