6.14 Merge with another file

VEGA ZZ can merge the loaded molecule with one or more parts of another molecule. Choosing File -> Merge menu item, it's possible select the file to merge (source) with the molecule already in memory (target). Trough a dialog box, it's possible select the fields included in the source molecule that will be read to merge with the target:

What merge ?

The source and the target molecules must be compatible to merge them, otherwise an error message is shown (they must have the same number of atoms). It's possible to merge source and target molecules with a different number of atoms, selecting an atom subset of the target and checking Consider selected atom only. Obviously, the subset target must be compatible with the source.
The All and None buttons are useful to check or uncheck all fields at once. The Merge button performs the merge, and the Cancel button aborts the operation without changes in the target molecule.
Not all merge fields are enabled because not all file formats contains all information. The following table highlights the fields that can be merged for each source file format:

 

Format Elements Atom names Atom types Atom charges Residue names Residue numbers Chain IDs Segments Molecule IDs Coordinates Connectivity Constraints
Alchemy              
AMMP            
CAR (old/new)        
ChemSol                
CIF/mmCIF       *  
CML 1.0/2.0                
Chem3D              
CPMD XYZ                    
CRD            
CRT                
CSSR              
GAMESS                  
Guassian input                  
Gaussian output                  
Gromos/Gromacs              
HyperChem        
IFF/RIFF 32/64 bit
MDL Molfile                
MDL Extended Molfile                
Mol2      
Mopac                  
MSF (Quanta)            
PDB       *  
PDB 2.2       *  
PDBA   *  
PDBF   *  
PDBQ       *  
PQR       *  
PQR XML            
QMC              
TINKER XYZ              
X-Plor PSF          
XYZ                    

* The connectivity can be merged only if it's present in the file.

WARNING:

  1. Isn't possible to merge molecules with a different number of atoms. If you want force the merge and the target atoms are more than source atoms, you can select a target atom subset and check Consider selected atom only.

  2. If source and target have got the same number of atoms, but differences in the element position are detected, a warning message is shown, allowing to choose to continue or to abort the merge.