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Chapter 50. Greater tutorial 03
50.1. Greater with a list of proteins
In this example we have supplied eleven PDB files in the Greater tutorial 03 directory. The names of the proteins are reported in a file called file.lst. Greater will be used here to perform atom type recognition, to check the 3D protein structures and to perform format conversions. Later on Greater will be used to perform Grid calculation on one of the proteins.
Go from your working directory in the Tutorial03 directory:
cd greater03
Begin by typing:
Greater
the Greater window interface will appear. In order to add the three targets for the computation select:
Target->Add multiple targets (or press the Add Multiple button).
Click on List file and select as input the file.lst. Be sure the filtering level is set to no filtering and then press OK and open. (Alternatively one can open an editor to insert PDB structure. The editor allow simple corrections and cut and paste operations).
Eleven new lines will appear on the Greater window with the eleven PDB files with the status "in progress". Please note the colour of the status bar. Structure 1AAQ is correct and ready for computation. The status bar shows no colour. Conversely the bar's colour turns yellow for 1ABE, 1ACO, 1AHA and 1BAF were warnings have been found, and red for the other macromolecules where serious problems in the structures have been detected. Greater suggests to check and to deeply inspect the structures with red bars.
Just click on the yellow line bar of 1ABE to select the structure and then click the right mouse button on the 1ABE status line. A subwindow appear. Select "view text files" and click on GRINLOUT button on the new window. Two blocks of yellow warning messages will be reported on the window. In this protein the residues ASN2 and LYS306 are incomplete: no side chain was reported for that residues. The missing atoms can be problematic when located close to regions important for the User, or in active site locations. In this case the User must edit the structure and try to correct it, when possible. However, sometime the problematic residues may be located in regions far distant from those of interest, and with a small impact on the focused User region. In the latter case the structure can be accepted as it is.
To check the 3D-location of the problematic residues in the protein structure, click on "Plot conflict". This command shows a 3D interactive representation of the selected protein structure, in which the 3D location of the problematic residues is highlighted with yellow crosses.
Repeat the operations for the 6RSA structure. The red colour bar in this case refers to serious errors that should be corrected before the use of the PDB file in sequential calculations. The 6RSA file contains about two hundred EXTRA ATOM in the residues. It is obvious that any calculation on this structure can be erroneous or misleading.
50.1.1. PDB filtering
From this version the PDB filtering automatically detects errors and introduces appropriate modifications in the PDB file. Although the method is quite sophisticate, the automatic use is not recommended when working with single or few structures. Conversely, the method can bereally useful when a lot of structures are processed as a "set". The filtering level can be customised (see the manual). In this tutorial we are using the semi-automatic filtering, which detects typing errors, non standard nomenclature, atom substitution, non standard position of fragments ATOM or HETATM records and so on, and repairs the PDB file without user assistance. Missing atom in aminoacid residues are still considered errors and a message will be reported. To repeat the importing using semi-automatic filtering select:
Add Multiple button, select the file file.lst and press Open, select the semi-automatic filtering and press OK. This time only two proteins show warnings, and no one reports serius errors. Please check the warnings in 1DWD structure.
50.1.2. Accept the warnings and-or the severe errors
Although may be risky to proceed in the calculation without solving conflicts in the structures, the experienced User may force Greater to do so using the command "Reimport all targets and Accept all errors". This command restarts the importing process for all the targets which were not imported correctly and it accepts all the errors. This command overrides the safety checks and changes the bar status from warning or error to ready. This is intended to be used only after careful inspection of the output files and at the own risk of the User.
After the selection of the probes and the output, the computation can start as reported in Tutorial 02.
You have now completed your third Tutorial. Well done!! We look forwards to hearing from you if we can help in any way.
Please, continue with Tutorial04.
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