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Questions and answers => General discussions (Q&As) => Topic started by: jyvdf3asdg2 on February 12, 2013, 05:30:59 pm

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Title: B-Factor values from PDB in output files?
Post by: jyvdf3asdg2 on February 12, 2013, 05:30:59 pm

Hi,

I've been looking through the documentation and can't seem to find any mention of this, but is there any way of getting the B-factor values for each base or base pair in the .outp files?

Thanks!

Title: Re: B-Factor values from PDB in output files?
Post by: xiangjun on February 12, 2013, 08:48:25 pm

The B-factor values are currently not included in 3DNA output file(s), and you are the first user to request such info. Where do you think is the appropriate place to put them? And in what format? How about atom occupancy?

Xiang-Jun

Title: Re: B-Factor values from PDB in output files?
Post by: jyvdf3asdg2 on February 13, 2013, 01:02:12 pm

Hi,

Thanks for the reply!

In the context of .outp files, it seems like they would need their own subsection for crystal parameters. Occupancy seems appropriate.

If I had to do it manually, I was going to calculate the B-factor averages for individual base moieties:

Base A: Sum average, Backbone Avg, Sugar Avg, Base Avg.
Base B: Sum average, Backbone Avg, Sugar Avg, Base Avg.

**************
Crystal pair parameters

Strand I

base B-Factor Occupancy ...
1 A 55.0 1.0
.
.
.

Strand II
base B-Factor Occupancy ...
1 T 50.0 1.0
.
.
.

Title: Re: B-Factor values from PDB in output files?
Post by: xiangjun on February 13, 2013, 01:34:02 pm

Thanks for your feedback.

Just to be sure: by ".outp", you mean the option "find_pair -p"-generated file "allpairs.ana" which is then fed into "analyze"? How about the default setting? i.e., the ".out" file?

I will think more about this request, and I may come up with something. If I decide to go for it, I'd output the B-factor average/occupancy for any input structure, not just crystal structures. Moreover, there would be a new command line option for such info, which is OFF by default to be compatible with previous 3DNA releases.

To help me help you in this endeavor, could you provide (at least) a concrete example with the values you want?

Xiang-Jun

Title: Re: B-Factor values from PDB in output files?
Post by: jyvdf3asdg2 on February 13, 2013, 05:01:19 pm

Quote from: xiangjun on February 13, 2013, 01:34:02 pm

Thanks for your feedback.

Just to be sure: by ".outp", you mean the option "find_pair -p"-generated file "allpairs.ana" which is then fed into "analyze"? How about the default setting? i.e., the ".out" file?

I will think more about this request, and I may come up with something. If I decide to go for it, I'd output the B-factor average/occupancy for any input structure, not just crystal structures. Moreover, there would be a new command line option for such info, which is OFF by default to be compatible with previous 3DNA releases.

To help me help you in this endeavor, could you provide (at least) a concrete example with the values you want?

Xiang-Jun

Hi,

Thanks so much for even considering this request!

I did not know the PDB even reported occupancy or temperature factor values for NMR/CryoEM structures.

I use .outp files because they tend to have all the base mispairs that the standard output fails to capture.

Command line is as you said:
>find_pair -p -original_coordinate %s.pdb %s.mbp
>analyze -c allpairs.ana

As for an example:

In the PDB format, these are the two values I'm interested in (moreso the B/temp-factor)

55 - 60        Real(6.2)       Occupancy.                           

61 - 66        Real(6.2)       Temperature factor (Default = 0.0).

As an example, I've included the pair extract from a random structure 1DQH.

For A(C 2) -- (G18)B, the B-factor averages would be:

A   C2   All Nucleobase Average   28.6875
      Base moeity average   24.095
      Sugar moeity average    30.0375
      Backbone moiety average   33.2125
         
         
B   G18   All Nucleobase Average   22.9326087
      Base moeity average   21.44
      Sugar moeity average   23.7675
      Backbone moiety average   25.21375

*This may not be correct, but I considered the backbone to be: P, OP1, OP2, O5', C5', C4', C3', O3'

Thanks so much!

