Tsjerk,
I substituted the .strip() method into my version instead of the [:-1] which
was originally meant to discard tailing \n in the entries in "converge.nam".
This seemingly identical approach worked! Guess I had more whitespace than I
thought? Oh well...
Thank you very much!
Matt
On Tue, Nov 10, 2009 at 6:08 PM, Tsjerk Wassenaar <tsje...@gmail.com> wrote:
> Hi Matt,
>
> Well, then you're in for some nasty debugging. That will probably end
> with you slapping yourself against the head, as I've done plenty ofc
> times on such occasions. I tried the same things using the same sort
> of code you posted, and it worked for me. Of course, I'd rather do
> something like:
>
> L = [ i.strip() for i in open("files.nam").readlines() if i.strip() ]
> for i in L: cmd.load( i, i )
>
> But those are details really.
> You may want to print the list of filenames right after reading them
> in, and again after changing the entries. That may give a clue of what
> goes wrong.
>
> Cheers,
>
> Tsjerk
>
> On Tue, Nov 10, 2009 at 6:05 PM, Mateusz Maciejewski
> <s0676...@sms.ed.ac.uk> wrote:
> > Dear Tsjerk,
> >
> > I actually also tried using full paths in the script, as in
> >
> >
> > for n in range(len(linie)): linie[n] = ["/path/to/my/files/" +
> > linie[n][:-1]]
> >
> >
> > Then in the PyMOL interpreter/ log window I was getting
> >
> >
> > ExecutiveProcessPDBFile-Error: Unable to open file
> > '/path/to/my/files/compstatin.pdb_14'.
> >
> >
> > in the traceback. Yes, the file is in the same directory as the pdb file
> and
> > the script. Again if in the script I put names of files I want to open in
> > the 'linie' list manually rather then make it read in from a file, then
> it
> > works fine. Puzzling.
> >
> >
> > Thanks,
> > Matt
> >
> >
> >
> > On Tue, Nov 10, 2009 at 4:51 PM, Tsjerk Wassenaar <tsje...@gmail.com>
> wrote:
> >>
> >> Hi Mateusz,
> >>
> >> The first guess would be that you're not in the right directory, since
> >> Pymol can't find the file. That seems a bit awkward, as I guess
> >> they're in the same directory as "converged.nam", or aren't they? To
> >> see what is in the directory, you can call cmd.ls() at the start of
> >> the script. For what it's worth, the script is syntactically correct,
> >> although it could be written a bit more neatly ;)
> >>
> >> Hope it helps,
> >>
> >> Tsjerk
> >>
> >> On Tue, Nov 10, 2009 at 5:08 PM, Mateusz Maciejewski
> >> <s0676...@sms.ed.ac.uk> wrote:
> >> > Hello,
> >> >
> >> > I'm writing a script in Python to be executed in PyMOL. Unfortunately
> I
> >> > got
> >> > stuck right at the beginning, when I'm trying to load .pdb's from
> >> > "converged.nam" file. The relevant bit of the script is the following:
> >> >
> >> >
> >> > from pymol.cgo import *
> >> > from pymol import cmd
> >> >
> >> > loadedStuff=open("converged.nam", 'r')
> >> > linie = loadedStuff.readlines()
> >> > for n in range(len(linie)): linie[n] = linie[n][:-1]
> >> > for n in range(len(linie)): print n, linie[n]
> >> > for n in linie: cmd.load(n,n)
> >> >
> >> >
> >> >
> >> > Unfortunately, it is not working - I keep on getting:
> >> >
> >> >
> >> >
> >> > 0 compstatin.pdb_14
> >> > 1 compstatin.pdb_72
> >> > 2 compstatin.pdb_91
> >> > 3 compstatin.pdb_93
> >> > 4 compstatin.pdb_78
> >> > 5 compstatin.pdb_34
> >> > 6 compstatin.pdb_32
> >> > 7 compstatin.pdb_7
> >> > 8 compstatin.pdb_47
> >> > 9 compstatin.pdb_31
> >> > 10 compstatin.pdb_5
> >> > ExecutiveProcessPDBFile-Error: Unable to open file
> 'compstatin.pdb_14'.
> >> > Traceback (most recent call last):
> >> > File "/usr/local/pymol/modules/pymol/parsing.py", line 407, in
> >> > run_file
> >> > execfile(file,global_ns,local_ns)
> >> > File "align.py", line 8, in ?
> >> > for n in linie: cmd.load(n,n)
> >> > File "/usr/local/pymol/modules/pymol/importing.py", line 575, in
> load
> >> > if _raising(r): raise pymol.CmdException
> >> > CmdException: <pymol.CmdException instance at 0x56fdc6cc>
> >> >
> >> >
> >> >
> >> > When I manually form a list containing all the compstatin entries than
> >> > it is
> >> > working, so it must be something with how it processes the list which
> it
> >> > gets from the file. I can't really understand why that is so,
> especially
> >> > given how it correctly pronts out the content of the list that
> captures
> >> > the
> >> > content of the file. I am obviously making some silly mistake here...
> >> > any
> >> > suggestions?
> >> >
> >> > Thank you,
> >> > Mateusz Maciejewski
> >> >
> >> > ----------------------------------------------
> >> >
> >> >
> >> >
> >> > Mateusz Maciejewski,
> >> > University of Edinburgh
> >> > Joseph Black Chemistry Bldg, West Mains Rd.,
> >> > Edinburgh EH9 3JJ, U.K.
> >> > Phone (44) (0) 131 650 4704 (group office)
> >> >
> >> >
> >> >
> ------------------------------------------------------------------------------
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> >> > trial. Simplify your report design, integration and deployment - and
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> >> > on
> >> > what you do best, core application coding. Discover what's new with
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> >> > _______________________________________________
> >> > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
> >> > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> >> > Archives:
> http://www.mail-archive.com/pymol-users@lists.sourceforge.net
> >> >
> >>
> >>
> >>
> >> --
> >> Tsjerk A. Wassenaar, Ph.D.
> >>
> >> Computational Chemist
> >> Medicinal Chemist
> >> Neuropharmacologist
> >>
> >
> >
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
> Computational Chemist
> Medicinal Chemist
> Neuropharmacologist
>
>
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