- Chimera-users - RBVI Mailing Lists

MD simulation fails with barostat
by Simon Wheeler 13 Mar '19

13 Mar '19

Hi everyone. I'm trying to run an MD simulation in Chimera. It works with no thermostat and no barostat and it works with just a thermostat. But when I try to run it with a barostat it gets about 15% of the way through the equilibration stage and then Chimera hangs and the simulation never finishes. I've applied periodic boundary conditions and specified the box size. Does anyone know what I'm doing wrong? Thanks, Simon

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CHIMERA ISSUES
by Acco . 13 Mar '19

13 Mar '19

Hello, I am a beginner with Chimera and I am looking for how to "bring to front" the residues that I have selected displaying the remaining structure of the protein in kind of blurred view. Is it possible to do this? Thank you in advance for your help Sincerely, Andrea

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how to load pseudobonds from command line?
by Michał Kadlof 12 Mar '19

12 Mar '19

Hello, I'd like to display my psudobond in chimera script. How can I do it? -- regards Michał Kadlof <m.kadlof(a)cent.uw.edu.pl>

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membrane boundaries
by Anaswara Ashok 12 Mar '19

12 Mar '19

Hi I would like to know if we could add membrane boundaries of proteins with chimera? -- Regards Anaswara Ashok

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OS differences in Chimera
by Marco J. Müller 11 Mar '19

11 Mar '19

Dear Chimera team, I do have a question regarding differences between OSes. Our group recently encountered a problem in the surface creation of proteins, which might be related to the OS. Recently, for some structures, directly obtained from the PDB (e.g. 6GB5, 1H97, 4YLJ) or prepared single-chain structures for docking runs, the surface creation of the proteins resulted in error 5 from mscalc.exe. This, however, seems to be an isolated problem of the Windows versions of ucsf chimera 1.12-1.13.1, as the same versions of chimera on macOS or Linux (Lubuntu) could successfully create these surfaces. Even more strangely, we are pretty sure that we could show surfaces of the very same files about half a year ago with these versions (1.12 and 1.13rc1). Did a recent update of Windows change the behavior of chimera? ChimeraX could actually show these surfaces on Windows, but gave us some other troubles. We did have a look at http://www.cgl.ucsf.edu/pipermail/chimera-users/2016-November/012874.html which did solve our problem for now, but we would like to know whether we can improve the reliability of chimera's functions, aside from tips mentioned in http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/surfprobs.html. An older post (http://www.cgl.ucsf.edu/pipermail/chimera-users/2010-December/005805.html) indicates that it is a numerical problem, is this still the case and means that it is indeed OS-dependent? Thank you in advance, Marco -- Marco J. Müller PhD student Technische Universität Braunschweig Institute of Medicinal and Pharmaceutical Chemistry https://www.tu-bs.de/pharmchem Beethovenstr. 55 | 38106 Braunschweig | Germany

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font problem
by 管泓翔 11 Mar '19

11 Mar '19

When I started chimera, it showed "Cannot find a usable font Aborted (core dumped)". How to fix the problem? Thank you HH

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Deterministic traversal of a chemical graph
by Jaime Rodríguez-Guerra Pedregal 08 Mar '19

08 Mar '19

Dear Chimera team, I have two questions regarding the same idea. I am trying to develop a script to find topologically equivalent residues in a structure (e.g. MOF, cages, and so on). To do this, I am using SplitMolecule.split.split_connected and then comparing the resulting pieces by number of atoms, empirical formula and, ultimately, I would like to compare the chemical graph (i.e. test for graph isomorphism). Is there any built-in function/object for that in Chimera? Since I didn't want to overcomplicate the algorithm, for now I am trusting that there won't be isomers in the structure and the empirical formula (actually a collections.Counter applied to atom.element.name<http://atom.element.name>) is enough of a test.This is working ok but, in some cases, the resulting pieces have totally different atom names because they come from a unified generic residue that encompasses all the pieces. As a result, I want to rename them in the same way consistently. My first attempt at this consists of finding the chimera.Root atom of each piece and then using chimera.Molecule.traverseAtoms to iterate over the piece. However, I've found that the Root is not always the same (topologically speaking) atom, so the naming scheme differs from piece to piece. Is there anyway to guarantee topologically equivalent traversals? I guess that both questions would lead to the same result, because it seems that I will need a chemical graph anyway. Thank you in advance, Jaime.

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Saving files from MD Movie
by Divjak Maja 06 Mar '19

