42 Results Found
  • Validation of Docking Poses via Interaction Motif Searching

    Given a set of docking poses for a single ligand can we separate correct poses from high scoring but incorrect poses by comparing protein-ligand interaction motifs?

    Last Modified: 14/02/2012 PDF

  • Validating protein-bound metals

    ​We compare the structure of a protein-bound metal and its coordination shell, with similar coordination structures in the CSD. This analysis may be useful in identifying errors in metal assignment or in coordination geometry in X-Ray derived protein models.

    Last Modified: 14/02/2012 PDF

  • Exploring symmetry related bias in conformational data from the CSD

    ​One frequently presented argument against using small molecule crystal structure data in conformer generation is that the close packing observed within crystal structures can significantly bias the observed conformations away from gas phase norms. We explore some well known cases where symmetry effects bias the distribution of conformational geometric information and to find the conditions that lead to this bias.

    Last Modified: 14/02/2012 PDF

  • How-to: reveal neigbouring molecules using Mercury

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    Using Mercury you may want to find out what is next to a molecule in a crystal structure however you would have to know what you were looking for and edit the contact options accordingly. This tool automatically reveals what is next to a molecule in any given direction, depending on where you choose.

    Produced by Andrew Bennett (a student at Dame Alice Owen's School, Potters Bar) during a work experience placement at CCDC.

  • How-to: Visualise the void space in a structure

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    ​A 'how to' video on visualising the void space in a structure using 'Mercury.'

    To visualise the void space of a functional structure you need to enter the Display tab and then click Voids. When the box has opened you simply need to tick Show Voids and then press OK. You can use the pack option (shown in video) to expand the structure and then turn on voids to see what the voids look like in the structure. You can then turn off the pack option to fully visualise the voids without the packed molecules in the way.

    Produced by Andrew Bennett (a student at Dame Alice Owen's School, Potters Bar) during a work experience placement at CCDC.

  • How-to: visualise crystal morphology

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    For some structures you may be interested in the physical shape of the crystal and the relationship between this shape and the structure at the molecular level. You can predict the shape of the crystal itself using the BFDH morphology option.

    Here each of the crystal faces is indexed and we can explore the packing of the structure as normal. If you have experimentally determined the crystal shape (by "face indexing") you may want to read in this information for display in Mercury. You can do this by opening the BFDH morphology dialogue and clicking on Open, then reading in your morphology file.

  • How-to: use lasso to select atoms in Mercury

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    A 'how to' video on using the Lasso Select in 'Mercury.'

    To use the lasso select in mercury you simply click on the lasso select icon in the top right of the Mercury window and then use the left click to draw around your atoms. You can use the lasso select on one molecule up to a whole crystal structure, in exactly the same way. Using the lasso select saves time as selecting individual atoms in a whole crystal structure can be unnecessarily time consuming.

  • How-to: Calculate the centroid of a functional group

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    A 'how to' video on calculating the centroid of functional structure using 'Mercury.'

    Produced by Andrew Bennett (a student at Dame Alice Owen's School, Potters Bar) during a work experience placement at CCDC.​

  • Mercury - How to change the colour of a measurement label

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    This is a short video showing how to change the colour of a measurement label in Mercury.

  • Mercury - How to change spacegroup settings

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    This is a short video showing how to change space group settings in Mercury