[Present interactions][PCA-loadings][PLS-loadings][PLS-partial weights][PLS-coefficients]
When the datafile imported into GOLPE contains a collection of ligand-residue interactions computed with AMBER or DISCOVER it is not possible to represent regular Grid plots. The variables are not associated to a certain point in a grid. Instead they are linked to a certain residue of a protein.
In these cases GOLPE can map the interaction energies or the results of the PCA and PLS models on the structures, producing colored structures in which the residues are colored in blue when the associated variable takes a low value and in red when the associated variable takes a high value, following a continuum blue to red color spectrum. to represent intermediate values.
GOLPE does this task including the value of the variable in the Temperature factor field of a PDB file (columns 61-66) and then starting the Grid plot application for representing this structure. When used in this way, the structure is colored "by property" by default, showing the color coded variable. Follow this link for a full description of the options and commands of this application. Alternatively, the modified PDB files can be imported in other molecular modeling packages, like InsightII, to produce different type of colored surfaces, etc...
All these plots require the input of a molecular structure that must contain residues with numbers matching the names given to the variables during the import. If the datafile represents the interaction of different ligands with the same receptor, there should be no problem on mapping the variables on a PDB file of this receptor. On the contrary, if the datafile contains many different proteins and homology keys were used, it is important to check the HomologyLog file to make sure that the names of the variables will match the names of the residues in the PDB file. Some manual editing of the residues names in the PDB structure could be required in this case.
Notice that this is a "tear-off menu", if you click on the dotted line on top of the menu you will transform the submenu in an independent window which will remain open until you specifically close it. This allows a fast access to the plots and is particularly useful when you plan to open many plots at the same time.
IMPORTANT: When the Grid plots represent this kind of data the plot intercommunication mechanism described as "clipboard" adapts itself in such a way that the variables selected in profiles or 2D plots produce to highlight the corresponding residues.
Plot>>>structure plots>>>Present interactions
This command produces a structure plot representing actual ligand-receptor interaction energies. The residues in the structure will be colored from blue (low values) to red (high values) according to the value of the corresponding variable. The User must chose the object and the block to use for the representation.
Find...
Press this button to open a standard file selection dialog. The file selected will be then presented in the input line immediately to the left to the button pressed. See the File>>>Open data file command for details about the file selection dialog.
original PDB file (.pdb)
Name of the file containing the structure of the receptor in PDB format. This file will be read but not written.
modified PDB file (.pdb)
Name of the output file. It will be identical to the original file but the contents in the Temperature factor field (columns 61-66). These will be replaced by the value of variable to represent, arbitrarily scaled. If no name is entered, the default file name (TMP.pdb) will be used.
block
Block of variables to use. Different blocks can represent steric or electrostatic energies of interaction, hydrogen bonds, etc... as defined when the data was first imported.
Objects:
The plot will represent the ligand-receptor interaction energy for the selected objects. Select one object from the list clicking on it.
When the dialog window shows the desired settings press the Create and Plot button to create the modified PDB file and start automatically the plotGrid application, or press the Create button to create the PDB file without starting plotGrid. Press the Exit button to close the dialog.
Plot>>>structure plots>>>PCA-loadings
Plot>>>structure plots>>>PLS-loadings
Plot>>>structure plots>>>PLS-partial weights
Plot>>>structure plots>>>PLS-coefficients
All these command produces structure plots representing different results of PCA or PLS models. The residues in the structure will be colored from blue (low values) to red (high values) according to the value of the corresponding variable. The User must chose the LV or model dimensionality and the block to use for the representation.
Find...
Press this button to open a standard file selection dialog. The file selected will be then presented in the input line immediately to the left to the button pressed. See the File>>>Open data file command for details about the file selection dialog.
original PDB file (.pdb)
Name of the file containing the structure of the receptor in PDB format. This file will be read but not written.
modified PDB file (.pdb)
Name of the output file. It will be identical to the original file but the contents in the Temperature factor field (columns 61-66). These will be replaced by the value of variable to represent, arbitrarily scaled. If no name is entered, the default file name (TMP.pdb) will be used.
model dimension
Select the LV or model dimensionality to use for obtaining the chemometrical property (PCA loading, PLS loading, PLS partial weight or PLS coefficient) that will be represented in the structure plot
block
Block of variables to use. Different blocks can represent steric or electrostatic energies of interaction, hydrogen bonds, etc... as defined when the data was first imported.
When the dialog window shows the desired settings press the Create and Plot button to create the modified PDB file and start automatically the plotGrid application, or press the Create button to create the PDB file without starting plotGrid. Press the Exit button to close the dialog.