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Author Topic: strange base name  (Read 1016 times)

Offline Trista

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strange base name
« on: December 15, 2016, 01:58:46 am »
Hi,
Some strange base name(B.G-14,B.A23/145) in the dssr output puzzles me a lot, and I cannot find any explanations in the DSSR manual.
What do the slash and dash mean?
What the difference between B.G14 and B.G-14?

Bests,
Trista

Offline xiangjun

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Re: strange base name
« Reply #1 on: December 15, 2016, 08:12:15 am »
Hi Trista,

Thanks for using DSSR and for posting your questions on the Forum. It's useful if you could provide a concrete example to help illustrate your problems.

Quote
Some strange base name(B.G-14,B.A23/145) in the dssr output puzzles me a lot, and I cannot find any explanations in the DSSR manual.

At the very beginning of each DSSR output, you will see the following note:

Code: [Select]
Note: Each nucleotide is identified by model:chainId.name#, where the
      'model:' portion is omitted if no model number is available (as
      is often the case for x-ray crystal structures in the PDB). So a
      common example would be B.A1689, meaning adenosine #1689 on
      chain B. One-letter base names for modified nucleotides are put
      in lower case (e.g., 'c' for 5MC). For further information about
      the output notation, please refer to the DSSR User Manual.
      Questions and suggestions are always welcome on the 3DNA Forum.

See also the section "3.14.4 The --idstr option" in the DSSR Manual for more info. For parsing DSSR output, one would use --idstr=long which separates fields by dot, in a fixed format.

Now back to your two specific questions:

Quote
What do the slash and dash mean?

As noted above, the default setting for id-string combines the residue name with the sequence number as specified in your input PDB/mmCIF file. This follows the convention such that A16 stands for adenine #16.

Here the number -14 is the sequence number which turns out to be negative. So the dash has no special meaning in DSSR output.

If the residue name has a number in it, as would be the case for A23, the a slash is add the separate name from sequence number. Otherwise A23/145 would be A23145.

Quote
What the difference between B.G14 and B.G-14?

B here mean chain id, G14 means G with sequence number 14, and G-14 means G with sequence number -14. So the only difference here is the sequence number, as specified in your PDB/mmCIF file.

Hope this clarify your confusions. Please follow up, providing a sample input file.

Xiang-Jun
« Last Edit: December 15, 2016, 08:19:15 am by xiangjun »
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

Offline Trista

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Re: strange base name
« Reply #2 on: December 15, 2016, 10:07:03 pm »
Thank you so much!
It helps a lot!

 

Created and maintained by Dr. Xiang-Jun Lu [律祥俊], Principal Investigator of the NIH grant R01GM096889
Dr. Lu is currently affiliated with the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.