Robin Stamler wrote:
I’m sure this is answered somewhere but I couldn’t find it.The ordering of atoms in a residue in Modeller output as in (a) is different from that usually seen in PDB files (b)This is a problem when using the output in some other servers. Can the Modeller output be changed?
Modeller always outputs atoms in the same order. This is defined by the CHARMM topology library (usually modlib/top_heav.lib) which you can of course alter if you want a different order.
We cannot output atoms in "PDB order" because there is no consistent ordering. If some servers cannot read atoms in different orders, then these servers are broken, and should be fixed.
Ben Webb, Modeller Caretaker -- modeller-care@salilab.org http://www.salilab.org/modeller/ Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage