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 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/
