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On Nov 7 2006, Nicholas Noinaj wrote:
If multiple copies are present, then (I think) phaser will simply output those solutions also in the .sol file ....but only the top solution will be output as a .pdb file. If mulitple solutions are present in the .sol file, you can use the parameters in the file to create coordinates for those additional solutions using PDBSET within CCP4. Then combine the files into a single coordinates file.
Actually, if you look for multiple components and Phaser succeeds in placing them, the PDB file will contain all of the components, as separate chains.
By default, Phaser will only produce a PDB file for the top solution (which, as I said, may contain several components), but this can be changed by specifying with the TOPFILES keyword that you want PDB and MTZ files for more than one solution. And you don't have to rerun the whole search to get PDB and/or MTZ files for more than one solution. If you run a packing job (MR_PAK), starting from the .sol file from your full run, with the number of topfiles set to a bigger number, Phaser will produce PDB files for those top solutions. If you want MTZ files as well, you can run a "phasing and refinement" (MR_RNP) job, again with the number of topfiles increased.
Randy Read
