Dear Charles, Thank you for your response. I have added the changes to the default protG "anneal.py" script, and now the extended conformation is loaded in VMD-Xplor. However, when it comes to " IVM.setTrajectory( VMDTraj(vobj,saveInterval=100) )" line, the script terminates with the following message:
TypeError: unbound method setTrajectory() must be called with IVM instance as first argument (got VMDTraj instance instead) Do you have any suggestions on this? Thank you, Vitaly ----- Original Message ----- From: [email protected] Date: Wednesday, January 6, 2010 12:37 pm Subject: Re: [Xplor-nih] Structure display during simulated annealing To: Vitaly Vostrikov <vvostri at uark.edu> Cc: xplor-nih at nmr.cit.nih.gov > -----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----- >
