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Author Topic: Base pair in 3LZ0 not recognised  (Read 342 times)

Offline mce1

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Base pair in 3LZ0 not recognised
« on: June 15, 2020, 01:04:37 pm »
Dear Xiangjun,

I'm trying to analyse the above structure (PDB 3LZ0) of a nucleosome core particle using w3DNA.

The structure contains 145bp of dsDNA. The two strands are designated chain I and J and numbered from -72 to 72 (including 0).

Under the first heading "Base Sequence" the 145bp sequence is reported correctly.

In all subsequent columns (Base-pair Identity etc.), however, base pair I:47/J:-47 is missing. Instead I:46/J-46 (Pair ID 119) is followed directly by I:48/J-48 (Pair ID 120). At this position no base-pair step parameters are reported:

Step ID   Step   Pair ID1   Pair ID2   Shift   Slide   Rise   Tilt   Roll   Twist   Context1   Context2
119   AG/CT   119      120      ----   ----   ----   ----   ----   ----   CAGC      GCTG

I suspect the pdb-file is somehow misformated at this position but cannot detect any problem by visual inspection. The base pair is also correctly displayed in pymol or Chimera, and even in the JSmol 3D View on the results page it is clearly there. I tried loading and re-saving the pdb with various editors, deleting heteroatoms and various other things, but that all did not fix the problem.

I wondered if you could have a look at the file and see if you can find the problem.

Your help would be much appreciated.

Regards,

Maik

Offline shuxiang

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Re: Base pair in 3LZ0 not recognised
« Reply #1 on: June 15, 2020, 03:25:44 pm »
Check the base pair I:47-J:-47 in visualization software such as pymol or vmd. The plane of the DC (J:-47) is rotated and also the distance between the two bases is beyond the criteria of base pair defined in 3DNA software. So 3DNA default setup treats I:47-J:-47 as not a pair base and ignores it.

Offline xiangjun

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Re: Base pair in 3LZ0 not recognised
« Reply #2 on: June 15, 2020, 09:29:20 pm »
Hi Maik,

In addition to what Shuxiang has suggested, have a look of FAQ entry How to fix missing (superfluous) base pairs identified by find_pair?. Specifically, using the 3DNA command-line find_pair/analyze programs should do the trick.

Best regards,

Xiang-Jun
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

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Offline mce1

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Re: Base pair in 3LZ0 not recognised
« Reply #3 on: June 16, 2020, 07:12:24 am »
Dear Xiang-Jun,

thanks a lot for the useful link!

After installing 3DNA and tweaking the parameter file the missing base-pair is recognised!

Thanks a lot again,

Maik

Offline xiangjun

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Re: Base pair in 3LZ0 not recognised
« Reply #4 on: June 16, 2020, 07:28:00 am »
Hi Maik,

Quote
After installing 3DNA and tweaking the parameter file the missing base-pair is recognised!

Glad to hear that it works. For the benefit of other viewers of this thread, could you please provide details on what you did to solve this specific problem?

Thanks also goes to Shuxiang, who is helping out this Forum from the sidelines.

Best regards,

Xiang-Jun
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

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* Original Poster, please provide a summary
* DSSR 2.0 has superseded the 3DNA v2.4 suite

 

Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (xiangjun@x3dna.org)
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.