- Chimera-users - RBVI Mailing Lists

Chimera does not start with mesa-11.2.2
by Jaime Rodríguez-Guerra Pedregal 23 May '16

23 May '16

Hi guys, just to let you know that mesa-11.2.2 is messing with Chimera startup sequence.: $ chimera --debug initializing general preferences loading Tix initializing graphics libGL error: unable to load driver: i965_dri.so libGL error: driver pointer missing libGL error: failed to load driver: i965 libGL error: unable to load driver: swrast_dri.so libGL error: failed to load driver: swrast X Error of failed request: BadValue (integer parameter out of range for operation) Major opcode of failed request: 154 (GLX) Minor opcode of failed request: 3 (X_GLXCreateContext) Value in failed request: 0x0 Serial number of failed request: 1410 Current serial number in output stream: 1411 $ `chimera --root`/bin/linuxdist /etc/os-release: NAME="Antergos Linux" VERSION="2015.11-ISO-Rolling" ID="antergos" ID_LIKE="arch" PRETTY_NAME="Antergos Linux" CPE_NAME="cpe:/o:antergosproject:antergos:2015.11" ANSI_COLOR="1;34;40" HOME_URL="https://antergos.com/" SUPPORT_URL="https://forum.antergos.com/" BUG_REPORT_URL="https://github.com/antergos" /etc/arch-release: Antergos Linux release 2015.11 (ISO-Rolling) /proc/cpuinfo: cpu: 8 GenuineIntel Intel(R) Core(TM) i7-4790 CPU @ 3.60GHz (x86_64) cpu MHz: 3884.625 cache: 8192 KB /proc/meminfo: MemTotal: 16296392 kB Graphics: 00:02.0 VGA compatible controller: Intel Corporation Xeon E3-1200 v3/4th Gen Core Processor Integrated Graphics Controller (rev 06) 01:00.0 VGA compatible controller: NVIDIA Corporation GM204 [GeForce GTX 970] (rev a1) I had to rollback to mesa-11.2.1 to make it work again. Cheers, Jaime Rodríguez-Guerra Pedregal Molecular modeling of transition metal systems group Department of Chemistry, Faculty of Sciences Edif. C · C7/153 Campus de la UAB · 08193 Bellaterra (Cerdanyola del Vallès) · Barcelona · Spain +34 93 581 28 57 www.uab.cat<http://www.uab.cat/> [http://www.uab.cat/vcard/Logo_ORCID_0.png] <http://orcid.org/0000-0001-8974-1566> [http://www.uab.cat/vcard/Logo_LinkedIn_0.png] <https://www.linkedin.com/in/jaimergp> This message may contain private or confidential information, and is addressed exclusively to its intended recipient. If you have received it in error, please notify the sender and delete it. Please bear in mind that you are not authorized to use it for any purposes. Please consider the environment before printing this email.

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How to convert Coot rotation matrix to something Chimera can read?
by Oliver Clarke 19 May '16

19 May '16

Hi all, I'd like to write a little python function in coot to open the current view with Chimera, because manually replicating in Chimera views that were identified in Coot is a little painful. The file handling aspects of this seem straightforward - the one aspect I haven't quite got yet is how to set the view in Chimera to match that seen in Coot. I would like to load up all molecules/maps that are displayed in coot, in their default orientations, and then apply the view matrix from coot using matrixset to get the equivalent view. Coot outputs a 3X3 rotation matrix which seems to be the same as that generated for an equivalent view by matrixget in Chimera, except that in Chimera the matrix is 3X4, with the last column representing the translation vector. This I cannot access directly within coot, but I can probably calculate it if I know what it represents. This is probably a stupid question, but is this simply the vector from the origin to the current center of rotation? Or is it something else? Cheers, Oliver.

