Hello, yes, I tangled with this about a year ago so my memory is a bit vague. I think you can get the mean protein B-factor from the refmac log file, but for ligands, etc, I had to write a script. I can dig it out this evening if that's any use.
Best wishes, Jon Cooper Sent from ProtonMail mobile -------- Original Message -------- On 26 Nov 2020, 14:10, Julia Griese wrote: > Hi all, > > I’m writing a Table 1 and getting a bit confused when it comes to number of > atoms and average B factors. Refmac has these in the table in the GUI, but > the atom numbers in that table seem to include H, and I’m only interested in > non-H atoms. > As an example, the PDB file says: > > REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. > REMARK 3 ALL ATOMS : 8351 > > Which agrees with the total count minus TER cards, so that seems to be > correct. However, the table in the GUI for this refinement run looks like > this: > > Chain mean B<br/>(No. atoms) > > AAA > 41.4( 2193 ) > > BBB > 57.7( 3499 ) > > CCC > 57.7( 3499 ) > > DDD > 41.7( 2212 ) > > EEE > 60.3( 923 ) > > FFF > 60.6( 920 ) > > aaa > 55.4( 1323 ) > > ddd > 56.0( 1346 ) > > GGG > 34.3( 1 ) > > GaG > 42.7( 1 ) > > GbG > 34.3( 1 ) > > GcG > 40.1( 1 ) > > GdG > 40.6( 1 ) > > GeG > 35.8( 1 ) > > GfG > 34.2( 1 ) > > GgG > 43.2( 1 ) > > HHH > 40.6( 136 ) > > You can easily see that this adds up to a lot more than 8351 atoms. The > numbers for the G chain (metal ions) and the H chain (water) are correct, > whereas the numbers for the macromolecule chains appear to include H. (If I > run a refinement with H output to the final file, I get approximately the > same number of atoms in total, though not quite.) But what I’m really > interested in is of course the number of non-H atoms per chain. I don’t want > to count all the atoms by hand… > > I used to use baverage to calculate average B factors (and that would also > give me the number of non-H atoms per chain), but can’t get that to work on > the command line and can’t find it in the i2 GUI. I don’t have the old ccp4i > anymore. > > So if anyone could either tell me how to get baverage to work, or if there is > another way to extract these numbers, I would much appreciate it! > > Best, > > Julia > > -- > Dr. Julia Griese > Assistant Professor > Department of Cell and Molecular Biology > Uppsala University > BMC, Box 596 > SE-75124 Uppsala > Sweden > > email: julia.gri...@icm.uu.se > phone: +46-(0)18-471 4043 > http://www.icm.uu.se/structural-biology/griese-lab/ > > När du har kontakt med oss på Uppsala universitet med e-post så innebär det > att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan > du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ > > E-mailing Uppsala University means that we will process your personal data. > For more information on how this is performed, please read here: > http://www.uu.se/en/about-uu/data-protection-policy > > --------------------------------------------------------------- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
