Hello Ning--
> For refinement, I have two questions here need your help to figure out. > 1.How to handle the only one tDB violation in my structure? > There is only one violation left in my structure, this violation is > located in transition region between helix and beta-strand, there > were no any experimental restraints for this residue, and the tDB > energy is about 4400 kcal/mol, the tDB energy is still about 4300 > kcal/mol even there is no tDB violations, would you please give me > some suggestions how to figure out this problem? BTW, what is the > acceptable number of tDB violations? A single violation is certainly not usually seen to be a problem. Do note that TorsionDB energies are relative only to other structure calculations on the same protein, and the values do not go to zero. One question is: is this TorsionDB violation seen in all structures? All the same, to more strongly force the torsion atoms in the transition region, a separate TorsionDB term could be created whose selection is only the linker region- and this second term could be given a larger energy scale value. > 2. How to add chainID to pdb file? > I have converted an ensemble of structure files to single pdb using > ens2pdb, and I tried using wwPDB server to do structure validation, > but failed. The errors show that there are missing chainID in this > pdb. I tried using "-remaneSegid" to solve this problem, it didn't > work. How can I add chainID? Could I get the pdb with chainID during > refinement process? > This should do it: ens2pdb -renameSegid 'segid ""' A file*.pdb > toSubmit.pdb Note that the first argument after -renameSegid is an atom selection. best regards-- Charles ######################################################################## To unsubscribe from the XPLOR-NIH list, click the following link: http://list.nih.gov/cgi-bin/wa.exe?SUBED1=XPLOR-NIH&A=1