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Re: [Chimera-users] Analysis of the contact maps from the MARTINI MD trajectory
by James Starlight 16 May '16

16 May '16

update: with the up-to-date chimera Trajectory is loaded fine now the question is related to the analysis of the binding interface. is it possible to make contact maps plots based on the 2 selections from the input trajectory assuming that I am using martini CG model? Gleb 2016-05-16 10:39 GMT+02:00 James Starlight <jmsstarlight(a)gmail.com>: > OK will try to update Chimera today ! > > What chimera's tools could be useful for the contact map based > analysis of md trajectories related to my case ? E.g to determine > binding interface between 2 proteins from long md simulation. > > Gleb > > 2016-05-13 19:52 GMT+02:00 Eric Pettersen <pett(a)cgl.ucsf.edu>: >> Hi Gleb, >> If you are using Gromacs 5 trajectories, you have to be using at least >> version 1.10.2 of Chimera. If you are using that version (or later), please >> use “Report a Bug” in Chimera’s Help menu to file a bug report and attach >> your topology file to the bug report. Thanks! >> >> —Eric >> >> Eric Pettersen >> UCSF Computer Graphics Lab >> >> >> On May 13, 2016, at 1:46 AM, James Starlight <jmsstarlight(a)gmail.com> wrote: >> >> Dear Chimera users! >> >> >> I am in charge with the analysis of protein-protein association during >> long molecular dynamic simulation where my system was parametrized >> using MARTINI CG force field. In particularly I am interesting to >> find residues on one of the protein which are crustal for the binding >> interface established during this MD. >> For that purpose I am trying to use Chimera to load trajectory and >> corresponded tpr file using MD movie plugin and than to >> map contact maps produced by Gromacs onto the 3D structure using Chimera. >> The problem that Chimera does not recognize properly the trajectory >> and topology. Briefly I have removed all solvent from both files >> before loading them to the Chimera using editconf and gmx convert-tpr >> obtaining eventually trajectory and topology with the same number of >> atoms. >> >> >> Than when I load it to Chimera that is the error which MD movie sent me: >> >> VERSION 5.0.2 >> using floats >> version 100, generation 26 >> 8 atoms >> Traceback (most recent call last): >> File "CHIMERA/lib/python2.5/site-packages/Pmw/Pmw_1_3/lib/PmwBase.py", >> line 1747, in __call__ >> File "CHIMERA/share/chimera/baseDialog.py", line 328, in command >> File "CHIMERA/share/chimera/baseDialog.py", line 543, in OK >> File "CHIMERA/share/Trajectory/EnsembleLoader.py", line 92, in Apply >> File "CHIMERA/share/Trajectory/formats/Gromacs/__init__.py", line >> 56, in loadEnsemble >> File "CHIMERA/share/Trajectory/formats/Gromacs/__init__.py", line >> 67, in loadEnsemble >> File "CHIMERA/share/Trajectory/formats/Gromacs/Gromacs.py", line 25, >> in __init__ >> File "CHIMERA/share/Trajectory/formats/Gromacs/Gromacs.py", line 86, >> in __init__ >> File "CHIMERA/share/Trajectory/formats/Gromacs/Gromacs.py", line >> 345, in _readTopology >> File "CHIMERA/share/Trajectory/formats/Gromacs/Gromacs.py", line >> 338, in _readString >> File "CHIMERA/lib/python2.5/xdrlib.py", line 197, in unpack_fstring >> raise EOFError >> EOFError >> EOFError >> >> File "CHIMERA/lib/python2.5/xdrlib.py", line 197, in unpack_fstring >> raise EOFError >> >> See reply log for Python traceback. >> >> Will be thankful for any suggestions! >> >> Gleb >> _______________________________________________ >> Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu >> Manage subscription: >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >> >>

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question
by zona cat 14 May '16

14 May '16

Good afternoon, My name is Daniel Heller, and I am working with Helen Berman at Rutgers University on a PDB project. We are trying to analyze multiple DNA binding proteins simultaneously (via matchmaker) and looking to visualize the surface electrostatic potential of each structure as a tiled picture. We are deleting the nucleotide chains for all proteins when complexed with DNA. However, I am only able to get the surface electrostatic coloring for one structure (the reference structure), subsequent structures will not apply the columbic coloring after i hit apply, they just maintain the monotone default surface structure . Could you please help me with this issue. Thank you very much,Dan

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Analysis of the contact maps from the MARTINI MD trajectory
by James Starlight 13 May '16

