Dear James, Many thanks for this! I will follow all the suggestions described above. With best wishes, Andre.
Em qua, 15 de mai de 2019 às 14:59, Holton, James M < jmhol...@slac.stanford.edu> escreveu: > The CCP4 program you are looking for is "cad". Using the "SCALE" keyword > you can apply an overall positive or negative B factor to any mtz data > set. Negative B factors are sharpening, which is what you are trying to do. > > There is also another program called "ecalc", which is specifically > designed for computing normalized structure factors like "U", which is > closely related to "E". > > As for which B factor to apply? Ostensibly the Wilson B factor and the > average atomic B factor should be the same number. The Wilson B, however, > is prone to systematic errors arising from how you decide which resolution > range to fit. There are also details about the distribution of B factors > in the model and the relative abundance of different atomic numbers. > However, I've always found these considerations dwarfed by the errors in > estimating the Wilson B. Depending on what you are trying to accomplish, > you might want to raise your B factor a bit anyway to reduce the overall > noise. > > > As for F000, another article describing its estimation is here: > https://doi.org/10.1073/pnas.1302823110 > > Script from that publication for calculating F000 is here: > https://bl831.als.lbl.gov/END/RAPID/scripts/find_F000.com > > This script requires the CCP4 Suite and the Phenix Suite version 1.6 or > lower. This was the last version of phenix.refine that reported k_sol and > B_sol for the bulk solvent. Without these, you cannot calculate the number > of electrons in the bulk solvent. > > Alternately, if you have run refmac you can look through the log for the > string: "Partial structure 1: scale = " > The "scale =" and "B =" numbers that follow are the k_sol and B_sol for > the bulk solvent. You can then provide these numbers on the command line > of the find_F000.com script above. Then again, if you have already run > refmac it might be simpler to provide the MSKOUT command-line parameter to > refmac. This will output the bulk solvent as a CCP4 map file. Once you > have that, all you need to do is run "mapdump" to report the average value > of the electron density in this map. You multiply this by the k_sol value > from the log and then multiply by the unit cell volume and you now have the > number of electrons in the bulk solvent. Add up all the atomic numbers in > your PDB file (including hydrogen) and you have the rest of the electrons > in your unit cell. The sum of all electrons in one unit cell is F000. > > HTH > > -James Holton > MAD Scientist > > On 5/15/2019 5:52 AM, Andre LB Ambrosio wrote: > > Dear Pavel, thank you so very much for the prompt feedback. > That would be extremely useful if you could script the Uhkl calculation in > CCTBX. > With best regards, > Andre. > > Em qua, 15 de mai de 2019 às 09:47, Pavel Afonine <pafon...@gmail.com> > escreveu: > >> Hi Andre, >> >> >>> - Is there any macromolecular crystallography software that can compute >>> Uhkl as above, or equivalent? >>> >> >> I estimate this can take about 10 minutes to script in CCTBX. I can write >> a script for you, if interested, and send off list. >> >> >>> - If not, would it be more correct to use the Wilson-B or the mean B >>> from the final model? >>> >> >> I'd guess mean B from the model is a better estimate. >> >> - How can F(000) be best estimated from the final model, which is not >>> necessarily always the most complete or best refined? Should we simply add >>> together the number of electrons for all the atoms refined in the >>> asymmetric unit (protein + ligands + solvent)? >>> >> >> See my previous email. >> >> Pavel >> >> > > > -- > Andre LB Ambrosio > > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > > > -- Andre LB Ambrosio ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
