Re: [ccp4bb] Off topic: PKa of protein-DNA complex.
Dear Yang, There are several. I also commend to you:- Crystallography Reviews, Volume 15, Issue 4 October 2009 , pages 231 - 259 An evaluation review of the prediction of protonation states in proteins versus crystallographic experiment Authors: Stuart J. Fisher; James Wilkinson; Richard H. Henchman; John R. Helliwell available at:- http://www.informaworld.com/smpp/content~db=all~content=a915050320~tab=content~order=page Best wishes, John Prof John R Helliwell DSc On Thu, Aug 12, 2010 at 6:11 PM, yang li robertcatru...@gmail.com wrote: Hi, Is there any server or program can calculate the theoretic PKa of the protein-DNA complex? Given the structure of the protein and the sequence of the DNA. Any suggestion will be appreciated! Best Yang -
Re: [ccp4bb] PEG in the pdb? zero occ
I agree that zero occupancy is a bit ugly, but useful when not sure whether you will ever see that LYS.. But I dont think it wlll displace bulk solvent - at least not in REFMAC where an atom with occ=0.0 will not contribute to the atom map. And I expect this is true for all other structure factor calculations using various programs.. Eleanor Ed Pozharski wrote: On Thu, 2010-08-12 at 08:57 +, MARTYN SYMMONS wrote: Zero occupancy is generally a deprecated way of dealing with missing density as it is confusing for less experienced user of the coordinates. I think zero occupancy can be useful during refinement as the atoms help fill space (or for example satisfy NCS restraint format requirement) but then these atoms can be stripped out before deposition. They should in any case never be included in B-factor refinement as they will skew the statistics and possibly the B-factor restraint model. Zero occupancy may be a bad idea for yet another reason - the atoms will displace bulk solvent and produce what is essentially a hole in the structure. It may be justified if you are trying to fill the empty internal cavities, but for atoms missing from density it seems like a wrong approach.
Re: [ccp4bb] PEG in the pdb? zero occ
Perhaps I was confused by the refinement exclude keyword which explicitly says that atoms excluded from refinement will contribute to the mask calculation. Thanks for the correction. I would still object to the zero-occupancy atoms on semantic grounds. Partial occupancy means that an atom spends this fraction of time an this position. Zero occupancy thus says that the atom is never near this particular point in space, which for disordered side chains is likely untrue. Cheers, Ed. I agree that zero occupancy is a bit ugly, but useful when not sure whether you will ever see that LYS.. But I dont think it wlll displace bulk solvent - at least not in REFMAC where an atom with occ=0.0 will not contribute to the atom map. And I expect this is true for all other structure factor calculations using various programs.. Eleanor Ed Pozharski wrote: On Thu, 2010-08-12 at 08:57 +, MARTYN SYMMONS wrote: Zero occupancy is generally a deprecated way of dealing with missing density as it is confusing for less experienced user of the coordinates. I think zero occupancy can be useful during refinement as the atoms help fill space (or for example satisfy NCS restraint format requirement) but then these atoms can be stripped out before deposition. They should in any case never be included in B-factor refinement as they will skew the statistics and possibly the B-factor restraint model. Zero occupancy may be a bad idea for yet another reason - the atoms will displace bulk solvent and produce what is essentially a hole in the structure. It may be justified if you are trying to fill the empty internal cavities, but for atoms missing from density it seems like a wrong approach. -- Edwin Pozharski, PhD University of Maryland, Baltimore
Re: [ccp4bb] what is the scaling factor generally used when calculating R factor?
Hi Hailiang, I posted this several times and here is another one.. The exact formula and all the related details are here: http://cci.lbl.gov/~afonine/FandR/Fmodel_and_Rfactor.pdf (there is a small typo in the formula found by Lothar, but I leave it for you to find -:) ) Also, here is another discussion related to R-factor mismatch that you might find helpful: http://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg16463.html Let me know if you have any questions. Finally, to answer your question, I would suggest to have a look at: /J. Appl. Cryst./ (2010). *43*, 669-676 which discusses the observations you have. Pavel. On 8/14/10 7:03 PM, Hailiang Zhang wrote: Hi, I have a very simple question about the R factor. I was trying to reproduce the R factor reported in the PDB file. I used phenix.fmodel incorporating solvent model, anisotropic scaling etc to calculate Fc, but frequenlty it doesn't match the PDB R factor. Now I am wondering what is the scaling factor generally used when calculating R factor? Thanks a lot! Best Regards, Hailiang