13 May '16

Dear Chimera users! I am in charge with the analysis of protein-protein association during long molecular dynamic simulation where my system was parametrized using MARTINI CG force field. In particularly I am interesting to find residues on one of the protein which are crustal for the binding interface established during this MD. For that purpose I am trying to use Chimera to load trajectory and corresponded tpr file using MD movie plugin and than to map contact maps produced by Gromacs onto the 3D structure using Chimera. The problem that Chimera does not recognize properly the trajectory and topology. Briefly I have removed all solvent from both files before loading them to the Chimera using editconf and gmx convert-tpr obtaining eventually trajectory and topology with the same number of atoms. Than when I load it to Chimera that is the error which MD movie sent me: VERSION 5.0.2 using floats version 100, generation 26 8 atoms Traceback (most recent call last): File "CHIMERA/lib/python2.5/site-packages/Pmw/Pmw_1_3/lib/PmwBase.py", line 1747, in __call__ File "CHIMERA/share/chimera/baseDialog.py", line 328, in command File "CHIMERA/share/chimera/baseDialog.py", line 543, in OK File "CHIMERA/share/Trajectory/EnsembleLoader.py", line 92, in Apply File "CHIMERA/share/Trajectory/formats/Gromacs/__init__.py", line 56, in loadEnsemble File "CHIMERA/share/Trajectory/formats/Gromacs/__init__.py", line 67, in loadEnsemble File "CHIMERA/share/Trajectory/formats/Gromacs/Gromacs.py", line 25, in __init__ File "CHIMERA/share/Trajectory/formats/Gromacs/Gromacs.py", line 86, in __init__ File "CHIMERA/share/Trajectory/formats/Gromacs/Gromacs.py", line 345, in _readTopology File "CHIMERA/share/Trajectory/formats/Gromacs/Gromacs.py", line 338, in _readString File "CHIMERA/lib/python2.5/xdrlib.py", line 197, in unpack_fstring raise EOFError EOFError EOFError File "CHIMERA/lib/python2.5/xdrlib.py", line 197, in unpack_fstring raise EOFError See reply log for Python traceback. Will be thankful for any suggestions! Gleb

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Suggestion for ChimeraX - interruptible Matchmaker?
by Oliver Clarke 12 May '16

12 May '16

Hi, Matchmaker takes a *really* long time when dealing with long chains, particularly if it has been (unwisely/accidentally) directed to find the best matching pair of chains. This is as expected, but as Chimera is unresponsive while this happens, if the wrong matchmaker parameters are accidentally selected, there is no way to recover the session except by waiting for the operation to complete or force-quitting the app. If feasible, maybe in ChimeraX it would be useful to execute this operation in a manner that allows for cancelling a structural alignment in progress? And perhaps displaying an estimate of time to completion in the taskbar? Cheers, Oli.

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Averaging multiple structures
by Yehuda Halfon 11 May '16

11 May '16

Hi there, I'm using Rosetta using comparative modeling of protein, and I get 1000 new PDBs. I wanted to upload all of them together and average them into one structure and to see if the average one is the better then the last one the software creates, which needs to be the best. Thanks, Yehuda

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building and positioning disordered sequence
by thereal sisterdot 11 May '16

11 May '16

Dear Chimera Users, i would like to do something in chimera, that is not exactly science but more graphics :-) i have a known structure with 5 positions that i know are crosslinking to a 100aa intrinsically disordered partner sequence. now just in order to better imagine how the disordered binding partner wraps around the structure, i would like to put 5 lysines in the open space near the known crosslinking positions in the pdb structure, and than somehow build the rest of the disordered partner sequence connecting those lysines. its not about getting a estimate of the structural arrangement of the partner. its just so i can better imagine how the partner sequence extends around the interacting residues (as the residues are not in a patch but really all over the 100 aa) or if the arrangement would be sterically possible. any ideas if and how i could achieve that in chimera ? i know that is sound more like a task for illustrator, but :-) THANKS A LOT!!! sisterdot

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Join models
by shazia sabir 10 May '16

10 May '16

Hi dear all, I have to join two models in one single model. For this I have to select N and C terminal of each of the model. But I couldn't find a way how to select/pick atom from N terminal of one model and C terminal of the other model. Please can anyone help me on that? kind Regards, Shazia.

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surfaces
by A G Szabo 10 May '16

10 May '16

I am trying to represent a large homodimer with 840 residues per subunit, as a surface. On a smaller protein, 350 residues I was able to get a surface representation and color different domains. When I try to produce the surface representation of the larger molecule, I receive an error message saying that I have to split it because it is too large a molecule. So how do I do that? Thanks AGS

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