As noted in post Rectangular block expressed in MDL molfile format, I added the -mol option (in v2.1) to convert 3DNA’s native alchemy to the better-supported MDL molfile format, to make the characteristic schematic representations more widely accessible. Along the line, I have recently further augmented alc2img with the -pdb option to transform alchemy to the PDB format.
While the macromolecular PDB format is certainly not convenient for specifying linkage details of small molecules, it’s nevertheless the best-documented and by far the most widely supported than molfile or alchemy in currently available molecular viewers. For example, the PDB format is consistently supported in Jmol, PyMOL, RasMol, DeepView, and UCSF Chimera. Moreover, the PDB format does have the CONECT section to provide information on atomic connectivity:
The CONECT records specify connectivity between atoms for which coordinates are supplied. The connectivity is described using the atom serial number as shown in the entry. CONECT records are mandatory for HET groups (excluding water) and for other bonds not specified in the standard residue connectivity table.
The alc2img -pdb option takes advantage of the CONECT records and specifies all ‘bond’ linkages explicitly. The usage is very simple — take the standard base-pair rectangular block file (‘Block_BP.alc’) as an example, the conversion can be performed as below:
alc2img -pdb Block_BP.alc Block_BP.pdb
Content of ‘Block_BP.alc’
12 ATOMS, 12 BONDS
1 N -2.2500 5.0000 0.2500
2 N -2.2500 -5.0000 0.2500
3 N -2.2500 -5.0000 -0.2500
4 N -2.2500 5.0000 -0.2500
5 C 2.2500 5.0000 0.2500
6 C 2.2500 -5.0000 0.2500
7 C 2.2500 -5.0000 -0.2500
8 C 2.2500 5.0000 -0.2500
9 C -2.2500 5.0000 0.2500
10 C -2.2500 -5.0000 0.2500
11 C -2.2500 -5.0000 -0.2500
12 C -2.2500 5.0000 -0.2500
1 1 2
2 2 3
3 3 4
4 4 1
5 5 6
6 6 7
7 7 8
8 5 8
9 9 5
10 10 6
11 11 7
12 12 8
Content of ‘Block_BP.pdb’
REMARK 3DNA v2.1 (c) 2012 Dr. Xiang-Jun Lu (http://x3dna.org) HETATM 1 N ALC A 1 -2.250 5.000 0.250 1.00 1.00 N HETATM 2 N ALC A 1 -2.250 -5.000 0.250 1.00 1.00 N HETATM 3 N ALC A 1 -2.250 -5.000 -0.250 1.00 1.00 N HETATM 4 N ALC A 1 -2.250 5.000 -0.250 1.00 1.00 N HETATM 5 C ALC A 1 2.250 5.000 0.250 1.00 1.00 C HETATM 6 C ALC A 1 2.250 -5.000 0.250 1.00 1.00 C HETATM 7 C ALC A 1 2.250 -5.000 -0.250 1.00 1.00 C HETATM 8 C ALC A 1 2.250 5.000 -0.250 1.00 1.00 C HETATM 9 C ALC A 1 -2.250 5.000 0.250 1.00 1.00 C HETATM 10 C ALC A 1 -2.250 -5.000 0.250 1.00 1.00 C HETATM 11 C ALC A 1 -2.250 -5.000 -0.250 1.00 1.00 C HETATM 12 C ALC A 1 -2.250 5.000 -0.250 1.00 1.00 C CONECT 1 2 4 CONECT 2 1 3 CONECT 3 2 4 CONECT 4 1 3 CONECT 5 6 8 9 CONECT 6 5 7 10 CONECT 7 6 8 11 CONECT 8 5 7 12 CONECT 9 5 CONECT 10 6 CONECT 11 7 CONECT 12 8 END
