- Chimera-users - RBVI Mailing Lists

Changing depth cue to side to side from front to back
by Trevor Harris 02 May '18

02 May '18

Hello, I would like to know if it is possible to change the depth cue to side to side rather than front to back. I don’t want to change the position of the molecule. Is it possible? Thanks, Trevor

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Label hydrogen bonds
by Pawan Mainkar 30 Apr '18

30 Apr '18

The following bug report has been submitted: Platform: windows_x86_64 Chimera Version: 1.11.2 Description Respected sir, I am a PhD student in the discipline of Biotechnology, actually sir i am working on Enzyme-inhibitor docking study and i did docking using Cluspro and then i want to check how much interaction by visualizing the inter molecular hydrogen bonds with proper labeling (like in structure hydrogen bond between D45-S89 with 2.3 Angstron) ,but sir am only able visualize only hydrogen bonds in Your software UCSF Chimera but am unable to label it with proper amino acid along with distance so i request you sir please tell me how to do that or provide me any video file regarding the same File attachment: Docking complex.docx

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Important Query
by Rida Zainab 30 Apr '18

30 Apr '18

Respected Sir, I am a research student trying to use chimera but I am having difficulties. Whenever I give an operation or task in chimera, the replylog opens always giving error. Suppose I tried to convert PDB file to Mol2 and there was error of replylog. I tried to do docking using autodock vina and it is not happening too. I am unable to do anything. Please tell me what's wrong? Big help needed. Regards, Rida.

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Suggestion for adding a volume map to morph conformation
by Trevor Harris 25 Apr '18

25 Apr '18

Hello, I would like to use the Morph Conformation show the changes of the molecular orbitals from starting material to transition state to product. I can show the changes structurally of the atoms which is great, but this would be amazing with the molecular orbitals overlaid the structures. If this option is available to add volumes into morph conformation, then I couldn’t find it. Would it be possible to add this feature? It would be similar to IBOView. Thank you! Trevor Harris Postdoctoral Fellow UPenn Chemistry, Chenoweth Group

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Problem running Modellerfrom Chimera (versión 1.11.2(build 41380) 2016-12-05 19:45 UTC. Platform Linux64)
by Sergio Garay 23 Apr '18

23 Apr '18

Hi all I've tried to run Modeller locally from Chimera (versión 1.11.2(build 41380) 2016-12-05 19:45 UTC. Platform Linux64. Windowing system: x11), but when it finishes, the model is not loaded inside Chimera. The log window give me the following output: *Model 0 (model1.pdb) appears to be a protein without secondary structure assignments.* *Automatically computing assignments using 'ksdssp' and parameter values:* * energy cutoff -0.5* * minimum helix length 3* * minimum strand length 3* *Use command 'help ksdssp' for more information.* *seq (len 437): added* *target (len 437): model1.pdb (#0) chain A* *seq (len 437): model1.pdb (#0) chain A* *target (len 437): added* *Target seq: added* *Template structures: * * model1.pdb (#0)* *Run locally, the Modeller binary location: /usr/bin/mod9.19* *Now, modeller is running locally...* *Wrote /tmp/tmp73g3JY/template_struc/model1.pdb_0_0.pdb* *MODELLER process output* *-----------------------* *-----------------------* *MODELLER process errors* *-----------------------* *Could not find platform independent libraries <prefix>* *Could not find platform dependent libraries <exec_prefix>* *Consider setting $PYTHONHOME to <prefix>[:<exec_prefix>]* *'import site' failed; use -v for traceback* The problem seems to be that Chimera can not load the models obtained . I can find the model inside the directory: /tmp/tmp73g3JY/template_struc/*model1.pdb_0_0.pdb* Thank you in advance. Sergio -- *Sergio GarayDr. en Ciencias BiológicasFacultad 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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Fwd: Re: run chimera remotely over nice dcv
by Greg Couch 23 Apr '18

23 Apr '18

Solution found! -------- Forwarded Message -------- Subject: Re: [Chimera-users] run chimera remotely over nice dcv Date: Sat, 21 Apr 2018 13:20:11 +0200 From: Mihajlo Vanevic <m.vanevic(a)uu.nl> To: Greg Couch <gregc(a)cgl.ucsf.edu> Dear Greg, Thank you very much for the prompt reply. About ssh -X, indeed putting the compatible libGL.so from local machine to Chimera's lib folder does the trick. About Nice DCV, I have contacted Nice DCV developers and will let you know if the problem is solved. With best wishes, Mihajlo On 04/20/2018 07:54 PM, Greg Couch wrote: > > Hi Mihajlo, > > We don't have any experience with Nice DCV, perhaps some other user on > the mailing list can help. But guessing at possible problems, make > sure that Chimera is displaying locally in Nice DCV virtual machine > (the DISPLAY environment variable should be ":0"), and the remote > display is done using the Nice DCV client. > > If, instead, you're using X11's remote display capability, then you > wouldn't need to use Nice DCV, any virtual machine technology would do > (or not do) -- the trick there is to have compatible OpenGL drivers on > both the virtual machine and your local computer (running the X11 > server). Assuming compatible versions of Linux on both ends, you > could copy libGL.so from your local machine to the Chimera's lib > directory on the remote machine, and it should work. > > Good luck, > > Greg > > On 4/20/2018 5:07 AM, Mihajlo Vanevic wrote: >> >> Dear Chimera users and developers, >> >> We are trying to run Chimera remotely on our cluster via Nice DCV >> visualization software: >> >> https://www.nice-software.com/products/dcv >> >> This package provides GPU acceleration for OpenGL and >> DirectX applications. It indeed works for most of apps, however with >> Chimera >> we get the following startup error >> >> X Error of failed request: GLXBadContext >> Major opcode of failed request: 152 (GLX) >> Minor opcode of failed request: 5 (X_GLXMakeCurrent) >> Serial number of failed request: 73 >> Current serial number in output stream: 73 >> >> Our cluster visualization node has nvidia GeForce GTX 1080 Ti cards >> and nvidia drivers 384.81 >> >> Chimera works if we use software mesa rendering, but it would be great if >> we can make it work remotely with hardware rendering. >> >> With kind regards, >> Mihajlo Vanevic >> Cryo-EM group, Utrecht University >>

