6.19 Merge with another file

VEGA ZZ can merge the molecule in the current workspace with one or more parts of another molecule. Choosing File Merge menu item, you can select the file to merge (source) with the molecule already in memory (target). In the dialog box, you can choose the fields included in the source molecule that will be read to be merged with the target:

 

What merge ?

 

The source and the target molecules must be compatible, 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 have the same number of atom of the source.
All and None buttons are useful to check/uncheck all fields at once. Merge button performs the merge.
Not all merge fields could be enabled, because not all file formats contains all information. The following table shows 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 Dot Dot   Dot           Dot Dot  
AMMP Dot Dot   Dot Dot         Dot Dot  
AutoDock 4 PDBQT Dot Dot Dot Dot Dot Dot Dot     Dot    
CAR (old/new) Dot Dot Dot Dot Dot Dot   Dot   Dot    
Chem3D Dot Dot Dot             Dot Dot  
ChemDraw CDX Dot                 Dot Dot  
ChemSol Dot Dot   Dot           Dot    
CIF/mmCIF Dot Dot     Dot Dot Dot Dot   Dot Dot*  
CML 1.0/2.0 Dot Dot               Dot Dot  
CPMD XYZ Dot                 Dot    
CRD Dot Dot   Dot Dot Dot       Dot    
CRT Dot Dot               Dot Dot  
CSSR Dot Dot   Dot           Dot Dot  
Fasta Dot Dot     Dot Dot       Dot Dot  
EMPIRE Dot     Dot           Dot    
GAMESS Dot     Dot           Dot    
Guassian input Dot     Dot           Dot    
Gaussian output Dot     Dot           Dot    
Gromos/Gromacs Dot Dot     Dot Dot       Dot    
HyperChem Dot Dot Dot Dot Dot Dot   Dot   Dot    
IFF/RIFF 32/64 bit Dot Dot Dot Dot Dot Dot Dot Dot Dot Dot Dot Dot
LiGen binary/text pocket Dot Dot Dot   Dot         Dot    
MDL Molfile Dot Dot               Dot Dot  
MDL Extended Molfile Dot Dot               Dot Dot  
Mol2 Dot Dot Dot Dot Dot Dot Dot     Dot Dot  
Mopac cartesian Dot     Dot           Dot    
Mopac internal Dot     Dot           Dot    
Mopac Gaussian Z-matrix Dot                 Dot    
MSF (Quanta) Dot Dot   Dot Dot Dot       Dot    
NAMD binary                   Dot    
PDB Dot Dot     Dot Dot Dot Dot   Dot Dot*  
PDB 2.2 Dot Dot     Dot Dot Dot Dot   Dot Dot*  
PDBA Dot Dot Dot Dot Dot Dot Dot Dot   Dot Dot*  
PDBF Dot Dot Dot Dot Dot Dot Dot Dot   Dot Dot*  
PDBL Dot Dot     Dot Dot       Dot    
PDBQ / Vina Dot Dot     Dot Dot Dot Dot   Dot Dot*  
PQR Dot Dot     Dot Dot Dot Dot   Dot Dot*  
PQR XML Dot Dot   Dot Dot Dot       Dot    
QMC Dot Dot   Dot           Dot Dot  
Spillo RBS Dot Dot     Dot Dot Dot     Dot    
TINKER XYZ Dot Dot Dot             Dot Dot  
X-Plor PSF Dot Dot Dot Dot Dot Dot         Dot  
XYZ Dot                 Dot    

* 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 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.