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<mailto: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 ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
