[ccp4bb] Adding TER card in PDB file

Hi all, I will greatly appreciate your help for the following: I am getting an error of not having TER card at the end of chain during precheck of PDB deposition. Hence, I would like to add TER card at the end of chain in my PDB file. Adding TER card manually is not problem but how to add "Atom

[ccp4bb] solvent excluded area and binding affinity

Hi All, I would greatly appreciate your comments on following: I would like to know the quantitative relation between "Solvent excluded area" (calculated by Areaimol at CCP4i) and "free energy of binding" or "binding affinity" of the DNA-protein or protein-protein interactions. Is there some free

[ccp4bb] align DNA structures

Hi all, I will highly appreciate your help regarding following: How to align two DNA structures in Pymol or Coot or any other softwares? ( I tried regular "align" in Pymol, but it doesn't work for DNA; it works great for protein structures.) Thanks a lot in advance ! Mike

[ccp4bb] Rfree in similar data set

Hi all, I will appreciate your comments on the following case: I have two datasets from the same or identical crystals. Initially, I refine a structure against the first data set and later on switch to another dataset for further refinements. Do you think, my Rfree will be biased as Rfree refle

[ccp4bb] DNA model building

Hi all, I would like to build the DNA (expected to be much deviated from standard B-DNA) into the electron density of our DNA-protein complex at ~3.0 A resolution by adjusting the torsion angles of the nucleotides. Any free software to do that? any other suggestions? thanks in advance. Mike