Hello Jun-- > I have some basic knowledge about python programming and > xplor-NIH. It is always a mystery to me how atom coordinates are > passed to IVM or other downstream objects.
Excellent question. The answer is that coordinate and other per-atom information is stored in a Simulation object (https://nmr.cit.nih.gov/xplor-nih/doc/current/python/ref/simulation.html) The Simulation xplor.simulation is used by default if no other Simulation is specified or defined. This is an XplorSimulation, with some special properties. It is possible to explicitly create a new XplorSimulation - see https://nmr.cit.nih.gov/xplor-nih/doc/current/python/ref/xplorSimulation.html There are also EnsembleSimulations and SymSimulations (used for energy terms acting on identical subunits, differing by rigid-body translations and rotations). > For example, we usually > load psf and generate starting extended structure by > protocol.initStruct and protocol.genExtendedStructure(). For most > python programing, we need a variable to hold the data in python, Most often, the Simulation is an optional argument- as it is for the IVM. In other cases, such as protocol.initCoords or genExtendedStructure, a non-current simulation can be specified in the simulation member of an atomSel.AtomSel object passed as the selection or sel argument, resepctively. There may be cases where it is simplest to change the current Simulation (using simulation.makeCurrent), so that it is not necessary to specify this information in a passed argument. I do hope this clears things up some. Charles ######################################################################## To unsubscribe from the XPLOR-NIH list, click the following link: http://list.nih.gov/cgi-bin/wa.exe?SUBED1=XPLOR-NIH&A=1
