On Saturday, October 4, 2003, at 10:21 AM, solomon wrote:
when i open a pdb format file like below: HETATM ................................. HETATM ................................. HETATM ................................. ... ... ... HETATM ................................. then I find that all the HETATM type atoms are bonding each other. All the HETATM need a ter card to split them. As for HETATM type, I think maybe there is some wrong with chimera. best regards gaokeng xiao
Dear Gaokeng, As far as know, Chimera will connect HETATM segments of all standard PDB files (i.e. those distributed by the RCSB) correctly. That being said, Chimera has to do a lot of guessing when it comes to connecting non-standard PDB files (which I'm pretty sure is the kind of file you're talking about here). One thing to keep in mind with HETATMs is that they don't necessarily imply a chain break. Also, they are supposed to have CONECT records detailing their connectivity. So for instance, part of PDB entry 1f1j looks like this: ATOM 3688 OG SER B 602 58.714 25.290 29.976 1.00 66.81 O TER 3689 SER B 602 HETATM 3690 C ACE C 701 29.751 29.860 -0.650 1.00 52.20 C HETATM 3691 O ACE C 701 28.552 30.100 -0.812 1.00 55.72 O HETATM 3692 CH3 ACE C 701 30.801 30.183 -1.675 1.00 52.54 C ATOM 3693 N ASP C 702 30.252 29.308 0.427 1.00 51.48 N The ACE residue in the HETATM records is connected to residue 702 (as detailed in the CONECT records for the file). So in summary, you can have sequences like these where the HETATM residues are connected: ATOM ATOM HETATM HETATM HETATM ATOM ATOM -or- HETATM HETATM HETATM ATOM ATOM Now the really big problem is that the SCOP web site returns "PDB" files with just these kinds of sequences but with _no_ CONECT records! So, Chimera guesses as best it can in this situation. The rule of thumb that it uses is that HETATMs are connected unless they occur somewhere after a TER card with no intervening ATOM record. Explicit CONECT records can add connectivity. So for your file of all HETATMs where nothing should be connected, there is a silver lining: in order to get nothing connected you just have to add a _single_ TER card at the beginning of the file, like this: TER HETATM ................................. HETATM ................................. HETATM ................................. --Eric