Paride, cmd.pseudoatom is only for creating atoms, not adding coordinates. What you're doing is creating a separate atom for each molecular state, which means N-atoms x M-states = a huge inefficiency!.
Look at what particle01.py is doing in terms of merely updating existing coordinates using alter_state. Then, the only additional trick to incorporate is to copy the first state before using alter_state to modify coordinates for the copied state. see examples/devel/particle02.py (just added) for a working example of what your code should do instead. Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:del...@delsci.info "Not yet a PyMOL Subscriber, but want to support the project? Email sa...@delsci.com to quote your lab, school, or employer. Thank you for sponsoring this open-source endeavor!" -WLD > -----Original Message----- > From: Paride Legovini [mailto:legov...@spiro.fisica.unipd.it] > Sent: Tuesday, November 06, 2007 4:48 PM > To: DeLano Scientific > Cc: pymol-users@lists.sourceforge.net > Subject: Re: [PyMOL] file format for homebrew MD software > > DeLano Scientific wrote: > > One option is to simply create and modify coordinates > real-time using > > Python. See example particle01.py > > I'm trying the code I'm pasting at the end of this email, but > I have a strange problem with pseudoatom: it is EXTREMELY > slow, and I mean that is takes AGES to read 100 files, eating > 100% of my CPU. Loading files with 'load' works fine. What's wrong? > > The dat files are just xyz coordinates and I'm experimenting > with no ten atoms per file. A partial example: > > $ cat data/step000011.dat > 0.097806 0.094156 0.934356 > 0.083930 0.020571 1.938765 > and so on... > > ---------- code starts here ---------- > > from glob import glob > from pymol import cmd > > file_list = glob("data/step*.dat") > > # for some reason file_list is unsorted. > file_list.sort() > > counter = 0 > > for file in file_list: > counter = counter + 1 > f = open(file, "r") > for line in f: > position = line.split() > cmd.pseudoatom("polymer", pos=position) > f.close() >
