This example is one of a few that shows how the PDBX library can be used to interface with Chimera, such that useful and interesting aspects of a molecule, e.g., certain connections among certain atoms, obtainable via parsing CIF files, can be located and used as the subject of a Chimera render or animation. This particular example shows how to find connections of certain types that involve certain entities by retrieving and iterating over the struct_conn category, which delineates connections in a molecule, and using the struct_asym and entity categories to determine the entity types involved in each connection. In this case, polymer-polymer covalent bonds are sought for Chimera to emphasize and animate. It is easy to extend this example, say, to handle a set of connection types of interest involving certain entity pairings, each to be displayed in a different color in Chimera, or to focus on connection types of interest only among certain atoms and entities of interest.
Save Connections2.py and the CIF data file. Run
python Connections2.py /path/to/file.cif, which generates a
/path/to/5HVP.com file which you can open with
Alternatively, you can save the script with Connections2.py, set the Chimera path, and run
which will automate the process
from pdbx.reader.PdbxContainers import ContainerBase
from pdbx.reader.PdbxContainers import DataCategory
getObj(self, name)Returns the DataCategory object specified by name.
getRowCount(self)Returns the number of rows in the category table.
getValue(self, attributeName=None, rowIndex=None)Returns the value of the attribute attributeName at row index rowIndex.
""" Connections2.py For some CIF file, generate a Chimera command (COM) file to iterate through and emphasize connections of specific connection types and involving specific types of entities. As an example, we will look for polymer-polymer covalent linkages. Method: For connections of interest, determine each partner atom's entity type by indexing into the struct_asym category table with the atom's asym_id to determine its entity ID. Then, index into the entity category table to determine its entity type. Lines with superscriptions contain footnoted references or explanations. """ from os.path import splitext from pdbx.reader.PdbxReader import PdbxReader from pdbx.reader.PdbxContainers import * from sys import argv, exit def prepareOutFile(file, name) : file.write("windowsize 500 500\n") # Set the window size to 500 x 500 px file.write("open %s\n" % name) # Open the CIF file file.write("preset apply pub 4\n") # Apply publication preset #4 file.write("color white\n") # Color the entire molecule white file.write("set bg_color gray\n") # Color the background gray file.write("repr bs\n") # Represent the atoms in ball-and-stick format file.write("savepos fullview\n") # Remember this position (the full view of the molecule) def writeConnection(selection, file) : sel = " | ".join(selection) file.write("sel %s\n" % sel) # Select the two partner atoms file.write("color byelement sel\n") # Color them by element file.write("sel sel za<3.0; wait 20\n") # Further select all atoms within 3.0 angstroms of the partner atoms file.write("focus sel; wait 25; ~disp ~sel\n"); # Focus in on the selection and hide all non-selected atoms file.write("turn y 5.25 68; wait 68\n") # Perform a basic y-axis turning animation file.write("disp ~sel; reset fullview 20\n") # Return to the full molecule view file.write("color white sel; ~sel; wait 20\n") # Uncolor and drop the selection # Check for improper usage if len(argv) != 2 : exit("Usage: python Connections2.py /path/to/file.cif"); # Open the CIF file cif = open(argv) # Create a list to store data blocks data =  # Create a PdbxReader object pRd = PdbxReader(cif) # Read the CIF file, propagating the data list pRd.read(data) # Close the CIF file, as it is no longer needed cif.close() # Retrieve the first data block block = data # Get the struct_conn category table, which delineates connections1 struct_conn = block.getObj("struct_conn") # Get the struct_asym category table, which details structural elements in the asymmetric unit2 struct_asym = block.getObj("struct_asym") # Get the entity category table, which details the molecular entities present in the crystallographic structure3 entity = block.getObj("entity") # Use the CIF file pathname to generate the Chimera command file (.COM) pathname (file, ext) = splitext(argv) comFileName = file + ".com" # Open the COM command file for writing comFile = open(comFileName, 'w'); # Write out some basic Chimera initialization commands prepareOutFile(comFile, argv) # Iterate over the rows in struct_conn, where each row delineates an interatomic connection for index in range(struct_conn.getRowCount()) : # A container to hold each partner atom's entity type entities =  # A container to hold each partner atom's Chimera selection string selection =  # Verify that the connection is covalent4 if struct_conn.getValue("conn_type_id", index) == "covale" : # Analyze the current row twice, once per partner for partner in ["ptnr1_", "ptnr2_"] : # Retrieve the partner atom's asym_id, with which we will index into struct_asym asym_id = struct_conn.getValue(partner + "auth_asym_id", index) # Add this atom's Chimera selection string to the container5,6 selection.append(":%s,%s.%s@%s.%s" % (struct_conn.getValue(partner + "auth_seq_id", index), struct_conn.getValue(partner + "auth_comp_id", index), asym_id, struct_conn.getValue(partner + "label_atom_id", index), struct_conn.getValue("pdbx_" + partner + "label_alt_id", index))) # Holds the atom's entity ID, which we will find in the struct_asym category table entityID = 0 # Find the atom's entity ID in the struct_asym category table for i in range(struct_asym.getRowCount()) : if struct_asym.getValue("id", i) == asym_id : entityID = (int)(struct_asym.getValue("entity_id", i)) break # Retrieve and store the atom's entity type entities.append(entity.getValue("type", entityID - 1)) # Write satisfactory entity pairings to the COM file (in this case polymer-polymer) if entities == "polymer" and entities == "polymer" : writeConnection(selection, comFile) # Write out the Chimera close command comFile.write("stop\n") # Close the COM file as all connections have been processed comFile.close()