[ccp4bb] alternative conformation refinement by phenix
Hi all, I am refining a DNA-protein complex structure by phenix. My protein is a nuclease and the DNA bound to protein is a mixture of the substrate and product. Partial DNA was cleavaged by the protein and others is keep a un-cleavaged strand. I am trying to rerine this mixture with phenix. My DNA sequence is *AG*NN. Half of DNA was cleavaged between AG and half DNA keep a uncleavaged strand as my sequence. Nucleic acid AG have two conformations in this structure and a water molecule located close to the phosphate group when it uncleavaged. I defined AADE and BADE, AGUA and BGUA with 0.5 occupancy. I also give the water mentioned above 0.5 occupancy. I try to refine this structure by phenix but failed. Please give me some suggestion about this DNA alternative confromation refinement? How should I define the occ.params file? Thank you in advance. Lisa
Re: [ccp4bb] alternative conformation refinement by phenix
On Fri, 2012-05-25 at 19:01 +0800, LISA wrote: try to refine this structure by phenix but failed. Not that I have an answer to your question, but you have to describe what you mean by failed. Maybe you should try refmac. Will also make your inquiry better suited for this forum (although it's perfectly ok to ask non-CCP4 questions and phenix developers hear you anyway). -- I'd jump in myself, if I weren't so good at whistling. Julian, King of Lemurs
Re: [ccp4bb] alternative conformation refinement by phenix
Hi Lisa, I am not an phenix expert and, as Ed mentioned, from the message that refinement failed it is hard to figure out what or how it failed. Nevertheless, here are a few suggestions. -do your alternate conformations make consistent sets? E.g. do the AADE and AGUA both belong to the linked set and the BADE and BGUA both belong to the broken set? -I would give the water a lower then 0.5 occupancy. For refmac it is claimed that the steric repulsions are switched off between atoms if the combined occupancies are less or equal to one. -tackle one problem at a time, i.e. remove the water first and see that the conneced/broken strands are being refined correctly. Once that is ok, you could add the water. my two cents, Herman From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of LISA Sent: Friday, May 25, 2012 1:02 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] alternative conformation refinement by phenix Hi all, I am refining a DNA-protein complex structure by phenix. My protein is a nuclease and the DNA bound to protein is a mixture of the substrate and product. Partial DNA was cleavaged by the protein and others is keep a un-cleavaged strand. I am trying to rerine this mixture with phenix. My DNA sequence is AGNN. Half of DNA was cleavaged between AG and half DNA keep a uncleavaged strand as my sequence. Nucleic acid AG have two conformations in this structure and a water molecule located close to the phosphate group when it uncleavaged. I defined AADE and BADE, AGUA and BGUA with 0.5 occupancy. I also give the water mentioned above 0.5 occupancy. I try to refine this structure by phenix but failed. Please give me some suggestion about this DNA alternative confromation refinement? How should I define the occ.params file? Thank you in advance. Lisa
Re: [ccp4bb] alternative conformation refinement by phenix
Hi LISA, if you send me more details I might be able to address your questions (as Phenix developer). Though a better place to post your Phenix related questions is a Phenix mailing list, not CCP4bb. P.S. Ugh, I find Ed's reply totally.. how to say it softer using my non-native-English... embarrassing. All the best, Pavel On Fri, May 25, 2012 at 4:01 AM, LISA science...@gmail.com wrote: Hi all, I am refining a DNA-protein complex structure by phenix. My protein is a nuclease and the DNA bound to protein is a mixture of the substrate and product. Partial DNA was cleavaged by the protein and others is keep a un-cleavaged strand. I am trying to rerine this mixture with phenix. My DNA sequence is *AG*NN. Half of DNA was cleavaged between AG and half DNA keep a uncleavaged strand as my sequence. Nucleic acid AG have two conformations in this structure and a water molecule located close to the phosphate group when it uncleavaged. I defined AADE and BADE, AGUA and BGUA with 0.5 occupancy. I also give the water mentioned above 0.5 occupancy. I try to refine this structure by phenix but failed. Please give me some suggestion about this DNA alternative confromation refinement? How should I define the occ.params file? Thank you in advance. Lisa
