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Protocols

diffmap specifications

Information


Unique identifier OMICS_26904
Name diffmap
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
License GNU General Public License version 3.0
Computer skills Advanced
Version 120330
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Nikolaus Grigorieff

diffmap citations

 (10)
call_split

Structural analysis of BRCA1 reveals modification hotspot

2017
Sci Adv
PMCID: 5606707
PMID: 28948225
DOI: 10.1126/sciadv.1701386
call_split See protocol

[…] en the H2O2-treated BRCA15382insC-BARD1 map and the untreated BRCA15382insC-BARD1 map. Maps were normalized and, to a common density range and differences, were generated using the publicly available DIFFMAP.exe. Difference densities in comparable regions at or above a 3σ threshold were considered significant (). A second difference map was calculated using the same procedures to visualize signifi […]

library_books

Molecular structure of human KATP in complex with ATP and ADP

2017
eLife
PMCID: 5790381
PMID: 29286281
DOI: 10.7554/eLife.32481.037

[…] nd one transporter module, which is equivalent to the volume enclosed in sector 4. The final composite map was sharpened by scaling to the synthetic map calculated from the refined atomic model using diffmap.exe (http://grigoriefflab.janelia.org/diffmap). The half-map equivalent of the composite map was prepared according to the procedure described above except half-maps from focused 3D refinement […]

call_split

Single protein detection in crowded molecular environments in cryo EM images

2017
eLife
PMCID: 5453696
PMID: 28467302
DOI: 10.7554/eLife.25648.032
call_split See protocol

[…] was used to calculate the reconstruction directly, using no refinement, classification, or imposed symmetry.The 3D difference map comparing the experimental reconstruction to a model was generated in Diffmap (http://grigoriefflab.janelia.org/diffmap). The real part of the electrostatic potential map of the DLP-VP1 complex used in this comparison was generated at 0.05 nm voxel pitch using TEM-simul […]

library_books

Structure of a human pre 40S particle points to a role for RACK1 in the final steps of 18S rRNA processing

2016
Nucleic Acids Res
PMCID: 5041492
PMID: 27530427
DOI: 10.1093/nar/gkw714

[…] d of Chimera. Difference maps between the 3D structures of the HASt-LTV1 pre-40S particle and the modified mature 40S subunit were calculated using either the ‘vop subtract’ option in Chimera, or the Diffmap program by N. Grigorieff. Both options yielded similar results. The difference map was superimposed to the modified mature 40S structure, and available X-ray or NMR structures of maturation fa […]

call_split

Structural organization of the dynein dynactin complex bound to microtubules

2015
PMCID: 4385409
PMID: 25751425
DOI: 10.1038/nsmb.2996
call_split See protocol

[…] Arp filament could be fit with high precision into the 24Å resolution negative stain dynactin reconstruction. By low pass filtering of the cryoEM reconstruction to a comparable resolution and using “diffmap” from the Grigorieff lab, it was possible to isolate density for the shoulder domain from the negative stain structure.Nine copies of a homology model of Arp1, based on an F-Actin as template […]

call_split

Effects of tubulin acetylation and tubulin acetyltransferase binding on microtubule structure

2014
Mol Biol Cell
PMCID: 3890346
PMID: 24227885
DOI: 10.1091/mbc.E13-07-0387
call_split See protocol

[…] he rotation and translations were then applied to the isolated dimers from the unsharpened (no B-factor applied) reconstructions. Differences between the aligned dimers were then calculated using the DIFFMAP program (Grigorieff lab, Brandeis University, Waltham, MA) after padding the dimer volumes by a factor of 2. Differences at the edges due to the alignment after the isolations were ignored. Al […]


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