Hi Edward
Thank you very much for the branch. I made some modifications and
included your and Sébastien's comments.
Unfortunately, I have a problem launching the relax functions. For
example by starting the noe calculation, an error appears:
Traceback (most recent call last):
File "/home/michael/Programme/relax_bieri_gui/gui_bieri/relax_gui.py",
line 2645, in exec_noe1
make_noe(self.res_noe1.GetValue(), self.noe_ref_1.GetValue(),
self.noe_sat_1.GetValue(), self.noe_ref_err_1.GetValue(),
self.noe_sat_err_1.GetValue(),
self.nmrfreq_value_noe1.GetValue(),self.structure_noe1.GetValue(),
self.unres_noe1.GetValue(), start_relax, self, 1, global_setting,
file_setting, sequencefile)
File
"/home/michael/Programme/relax_bieri_gui/gui_bieri/res/calc_noe.py",
line 66, in make_noe
pipe.create(pipename, 'noe')
NameError: global name 'pipe' is not defined
relaxGUI is not able to feed the commands into relax. Do I have to
import other modules?
Imported relax modules:
from float import floatAsByteArray
from generic_fns.mol_res_spin import generate_spin_id, spin_index_loop,
spin_loop
from generic_fns import pipes, spectrum
from relax_errors import RelaxError
Do you have an idea how to solve this problem?
I have another problem relating the OMP data. relaxGUI calculated
local_tm model, but it is not able to calculate the others (also the
scripts can't calculate). There seems to be a problem with the pdb file,
I just don't see at the moment:
Internal relax PDB parser.
Opening the file '/home/mbieri/LinuxBox/OMP/1F35_mono.pdb' for reading.
RelaxWarning: The atom number 80 from the CONECT record cannot be found
within the ATOM and HETATM records.
RelaxWarning: The atom number 88 from the CONECT record cannot be found
within the ATOM and HETATM records.
Traceback (most recent call last):
File "relaxGUI.py", line 4126, in exec_model_free
start_model_free(self, which_model)
File "relaxGUI.py", line 1533, in start_model_free
Model()
File "relaxGUI.py", line 1125, in __init__
structure.read_pdb(PDB_FILE)
File "/usr/local/relax-1.3.4/prompt/structure.py", line 464, in read_pdb
generic_fns.structure.main.read_pdb(file=file, dir=dir,
read_mol=read_mol, set_mol_name=set_mol_name, read_model=read_model,
set_model_num=set_model_num, parser=parser)
File "/usr/local/relax-1.3.4/generic_fns/structure/main.py", line 247,
in read_pdb
cdp.structure.load_pdb(file_path, read_mol=read_mol,
set_mol_name=set_mol_name, read_model=read_model,
set_model_num=set_model_num, verbosity=verbosity)
File "/usr/local/relax-1.3.4/generic_fns/structure/internal.py", line
628, in load_pdb
mol.fill_object_from_pdb(mol_records)
File "/usr/local/relax-1.3.4/generic_fns/structure/internal.py", line
1373, in fill_object_from_pdb
self.atom_connect(index1=self.__atom_index(record[1]),
index2=self.__atom_index(record[i+2]))
File "/usr/local/relax-1.3.4/generic_fns/structure/internal.py", line
1332, in atom_connect
if index2 not in self.bonded[index1]:
TypeError: list indices must be integers
I tried both, the monomer (extracted in pymol) and the dimer.
Thank you for your help!
Cheers
Michael
Edward d'Auvergne schrieb:
Michael,
I have been modifying your GUI branch to launch the GUI from relax.
All your code and pictures from file #7341
(https://gna.org/support/download.php?file_id=7341) attached to task
#6847 (https://gna.org/task/?6847#comment4) is now committed to the
SVN repository. So to launch the GUI, you can type any one of the
following:
$ relax -g bieri
$ relax --gui bieri
$ relax -b
$ relax --bieri
You can see all my changes on the relax-commits mailing list
(https://mail.gna.org/public/relax-commits), which I would recommend
you subscribe to so you can see all the changes occurring to your
branch. Not all elements of the interface may work, but the GUI
should launch independently of where relax is installed or where you
run it from. If you haven't already, you can check out your branch by
typing:
$ svn co svn+ssh://michaelbieri@xxxxxxxxxxx/svn/relax/branches/bieri_gui
Later on I will make lots of code cleanups/modification
recommendations and suggestions for renaming of files and directories,
as well as for reorganising the separate GUI elements into separate
modules. For example increasing the comment count and clearly
describing in human understandable terms what a statement or block of
statements are doing (this is part of the design of relax so that
non-programmers can understand and contribute). And using the
standard relax variable, class, module etc. naming conventions.
Regards,
Edward
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Re: Launching the GUI from relax.