Dear Sasha, i try to answer one by one your question :
1) Not sur to understand what you mean by "validate DNA constraints", if it's about the geometry parameters liken angle bond length, you have to use Moleprobity for example. 2) Fitting DNA in density, you can use coot, it's exactly the same spirit as protein building. You have to be careful of the possible "special" case like hoogsteen bases pair, or fliping base, but out of that, most of the DNA building is comparable with protein. 3) The kind of parameters, is the same as for protein. But, you have to be carefull that refmac "understand" well that you pdb file contain DNA. I do not use Refmac, but i think with the right library for restraint (the same as ccp4 or coot) it should be OK. If it's possible, sometimes it could be good to use TLS group for DNA refinement. 4) I think it's always good to use up-to-date version of the programm. You can use the ccp4 method to install all the programm at the same time. But if it's timpossible for you, i can't rememeber which version it was, but i worked with DNA protein structure 5 years ago, and it was already more or less good. Hope to help. ________________________________________ De : CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] de la part de Sasha Pausch [sashapau...@gmail.com] Envoyé : mercredi 30 juillet 2014 19:45 À : CCP4BB@JISCMAIL.AC.UK Objet : [ccp4bb] Protein-DNA structure solution Hello CCP4bb I am solving a 3.2A resolution crystal data for a protein DNA complex. I would like to know- 1) How to validate the DNA constraints in the crystal structure? 2) How to fit DNA into density? How different it is from protein fitting into density? 3) What kind of parameters to consider for refining DNA in Refmac for a Protein-DNA complex? 4) Which versions of refmac and COOT support DNA refining and model building? Thank you in advance, Sasha Pausch