06 Mar '19

Hello! I have been using Chimera for analysis of H-Ras morphing from its GDP-bound inactive state to the GTP-bound active state. It works very nicely and a lovely movie is produced. What I am having difficulty with however, is saving the output of the morph as a series of PDB files that I can import to Autodesk Maya with the molecular Maya plugin. When I try to save from the movie window ie using file >save PDB, all I get is one PDB file containing a single structure. I also tried to save using the main window file > save PDB > save all frames and the same thing happens. I then tried selecting each frame individually and saving with unique numbered file names, but again, when trying to import into Maya, all I get is one structure, not a changing structure. Even the first and last frame PDBs are the same. Could you please advise as to how to save the morph output as a useful PDB series, I must be missing something? Thanks so much and best wishes, Maja Dr Maja Divjak BAppSc(Hons), PhD, Grad Cert 3D Animation (AFTRS) Biomedical Animator Office of Cancer Research [Description: cid:image001.jpg@01D35ECE.31407C60] Phone +61 3 8559 5961 Email maja.divjak(a)petermac.org<mailto:maja.divjak@petermac.org> 305 Grattan Street Melbourne Victoria 3000 www.petermac.org<http://www.petermac.org/> Disclaimer: This email (including any attachments or links) may contain confidential and/or legally privileged information and is intended only to be read or used by the addressee. If you are not the intended addressee, any use, distribution, disclosure or copying of this email is strictly prohibited. Confidentiality and legal privilege attached to this email (including any attachments) are not waived or lost by reason of its mistaken delivery to you. If you have received this email in error, please delete it and notify us immediately by telephone or email. Peter MacCallum Cancer Centre provides no guarantee that this transmission is free of virus or that it has not been intercepted or altered and will not be liable for any delay in its receipt.

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Re: [Chimera-users] Chimera installation on Windows Sub System Ubuntu
by Tom Goddard 04 Mar '19

04 Mar '19

The OpenGL graphics library is an operating system library. If you install it then Chimera should find it. There is nothing more you would have to do. Tom > On Mar 4, 2019, at 1:00 PM, Rosenberg, Mark F <mark.rosenberg(a)imperial.ac.uk> wrote: > > Hi Tom > Sorry to bother you again. > I have found installed/ the library. How do I tell Chimera where to look for it please when building ? > Thank you again. > Mark > > Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10 > > From: Tom Goddard <goddard(a)sonic.net> > Sent: Monday, March 4, 2019 6:54:44 PM > To: Rosenberg, Mark F > Cc: Rosenberg, Mark F; chimera-users(a)cgl.ucsf.edu BB > Subject: Re: Chimera installation on Windows Sub System Ubuntu > > The error installing on the Ubuntu virtual machine means that the opengl graphics library libGL.so.1 was not found. Probably you need to install a graphics driver for the Ubuntu virtual machine in order for Chimera to start. > > Tom > > >> On Mar 4, 2019, at 9:40 AM, Rosenberg, Mark F wrote: >> >> >> Dear Tom >> Hope you are well. I think I have been at this for days. I am trying to install Chimera on a Windows installation but I have had a few bugs which I have submitted to Bugs. >> >> I thought in the meantime , I could try and install Chimera in the Windows Subsystem with Ubuntu. >> >> I have got so far but I keep on getting the below error. >> >> I have tried to see if I am missing any libraries to no avail. >> >> Do you have any suggestions please ? >> >> Thank you very much. >> >> Kind Regards >> >> Mark >> >> Traceback (most recent call last): >> File "/opt/Chimera/share/__main__.py", line 73, in <module> >> value = chimeraInit.init(sys.argv) >> File "/opt/Chimera/share/chimeraInit.py", line 666, in init >> import chimera >> File "/opt/Chimera/share/chimera/__init__.py", line 16, in <module> >> from _chimera import BBox, Camera, Color, ColorGroup, DirectionalLight, LODControl, Lens, LensViewer, Light, Material, MaterialColor, Model, NoGuiViewer, OGLFont, OSLAbbreviation, OpenModels, OpenState, PathFinder, PixelMap, Plane, Point, PositionalLight, Selectable, SharedState, SpotLight, Sphere, Texture, TextureColor, TrackChanges, Vector, Viewer, X3DScene, Xform >> ImportError: libGL.so.1: cannot open shared object file: No such file or directory >> Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10

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Re: [Chimera-users] Chimera installation on Windows Sub System Ubuntu
by Tom Goddard 04 Mar '19

04 Mar '19

The error installing on the Ubuntu virtual machine means that the opengl graphics library libGL.so.1 was not found. Probably you need to install a graphics driver for the Ubuntu virtual machine in order for Chimera to start. Tom > On Mar 4, 2019, at 9:40 AM, Rosenberg, Mark F wrote: > > > Dear Tom > Hope you are well. I think I have been at this for days. I am trying to install Chimera on a Windows installation but I have had a few bugs which I have submitted to Bugs. > > I thought in the meantime , I could try and install Chimera in the Windows Subsystem with Ubuntu. > > I have got so far but I keep on getting the below error. > > I have tried to see if I am missing any libraries to no avail. > > Do you have any suggestions please ? > > Thank you very much. > > Kind Regards > > Mark > > Traceback (most recent call last): > File "/opt/Chimera/share/__main__.py", line 73, in <module> > value = chimeraInit.init(sys.argv) > File "/opt/Chimera/share/chimeraInit.py", line 666, in init > import chimera > File "/opt/Chimera/share/chimera/__init__.py", line 16, in <module> > from _chimera import BBox, Camera, Color, ColorGroup, DirectionalLight, LODControl, Lens, LensViewer, Light, Material, MaterialColor, Model, NoGuiViewer, OGLFont, OSLAbbreviation, OpenModels, OpenState, PathFinder, PixelMap, Plane, Point, PositionalLight, Selectable, SharedState, SpotLight, Sphere, Texture, TextureColor, TrackChanges, Vector, Viewer, X3DScene, Xform > ImportError: libGL.so.1: cannot open shared object file: No such file or directory > Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10

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