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 _______________________________________________________ Reply to this item at: <http://gna.org/support/?3112> _______________________________________________ Message sent via/by Gna! http://gna.org/ _______________________________________________ relax (http://www.nmr-relax.com<http://www.nmr-relax.com/>) This is the relax-devel mailing list relax-devel@xxxxxxx<mailto:relax-devel@xxxxxxx> 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