-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1
Hello Vitaly-- > I have a somewhat naive question: is it possible to toggle the display of the > molecule during the simulated annealing? > > Certainly the efficiency will suffer, but I am looking for a way to > introduce > the students to structure calculations. I vaguely recall that such > display w > as used in Dynamo from NMRPipe package, but maybe I am mistaken on this. It is possible to visualize a molecular structure during structure determination. It's not so much toggling, however. In the Python interface: 1) Make this modification: (documented here: http://nmr.cit.nih.gov/xplor-nih/doc/current/python/ref/vmdInter.html) after loading PSF info: from vmdInter import VMDInter, VMDTraj vmd=VMDInter() vobj=vmd.makeObj("struct") #creates a new VMD molecule # named ``struct'' vobj.bonds("name C or name N or name CA") #draw backbone atoms then, for each IVM object add a line ivm.setTrajectory( VMDTraj(vobj,saveInterval=100) ) you may wish to make saveInterval smaller. 2) then, with a running VMD-XPLOR instance, a) run the python script within the XPLOR window, using pyth execfile('script.py') or b) using an external instance of Xplor-NIH, run the script, adding -port <num> -host <name> parameters to the command-line. The host is the hostname of the machine where VMD-XPLOR is running, and the port number can be found out from the running VMD-XPLOR instance using Control -> Info It is not yet possible to directly generate a trajectory file from the IVM, although this is possible using the old XPLOR interface. best regards-- Charles -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Processed by Mailcrypt 3.5.8+ <http://mailcrypt.sourceforge.net/> iEYEARECAAYFAktE2GgACgkQPK2zrJwS/lZskgCeKlwrQaUr4MmhC8tRrdLozTF+ VKIAn1x5gR/RW7UGshYFhZTxF23UCW31 =g5pc -----END PGP SIGNATURE-----
