Dear Stefano.
>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 <[email protected]>
:
> 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
>
>
>
>
> _______________________________________________________
>
> Reply to this item at:
>
> <http://gna.org/support/?3112>
>
> _______________________________________________
> Message sent via/by Gna!
> http://gna.org/
>
>
> _______________________________________________
> relax (http://www.nmr-relax.com)
>
> This is the relax-devel mailing list
> [email protected]
>
> To unsubscribe from this list, get a password
> reminder, or change your subscription options,
> visit the list information page at
> https://mail.gna.org/listinfo/relax-devel
>
_______________________________________________
relax (http://www.nmr-relax.com)
This is the relax-devel mailing list
[email protected]
To unsubscribe from this list, get a password
reminder, or change your subscription options,
visit the list information page at
https://mail.gna.org/listinfo/relax-devel
