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Information
| Unique identifier | OMICS_06370 |
|---|---|
| Name | Coot |
| Alternative name | Crystallographic Object-Oriented Toolkit |
| Software type | Package/Module |
| Interface | Command line interface |
| Restrictions to use | None |
| Operating system | Unix/Linux |
| Computer skills | Advanced |
| Stability | Stable |
| Maintained | Yes |
Subtool
- SSM
Versioning
No version available
Maintainer
- person_outline Paul Emsley
Publications for Crystallographic Object-Oriented Toolkit
Handling ligands with Coot.
Features and development of Coot.
Coot: model-building tools for molecular graphics.
Coot citations
(5925)Activity of acetyltransferase toxins involved in Salmonella persister formation during macrophage infection
[…] ined with PHENIX Phaser software using molecular replacement function and a polyalanine scaffold of TacT (PDB 5FVJ) as a model. The model was then modified using AutoBuild and manually improved using Coot and refined using PHENIX and Refmac, against the high-resolution native data to give a final structure with an Rfree of 23.1% and good geometry (Supplementary Table ). The relatively high final […]
Targeting G protein coupled receptor signaling at the G protein level with a selective nanobody inhibitor
[…] ssion: 1A0R, 5M2W) with the CCP4 program PHASER,. Initial models were improved by multiple rounds of REFMAC ver. 5.8 refinement against the Gβ1γ1-Nb5 complex dataset and manual model adjustments with Coot 0.8.8. The final models had agreement factors Rfree and Rcryst of 24.7% and 20%, respectively. The stereochemical quality of the Gβ1γ1-Nb5 complex model was assessed with the Molprobity and wwPDB […]
X ray structure of a carpet like antimicrobial defensin–phospholipid membrane disruption complex
[…] chrotron (MX2) and processed using XDS. The structure was solved by molecular replacement with PHASER using the structure of NaD1 in its dimeric form as a search model. The final model was built with Coot and refined with Phenix to a resolution of 2.5 Å with the final Rwork and Rfree values of 0.2031 and 0.2519, respectively. All data collection and refinement statistics are summarized in Table . […]
Structure of a cleavage independent HIV Env recapitulates the glycoprotein architecture of the native cleaved trimer
[…] +PGT122 complex structure was determined by MR with PGV19 (determined in this study) and BG505 SOSIP.664+PGT122 from PDB 4TVP. The structures were refined using Phenix and model building performed in Coot. MolProbity, Privateer, and pdb-care were used for structure validation. The refinement statistics are reported in Supplementary Table . […]
Ratchet free solid state inertial rotation of a guest ball in a tight tubular host
[…] tructions. The non-hydrogen atoms were analyzed anisotropically, and hydrogen atoms were input at the calculated positions and refined with a riding model. Electron density mapping was performed on a COOT software program. The Hirshfeld surface analyses were performed using the CrystalExplorer software program. The refinement data are shown in Supplementary Tables –. […]
Structure guided Discovery of Dual recognition Chemibodies
[…] e molecular replacement program Phaser using a previously reported complex structure of rat DPP-IV with Fab 11A19 (PDB code: 4FFV) as a search model. Model building and refinement were carried out in COOT and REFMAC in CCP4, respectively. All structural figures were prepared using PyMOL (Schrodinger Inc, San Diego, CA). […]
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