Hello Charles, Thank you so much. The same TorsionDB violation is in almost all structures and I will try this.
Thanks again, Ning > On Aug 28, 2019, at 5:55 AM, Charles Schwieters <[email protected]> > wrote: > > > 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
