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Does anyone know any freeware like RasMol or JMol with the following features?:
-it should allow protein visualization including protein sequence.
-it should allow to mark specific subsequences of the entire protein sequence, the corresponding sequence should be painted in any distinguished colour in the protein model.
-it should allow to edit the protein sequence (i.e. to mutate amino acids) and the changes should be reflected in changes in the structure.
I know that the last point is particularly demanding and that taking it seriously it is not possible (since we cannot deduce the structure of a protein given its sequence). But what I need is a "simplistic" software that tells me whether any changes will affect a given structure locally or not. For instance, in an alpha-helix, whether the change of an amino acid retains the helix structure or whether the helix is disrupted. I guess that taking into account the nature of the chemical group plus the size of the amino acid should be sufficient to answer my questions. But I don´t want to calculate them by myself.
Edited by Chelo, 08 June 2011 - 08:28 AM.
