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The chain selects the part of the molecule to be used for RMSD calculation. If you do not provide the chain, the entire molecule will be used.
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Generally, every name for which a PDB file is contained in the zip/tgz file that you upload. Please, provide the full name with ending.
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No, the RMSD is calculated in absolute coordinates.
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This really depends on your sampling. Probably you want to start with a rather large value and decrease it in a few steps. The smaller the RMSD value the longer will be your pathway. On the other hand, if you use very small RMSD values, it may force the algorithm to include high energy conformations. In that way, you would introduce artificial barriers. It will require finding the best balance.
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SmoothT creates low-energy pathways. Thus, the 'energy' for every PDB has to be provided. This can be calculated with any approach, MD or Rosetta for example, but has to be consistently the same scheme for all PDBs. The identifier is needed to find the energy value.
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Not on the server. If you download SmoothT you can use a pair of proteins for which you have an alignment.
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Probably there were no values for the energy identifier in your PDB file.
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Make sure that all PDB files have the same order, otherwise the NGL viewer gets confused.
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If the other FAQs could not help solving your problem, drop us an email.
