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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Does GOLD calculate or use atomic charges?
… GOLD ignores both formal and partial charges. It deduces whether an atom has a formal charge by counting the bond order of the atom and comparing the result …
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I find searching for polymeric structures difficult and I get results I don't fully understand. Can you explain how polymeric structures are defined so I can tailor my searches to be more effective?
… Polymers and extended structures are defined within the CSD with the use of the polymeric bond type. We have prepared a document that details how to search …
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Having built up a network of molecules, can I delete one of them?
… Yes - right click on any of the atoms or bonds in the molecule you want to delete, then select Delete this Molecule from the pop-up menu. …
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What level of disorder needs to be present to trigger the disorder filter in the CSD?
… for certain parameters. The level of disorder referred to in this case is essentially any structure in which there are multiple sites for any non-hydrogen atom …
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I'm using the porphyrin template provided with ConQuest as part of my substructure but the search seems to be missing hits I know are there: what is going on?
… however it may miss cases where some of the bonds are aromatic. To avoid this issue, the porphyrin template bonds should be re-typed as Any. The template can …
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What are the strengths/weaknesses of similarity searching in WebCSD?
… . The fingerprints used by WebCSD for similarity searching are created using atom types, bond types and bonded paths through the molecules. This definition for the fingerprints …
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Can GOLD handle metals?
… should not have any bonds to coordinating atoms. If these are present in the original PDB file, they must be deleted. Further information can be found …
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How should I reference IsoStar?
… IsoStar: A library of information about non-bonded interactions I. J. Bruno, J. C. Cole, J. P. M. Lommerse, R. S. Rowland, R. Taylor and M. L. Verdonk, J …
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What is the best way of reducing the number of hits if a search gives more than I want?
… options such as 'Number of Bonded Atoms'). Alternatively, you can restrict the search to only the most experimentally precise structures, e.g. by setting an upper …
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What should I input to Mogul?
… In general you should input complete molecules, ions or crystal structures to Mogul rather than substructures. The geometrical preferences of a bond length …
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