Re: r11120 - /branches/bieri_gui/gui_bieri/analyses/auto_model_free.pyRe: r11120 - /branches/bieri_gui/gui_bieri/analyses/auto_model_free.pyMaybe the heading for the dialog could be changed to "Parameter file columns"? Or change "Molecule Name" to "Molecule name column"? I don't think it is obvious that these are column numbers, and this will result in many confused relax-user emails. I think we should make this more obvious, and it won't take much to do this. As relax automatically sets the columns in its output files, if you have a sequence file which contains first the atom name and then the molecule name, then this will cause the GUI code to fail. The columns will be different. Or if you only have atom names in your sequence file, i.e. your molecule has no residues, this will also fail. Or if the sequence data is simply column 1 for the protein residue number and column 2 for the residue name, then this should also trigger the problem. From what I can see from assemble_data() in gui_bieri.analyses.auto_model_free, this will cause a big bug. The only way this can work is if the user inputs sequence data in exactly the correct format. I'll have to test this to confirm. Could you try changing the column ordering in the initial sequence file and see what happens? Regards, Edward On 28 April 2010 00:26, Michael Bieri <michael.bieri@xxxxxxxxxxxxx> wrote:
I would leave it as it is. The settings dialogs are more for advanced users. Instead, I would design a import sequence dialog, as mentioned before. The default settings are for a whole analysis using relax (noe, r1 and r2 parameter files are created with relax and in the corresponding format, only the sequence could be read independently. So far, it has to be in the first column). What do you think? Cheers Edward d'Auvergne wrote:Hi, I think for the parameter file settings dialog box we need to be clearer. I think there could be some text introduced before the text entry boxes explaining what this is. Something like: "Please enter the column numbers of your data files corresponding to the following molecular information:" This dialog could in the next iteration be used for each *.read() user function call. This would be more useful as the sequence could be read out of a PDB file, and the relaxation data could come from Sparky output files, or Excel csv files the user used to fit the data with. I think we could also introduce in this dialog the column separator, with explanatory text, which defaults to 'whitespace', but could be changed to ',', '\t', etc. This could even be a pre-select list the user chooses from. What do you think? Cheers, Edward On 22 April 2010 06:43, <michael.bieri@xxxxxxxxxxxxx> wrote:Author: michaelbieri Date: Thu Apr 22 06:43:24 2010 New Revision: 11120 URL: http://svn.gna.org/viewcvs/relax?rev=11120&view=rev Log: Parameter file settings are used and can be changed. Modified: branches/bieri_gui/gui_bieri/analyses/auto_model_free.py Modified: branches/bieri_gui/gui_bieri/analyses/auto_model_free.py URL: http://svn.gna.org/viewcvs/relax/branches/bieri_gui/gui_bieri/analyses/auto_model_free.py?rev=11120&r1=11119&r2=11120&view=diff ============================================================================== --- branches/bieri_gui/gui_bieri/analyses/auto_model_free.py (original) +++ branches/bieri_gui/gui_bieri/analyses/auto_model_free.py Thu Apr 22 06:43:24 2010 @@ -545,6 +545,9 @@ data.bond_length = 1.02 * 1e-10 data.csa = -172 * 1e-6 + # Import parameter file settings. + param = ds.relax_gui.file_setting + # The relaxation data (data type, frequency label, frequency, file name, dir, mol_name_col, res_num_col, res_name_col, spin_num_col, spin_name_col, data_col, error_col, sep). These are the arguments to the relax_data.read() user function, please see the documentation for that function for more information. data.relax_data = [] for i in range(3): @@ -557,9 +560,9 @@ continue # Append the relaxation data. - data.relax_data.append(['R1', str(frq), float(frq)*1e6, files[1], None, None, 2, 3, 4, 5, 6, 7, None]) - data.relax_data.append(['R2', str(frq), float(frq)*1e6, files[2], None, None, 2, 3, 4, 5, 6, 7, None]) - data.relax_data.append(['NOE', str(frq), float(frq)*1e6, files[0], None, None, 2, 3, 4, 5, 6, 7, None]) + data.relax_data.append(['R1', str(frq), float(frq)*1e6, files[1], None, None, param[1], param[2], param[3], param[4], param[5], param[6], None]) + data.relax_data.append(['R2', str(frq), float(frq)*1e6, files[2], None, None, param[1], param[2], param[3], param[4], param[5], param[6], None]) + data.relax_data.append(['NOE', str(frq), float(frq)*1e6, files[0], None, None, param[1], param[2], param[3], param[4], param[5], param[6], None]) # Unresolved resiudes file = DummyFileObject() _______________________________________________ relax (http://nmr-relax.com) This is the relax-commits mailing list relax-commits@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-commits_______________________________________________ relax (http://nmr-relax.com) This is the relax-devel mailing list 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_______________________________________________ relax (http://nmr-relax.com) This is the relax-devel mailing list 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