Hi Paul, unfortunately, mrage does not currently handle nucleic acids. However, I am wondering whether it would be beneficial to add this feature. My understanding is that for nucleic acids, the sequence-structure relation is not the same as for proteins, therefore the majority of MRage's features, such as homology search and template editing are not applicable, but I am glad to listen to the experts on the field, and add features that would be make the program more useful (with this said, I am currently adding support for sculptor to process nucleic acid chains, although right now this is not more than renaming to the expected sequence; any advice on further possibilities is gratefully received). If you just have one model, and want to run it through MRage, you can do this by leaving out the component sequence, and specify the model structure as a "processed model" (I am not sure that the GUI lets you do this, but you can do it from the command line); in this case, the molecular weight is calculated from the structure (and a warning will be printed to the logfile). This will still assume that the structure is protein, and hence estimate SigmaN incorrectly, but the error is rather small. However, unless you have a large number of pre-made models and want to run it on a cluster, this is unlikely to give better results than running Phaser to do the same. Best wishes, Gabor On 2014-11-16 15:17, Paul Paukstelis wrote:
I'm trying to run mrage with nucleic acid models. With phaser, it is possible to specify the molecule type, but this option doesn't exist in mrage (from what I can see). Providing a sequence file automatically assumes protein one letter codes. Any suggestion on how to clearly define a sequence file as a nucleic acid?
Thanks,
--paul _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb