FAQs
For questions not addressed by a support solution here, please Contact Us. Please do include a description of the problem as well as your operating system and version.
What can we help you with?
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How do I know whether to flip or rotate Ring-NHR, Ring-NR1R2 and protonated carboxylic acids when setting ligand flexibility?
… When setting ligand flexibility, by default, all planar Ring-NHR, Ring-NR1R2 and carboxylic acids are set to 'Flip' i.e. to rotate through 180 degrees only …
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Does GOLD allow for protein flexibility?
… GOLD allows for partial protein flexibility in all dockings. Specifically GOLD rotates the torsion angles of serine, threonine and tyrosine hydroxyl groups …
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Mercury 2020.1 is slow on MacOS
… We are aware of a stutter-like behavior when rotating structures in Mercury 2020.1. This has been fixed in later releases. You can download the latest …
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Can I perform a rigid ligand docking using GOLD?
… to the Ligand Flexibility option under Global Options in the GOLD Setup interface. Upon activating the "Fix Ligand Rotatable Bonds" tick box, you are presented …
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How do I generate a movie using Mercury?
… ... then tick the Generate Animation Frames checkbox before clicking on Render. Recommended settings for generation of smooth and effective movies are rotation about …
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How do the default settings for GOLD differ in the MOE interface compared to standalone GOLD?
… corners: flip v.s. fixed Ligand carboxylic OH groups: fully rotatable v.s. flip Ligand pyramidal nitrogen groups: allow inversion v.s. fixed Torsional …
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Why is it not possible to return the crystallographic binding pose of the ligand?
… Solutions option to find other reasonable binding poses. The ligand is large and has many rotatable bonds. If so, try a longer docking protocol. The ligand …
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Electron Diffraction Data in the CSD
… in the following CIF fields: CIF field Information to include _diffrn_measurement_method The method used to measure the data e.g. ‘Rotation Electron Diffraction …
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