Re: [ccp4bb] Mean B factors and number of atoms (Refmac/baverage)
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(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=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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/
Re: [ccp4bb] Mean B factors and number of atoms (Refmac/baverage)
Answer to self: the number of non-H atoms per chain can be found in the PDB validation report! Duh! I guess I’ll trust the average B values reported by Refmac. /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/ From: CCP4 bulletin board on behalf of Julia Griese Reply-To: Julia Griese Date: Thursday, 26 November 2020 at 15:11 To: "CCP4BB@JISCMAIL.AC.UK" Subject: [ccp4bb] Mean B factors and number of atoms (Refmac/baverage) 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(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=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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/
Re: [ccp4bb] Mean B factors and number of atoms (Refmac/baverage)
Hi Julia,
For a table 1 you should make a sensible split of the atoms over which you
calculate the mean. You might need to pool certain chains. There is not really
convenient tool for that because the choice depends on the biology/biochemistry
of your system. In practice, the easiest way is using the command line on just
the ATOM/HETATM records (atom_site in mmCIF format) in which you are
interested. Calculating the mean of a column of values is pretty
straightforward in awk.
Example for all atoms in a PDB file:
grep ^[HA][TE][OT][MA] 100d_final.pdb | cut -c 61-66 | awk '{sum = sum + $1}
END {print sum/NR}'
Or mmCIF:
grep [HA][TE][OT][MA] /DATA/pdb_redo/00/100d/100d_final.cif | awk '{sum = sum
+ $16} END {print sum/NR}'
HTH,
Robbie
From: CCP4 bulletin board On Behalf Of Julia Griese
Sent: Thursday, November 26, 2020 15:11
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Mean B factors and number of atoms (Refmac/baverage)
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(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<mailto: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
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E-mailing Uppsala University means that we will process your personal data. For
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[ccp4bb] Mean B factors and number of atoms (Refmac/baverage)
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(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=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/
