Dear Troels,
thank you very much for the answer.
Now that I understand better the source of the problem, I will try again
using the GUI. The question is: would it be better for the PDB contain only
one molecule without the Zn? (after all, as far as I understand, it is used
only to build the list of spin, correct?) and should the PDB already have the
protons added or not?
Stefano
PS: I will try to use your list of instructions as a script file
From the PDB file, I see that there is an A+B (protein) and C chain (ZN).
The A and B chain is two molecules I guess.
This helped me solve it in the relax prompt:
help(pipe.create)
pipe.create('new','relax_disp')
help(structure.read_pdb)
# The smallest possible info
structure.read_pdb(file='BpUreE_apo_model_full.pdb')
# Defining molecule 1
structure.read_pdb(file='BpUreE_apo_model_full.pdb', dir=None, read_mol=1,
set_mol_name='SpUreE_SC', read_model=None, set_model_num=None, alt_loc=None,
merge=False)
# Defining names for the two molecules
structure.read_pdb(file='BpUreE_apo_model_full.pdb', dir=None,
set_mol_name=['SpUreE_SC_1','SpUreE_SC_2'])
structure.read_pdb(file='BpUreE_apo_model_full.pdb', dir=None, read_mol=None,
set_mol_name=['SpUreE_SC_1','SpUreE_SC_2'], read_model=None,
set_model_num=None, alt_loc=None, merge=False)
I hope it helps :-)
Best
Troels
2014-02-08 11:41 GMT+01:00 stefano ciurli
<NO-REPLY.INVALID-ADDRESS@xxxxxxx<mailto:NO-REPLY.INVALID-ADDRESS@xxxxxxx>>:
URL:
<http://gna.org/support/?3112>
Summary: unable to upload PDB
Project: relax
Submitted by: stefanociurli
Submitted on: Sat 08 Feb 2014 10:41:02 AM UTC
Category: None
Priority: 5 - Normal
Severity: 3 - Normal
Status: None
Privacy: Private
Assigned to: None
Originator Email:
Open/Closed: Open
Discussion Lock: Any
Operating System: Mac OS
_______________________________________________________
Details:
Hello,
following my previous email, this is the log message I get.
Please help!
SC
relax>
structure.read_pdb(file='/Users/stefano/Desktop/13-BpUreE-NMR/Manuscript/Figure
7 - Dynamics/relax/BpUreE_apo_model_full.pdb', dir=None, read_mol=None,
set_mol_name='SpUreE_SC', read_model=None, set_model_num=None, alt_loc=None,
merge=False)
Internal relax PDB parser.
Opening the file '/Users/stefano/Desktop/13-BpUreE-NMR/Manuscript/Figure 7 -
Dynamics/relax/BpUreE_apo_model_full.pdb' for reading.
Traceback (most recent call last):
File "gui/interpreter.pyc", line 303, in run
File "pipe_control/structure/main.pyc", line 722, in read_pdb
File "lib/structure/internal/object.pyc", line 1840, in load_pdb
IndexError: list index out of range
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Re: [sr #3112] unable to upload PDB