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Bug #457

Option -bfac messes up residue name and number

Added by Erik Marklund over 9 years ago. Updated over 9 years ago.

Status:
Closed
Priority:
Normal
Category:
analysis tools
Target version:
Affected version - extra info:
Affected version:
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Description

My colleague and I found two major issues with the b-factor calculations in g_confrms.

1)

When executing g_confrms -f1 -f2 -bfac the resulting pdb file gets the wrong residue names and residue numbers. More specifically, the name and number of the first residue gets copied to all other residues.

2)

Furhtermore, I suspect that the bfactors are too small.
g_confrms reports that "Atomic MSD's range from 0.00113108 to 0.827677"

An atomic MSD of u=0.827677 nm^2 would mean that the corresponding bfactor would be u*pi^2*8 = 65.35 nm^2, or 6535 Å. However, the largest b-factor I can find in the pdb file is 21.78. Remember that pdb uses Å, not nm. Let's calculate the MSD v from this. 21.78 Å^2 = pi^2*8 * v => v = 0.28 Å^2, or 0.0028 nm^2. Clearly v != u and something must be wrong.

These errors seem quite reproducible with different input pdb-files.

History

#1 Updated by Erik Marklund over 9 years ago

(In reply to comment #0)

My colleague and I found two major issues with the b-factor calculations in
g_confrms.

1)

When executing g_confrms -f1 -f2 -bfac the resulting pdb file gets the wrong
residue names and residue numbers. More specifically, the name and number of
the first residue gets copied to all other residues.

2)

Furhtermore, I suspect that the bfactors are too small.
g_confrms reports that "Atomic MSD's range from 0.00113108 to 0.827677"

An atomic MSD of u=0.827677 nm^2 would mean that the corresponding bfactor
would be u*pi^2*8 = 65.35 nm^2, or 6535 Å. However, the largest b-factor I can
find in the pdb file is 21.78. Remember that pdb uses Å, not nm. Let's
calculate the MSD v from this. 21.78 Å^2 = pi^2*8 * v => v = 0.28 Å^2, or
0.0028 nm^2. Clearly v != u and something must be wrong.

These errors seem quite reproducible with different input pdb-files.

Based on the superimposed structures from g_confrms, I calculated the bfactors and msd in python and got a maximum atomic MSD of 6535.80813206, just like in the calculations above. This supports that that g_confrms does something fishy when calculating bfactors.

#2 Updated by David van der Spoel over 9 years ago

There was a spurious factor of hundred lingering there indeed. Can you please upload an example to test before I commit fix?

#3 Updated by Erik Marklund over 9 years ago

There should be a factor 1/3 in my calculations, which together with the factor 100 explains the discrepancy. I'll send you some pdb-files by e-mail, David.

#4 Updated by David van der Spoel over 9 years ago

Fixed in git.

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