2D sdf to 3D PDB - bonds

User bc49d72cd2

28-07-2006 11:12:51

hi all,





I am trying to convert my 2D molecules in sdf to 3D PDB. Everything works fine but in the end it seems that I am loosing bond information on pdb. All the double bonds, triple bonds are converted to single bonds. Am i missing something?





Here is the line of command:





molconvert -3:[timelimit]0 pdb xxx.sdf -o xxx.pdb





thanks for the help...


emre

ChemAxon 7c2d26e5cf

28-07-2006 17:18:14

We will check the issue.

ChemAxon a3d59b832c

28-07-2006 20:01:26

Hi Emre,





Our PDB expert is on holiday at the moment, but I will try to do my best.


My colleague may correct my answer when he is back.





It seems to me, that bond type information is missing from the PDB file format. See the PDB specification on the PDB website about the CONECT lines:


http://www.rcsb.org/pdb/file_formats/pdb/pdbguide2.2/part_69.html





Programs usually have two ways of determining the bond types:


1. Protein or nucleic acid atoms correctly described in the PDB file has the residue information available, so standard protein bond types are "known" from the residue information of their atoms.


2. For between non-protein and non-nucleic atoms, bond types can be guessed based on the interatomic distances. Our PDB import can do the same, using the b option:





http://www.chemaxon.com/marvin/doc/user/pdb-doc.html





So, you have to specify the file format and options as pdb:b for import, for example:





msketch xxx.pdb{pdb:b}





I hope this helps,


Szabolcs

ChemAxon efa1591b5a

28-07-2006 22:20:34

Hi,





holiday != not working ;-)





Szabolcs provided detailed and certainly correct answer. There only one comment form me: if possible, do not use PDB to store small molecules. It was designed to best represent macromolecules (peptides and nucleic acids).





Thanks


Miklos

User bc49d72cd2

29-07-2006 10:57:32

hi again,





first of all, thanks to all for your help...





it's actually a good idea to use other formats for small non-protein molecules. However, I guess I can't, but still I will try to do that.





for the connect entries in PDB, I guess there is a way to show bond types (at least double and triple bonds) as:





CONECT 3 6 6 10 2


CONECT 6 3 3 ...





This way, I could say 3rd atom is double bonded to 6th atom. This would actually help me; but still I am not sure it is a correct representation.





...





"msketch xxx.pdb{pdb:b}"





doesn't seem to be usefull for me, because I will process these molecules with other programs to add hydrogens/solubilization parameters and etc. and the bond info will be required. Also, please check the attachements, because with the {pdb:b} it still looks different than the original bonds





thanks...

ChemAxon efa1591b5a

31-07-2006 20:54:11

Hi,





technically it would be possible, but it violates the PDB standard, so we have no plans to implement it.


You may wish to check the PDB file format specification, the CONECT record is discussed here: http://www.pdb.org/pdb/file_formats/pdb/pdbguide2.2/part_69.html





Best regards,


Miklos