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Error in Windows saving a session
by Joel Mackay 21 Apr '18

21 Apr '18

Hi all Have other people seen (and solved!) this error before (below)? I'm having it crop up pretty much all the time now when I try to save a session (on my Win7 machine - running Chimera 1.11.2. Thanks Joel WindowsError Exception in Tk callback Function: <function command at 0x00000000155434A8> (type: <type 'function'>) Module: <module 'chimera.baseDialog' from 'C:\Program Files\Chimera 1.11.2\share\chimera\baseDialog.pyc'> (line: 447) Args: () Traceback (innermost last): File "C:\Program Files\Chimera 1.11.2\bin\lib\site-packages\Pmw\Pmw_1_3_3\lib\PmwBase.py", line 1747, in __call__ return apply(self.func, args) File "C:\Program Files\Chimera 1.11.2\share\chimera\baseDialog.py", line 449, in command getattr(s, buttonFuncName(txt))() File "C:\Program Files\Chimera 1.11.2\share\OpenSave\__init__.py", line 264, in Save getattr(self, self.keepEquiv())() File "C:\Program Files\Chimera 1.11.2\share\chimera\baseDialog.py", line 704, in OK self.Apply() File "C:\Program Files\Chimera 1.11.2\share\OpenSave\__init__.py", line 183, in Apply self.command(1, self) File "C:\Program Files\Chimera 1.11.2\share\SimpleSession\gui.py", line 41, in _saveCB saveSession(paths[0], **kw) File "C:\Program Files\Chimera 1.11.2\share\SimpleSession\save.py", line 135, in saveSession os.rename(tsave, filename) WindowsError: [Error 32] The process cannot access the file because it is being used by another process WindowsError: [Error 32] The process cannot access the file because it is being used by another process File "C:\Program Files\Chimera 1.11.2\share\SimpleSession\save.py", line 135, in saveSession os.rename(tsave, filename) See reply log for Python traceback. ------------------------------------------------------------------------------------------------------------------------------ Professor Joel Mackay | NHMRC Senior Research Fellow Chair, Biochemistry, Cellular and Molecular Biology Cluster School of Life and Environmental Sciences THE UNIVERSITY OF SYDNEY A: School of Life and Environmental Sciences | Rm 674, Building G08 | Butlin Ave The University of Sydney | NSW | 2006 | Australia T: +61 2 9351 3906 | F: +61 2 9351 5858 | S: joelmackay E: joel.mackay(a)sydney.edu.au | W: www.mmb.usyd.edu.au/mackay/

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run chimera remotely over nice dcv
by Mihajlo Vanevic 20 Apr '18

20 Apr '18

Dear Chimera users and developers, We are trying to run Chimera remotely on our cluster via Nice DCV visualization software: https://www.nice-software.com/products/dcv This package provides GPU acceleration for OpenGL and DirectX applications. It indeed works for most of apps, however with Chimera we get the following startup error X Error of failed request: GLXBadContext Major opcode of failed request: 152 (GLX) Minor opcode of failed request: 5 (X_GLXMakeCurrent) Serial number of failed request: 73 Current serial number in output stream: 73 Our cluster visualization node has nvidia GeForce GTX 1080 Ti cards and nvidia drivers 384.81 Chimera works if we use software mesa rendering, but it would be great if we can make it work remotely with hardware rendering. With kind regards, Mihajlo Vanevic Cryo-EM group, Utrecht University

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Adding quadrant lines to atoms
by Trevor Harris 20 Apr '18

20 Apr '18

Hi, Is there a way to add quadrant lines to atoms similar to how Houkview does it in CylView, pictured below. If not, could you add this feature as an option? All the best, Trevor Harris

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Superimpose map with fitted atoms
by Luca Pellegrini 20 Apr '18

20 Apr '18

Hi, I’d like to superimpose a cryoEM map with fitted atoms onto a second cryoEM map. I do this using ‘fit in map’, but only the map moves, the fitted structure does not. Is there a way to update the coordinates of the fitted structure according to the map superposition? Best wishes, Luca Luca Pellegrini, PhD Department of Biochemistry University of Cambridge 80 Tennis Court Road Cambridge CB2 1GA UK Email: lp212(a)cam.ac.uk Phone: 0044-1223-760469 https://www.bioc.cam.ac.uk/pellegrini-group/pellegrini-group @PellegriniLab

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