- Chimera-users - RBVI Mailing Lists

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 05 Mar '19

05 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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How to setup appropriate parameters during auto dock vina
by temban billyhp 02 Mar '19

02 Mar '19

Hi, How should I vary docking parameters when carrying out ligand/receptor docking in order to obtain correct results. Is there any logical trend to follow. I have always used the default mode. Best regards Sent from Yahoo Mail on Android

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Re: [Chimera-users] Morph Help
by Elaine Meng 01 Mar '19

01 Mar '19

Hi Debamita (Paul), You may not always be able to get the trajectory you want. All I can suggest is to try: (1) changing morph parameters. You did not say whether you were using Chimera or ChimeraX. Both allow changing method and core fraction, or forcing Cartesian intermediates (the latter has not been useful in the cases I’ve worked on, however). ChimeraX also allows changing hinge spacing. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/morph/morph.html> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/morph.html> (1b) Chimera has an option to minimize each frame, but it also has limited ability to “rescue” bad conformations, and it will take a lot longer to calculate your morph trajectory. (2) more difficult, if (1) does not solve your problem: manually create intermediate states to “guide” the overall trajectory and then morph in more stages involving these intermediates. I.e instead of morphing 1->2, create 1a and possibly 1b etc. then morph 1->1a->1b->2. I hope this helps. For future reference, to make it more likely you get your questions answered, please send to chimera-users(a)cgl.ucsf.edu or chimerax-users(a)cgl.ucsf.edu (depending on which program you’re asking about). Thanks, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Feb 25, 2019, at 12:30 PM, Paul, Debamita <Debamita_Paul(a)baylor.edu> wrote: > > Hi, > > I am trying to morph two structures having a DNA lesion (6-4 Photoproduct). However the movie is showing weird geometry in the intermediate steps. Is there a way I can provide the parameter file for the 6-4 so that the geometry is not messed up. > > Thanks > Debamita

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Chimera using question
by Khải Trần Gia 28 Feb '19

28 Feb '19

Dear Mr/Mrs, I am a person using Chimera to adding missing residues to a protein from Protein Data Bank. My protein has 2 chains: A and B which both have missing residues. I have used Chimera tools compliment with Modeller to adding missing residues in both chain. The problem is I want to save the whole protein which consists of 2 fixed chains, however when I saved with PDB it only show 1 chain. How can I do that? I am looking forward for your replying. Thank you. Best regards, Khai.

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Chimera Help
by Debamita Paul 28 Feb '19

28 Feb '19

morphg5-xtal_0222_new.pdb <https://drive.google.com/a/cornell.edu/file/d/1t0Up4tsMWqLe7ipmUEfRzth0OFNN…> morphg5-xtal_0222_new.pdb <https://drive.google.com/a/cornell.edu/file/d/1C_cQTG9d5k10rKOQnW_XayfDGZt1…> Hi Dr. Meng, I emailed you earlier about having trouble in morphing two structures of a DNA bound protein. The DNA has 6-4 photo lesion. I am attaching the pdb files and the morph results (64_IB to 6cfi). You can see in the morph

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Can Chimera read electron density difference map files from RIDL?
by Murpholino Peligro 28 Feb '19

28 Feb '19

Here is what RIDL is https://github.com/GarmanGroup/RIDL I can open the map in coot specifying is a difference map and it opens nicely over the protein. In chimera I can open the map but .....all my clicks won't reproduce the coot behavior :P ... Thanks

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Seeking for help
by temban billyhp 27 Feb '19

27 Feb '19

SirI prepared the DNA molecule using the dock prep with its default options but when I lunched auto dock vina alongside with my ligand, I received a message that auto dock vina cannot prepare the receptor due to an error. How can I solve this problem. I will be greatful listening from you. Best wishes. Sent from Yahoo Mail on Android

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