Regards,

Isaac

Title: Re: B-Factor values from PDB in output files?
Post by: xiangjun on February 13, 2013, 06:24:58 pm

Thanks for your feedback -- that helps me in making decisions. I could add the new functionality to 3DNA's "analyze" program, or more sensibly, to the new RNA-focused component (DSSR) I am currently working on. I aim to get DSSR (alpha test version) out by the end of the month, or even possibly by next week.

NMR structures in PDB seem to have the b-factor columns filled. Calculating the average values of b-factors regardless structure type would make coding simple and consistent.

Xiang-Jun

Title: Re: B-Factor values from PDB in output files?
Post by: jyvdf3asdg2 on February 13, 2013, 07:12:21 pm

Either way would be great, thanks!

What will the output format for the new program look like? Will it be similar to 3DNA's?

Thanks

Title: Re: B-Factor values from PDB in output files?
Post by: xiangjun on February 19, 2013, 10:58:31 pm

I have looked into the B-factor issue, and noticed a numerical inconsistency for the sugar moiety. Using the example nucleotide C2 on chain A (A.C2) of PDB entry 1dqh (http://www.rcsb.org/pdb/explore/explore.do?structureId=1dqh), you reported a mean B-factor for sugar moiety of 30.04.

Quote

As an example, I've included the pair extract from a random structure 1DQH.

For A(C 2) -- (G18)B, the B-factor averages would be:

A   C2   All Nucleobase Average   28.6875
      Base moeity average   24.095
      Sugar moeity average    30.0375
      Backbone moiety average   33.2125

The atomic records for the A.C2(1dqh) are as below:

ATOM     21  P     C A   2      37.584  10.166  36.231  1.00 35.40           P  
ATOM     22  OP1   C A   2      38.502   9.371  35.370  1.00 37.17           O  
ATOM     23  OP2   C A   2      37.371  11.599  35.951  1.00 34.58           O  
ATOM     24  O5'   C A   2      36.188   9.406  36.193  1.00 33.54           O  
ATOM     25  C5'   C A   2      36.118   7.997  36.285  1.00 32.07           C  
ATOM     26  C4'   C A   2      34.683   7.567  36.457  1.00 30.69           C  
ATOM     27  O4'   C A   2      34.156   8.055  37.727  1.00 29.94           O  
ATOM     28  C3'   C A   2      33.728   8.137  35.431  1.00 30.66           C  
ATOM     29  O3'   C A   2      33.789   7.366  34.249  1.00 31.59           O  
ATOM     30  C2'   C A   2      32.391   7.983  36.148  1.00 28.79           C  
ATOM     31  O2'   C A   2      31.937   6.639  36.197  1.00 29.01           O  
ATOM     32  C1'   C A   2      32.779   8.394  37.563  1.00 27.55           C  
ATOM     33  N1    C A   2      32.625   9.836  37.823  1.00 25.64           N  
ATOM     34  C2    C A   2      31.353  10.331  38.113  1.00 24.78           C  
ATOM     35  O2    C A   2      30.382   9.563  38.052  1.00 23.25           O  
ATOM     36  N3    C A   2      31.210  11.641  38.434  1.00 24.08           N  
ATOM     37  C4    C A   2      32.265  12.446  38.446  1.00 23.49           C  
ATOM     38  N4    C A   2      32.070  13.718  38.781  1.00 22.55           N  
ATOM     39  C5    C A   2      33.573  11.981  38.110  1.00 24.21           C  
ATOM     40  C6    C A   2      33.702  10.676  37.806  1.00 24.76           C  

The sugar moiety (colored red) has actually a mean B-factor of 30.43, which is different from your number (30.04). Any explanation?

Xiang-Jun

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