UCSF Chimera protocols

View UCSF Chimera computational protocol

UCSF Chimera statistics

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chevron_left Multiple amino acid sequence alignment Protein-ligand docking 3D macromolecule reconstruction Molecule viewers Structure visualization Pairwise sequence alignment chevron_right
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UCSF Chimera specifications

Information


Unique identifier OMICS_03803
Name UCSF Chimera
Software type Package/Module
Interface Command line interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux, Mac OS
Computer skills Advanced
Stability Stable
Maintained Yes
Wikipedia https://en.wikipedia.org/wiki/UCSF_Chimera

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Maintainer


  • person_outline Thomas E. Ferrin <>

Additional information


Tuto: http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/frametut.html

Publication for UCSF Chimera

UCSF Chimera in pipelines

 (130)
2018
PMCID: 5758568
PMID: 29311594
DOI: 10.1038/s41467-017-02553-6

[…] 129,663 particles yielded a 5.1 å, state2 with 33,587 particles yielded a 6.9 å and state3 with 15,678 particles yielded a 8.3 å (supplementary figure )., masks for 3d refinement were created by ucsf chimera and relion program. pdb data file of whole complex (pdbid: 5gar) was converted to a density map by molmap command of chimera software applying 20–30 å lowpass filter. then, in relion, […]

2018
PMCID: 5762779
PMID: 29321502
DOI: 10.1038/s41467-017-02474-4

[…] ation, at a cutoff of 0.143. this final em map was deposited in em data bank (emd-7005). all rigid-body fitting of atomic models into em density, as well as generation of figures were performed using ucsf chimera., pex1/pex6 atpase activity was monitored using an atp/nadh coupled enzyme assay in which the regeneration of hydrolyzed atp is coupled to the oxidation of nadh. the reaction contains 5 n […]

2018
PMCID: 5799202
PMID: 29402941
DOI: 10.1038/s41598-018-20802-6

[…] by bioedit (isis pharmaceuticals, inc.). superposition of structures was done using discovery studio 4.0 client (accelrys software inc., san diego, ca) and the r.m.s. deviation were generated using ucsf chimera (http://www.cgl.ucsf.edu/chimera/)., publisher's note: springer nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations., this work […]

2018
PMCID: 5805719
PMID: 29422607
DOI: 10.1038/s41598-018-21053-1

[…] reconstruction (ihrsr) was carried out in spider, using an f-actin model as an initial reference. the process was repeated for 20 rounds, with convergence usually occurring within 10 rounds. ucsf chimera was used for visualization, analysis, and atomic fitting of 3d volumes., accurate matching of reconstructions to each other was essential to determine whether mybp-c n-termini resulted […]


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UCSF Chimera in publications

 (1543)
PMCID: 5951799
PMID: 29760474
DOI: 10.1038/s41467-018-04300-x

[…] supplementary table . atomic coordinates and structure factors have been deposited with the protein data bank, accession code 6en3. molecular graphics and structural analyses were performed with the ucsf chimera package., synchrotron x-ray scattering data for recombinant purified endosd233a/e235l were collected on the b21 beamline of the diamond light source, uk. data collection was performed […]

PMCID: 5944921
PMID: 29746590
DOI: 10.1371/journal.ppat.1006986

[…] projection images were refined and reconstructed to a final average resolution of ~4.2 å (0.143 fsc cut-off)., an initial model was generated based on pdb id 5cez [] and pdb id 3se9 [] using ucsf chimera [], modeler [] and coot []. a library of 200 homologous 7-mer peptide fragment coordinates per relevant residue were compiled and used in iterative centroid-representation density-guided […]

PMCID: 5940828
PMID: 29740047
DOI: 10.1038/s41598-018-25336-5

[…] the docking was performed using the ‘accurate’ parameter at otherwise default parameters, with no region of interest defined (blind docking). modeling and docking results were visualized using ucsf chimera v1.12 software., , electronic supplementary material , supplementary information accompanies this paper at 10.1038/s41598-018-25336-5., publisher's note: springer nature remains […]

PMCID: 5935710
PMID: 29728606
DOI: 10.1038/s41467-018-04139-2

[…] the native yaxb dataset was recorded at 4 å resolution and phased by molecular replacement on the paxb crystal structure (chain a). homology modeling was performed with modeler interfaced through ucsf chimera and the obtained coordinates applied for patterson search calculations in phaser. though appropriate rotation solutions were achieved, the full-length model was unable to be positioned […]

PMCID: 5929558
PMID: 29715318
DOI: 10.1371/journal.pone.0196484

[…] and after the simulation. after the minimization and production in the pdb coordinated of the complexes were saved from the .rst files and were analyzed by using an online server pdbepisa [] ucsf chimera [] and pymol [] visualization software., the antigenic epitopes were determined by using tongaonkar’s method [] using the physiochemical properties of amino acids. experimental precision […]


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UCSF Chimera institution(s)
Computer Graphics Laboratory, Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA

UCSF Chimera review

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krawutzi

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Desktop
Very useful and intuitive program, commandline is available and tight integration with python