[gmx-users] Why "do_dssp" gives one more residue?

[Justin Lemkul]

On 2/21/18 12:34 PM, ZHANG Cheng wrote:
> Dear Qinghua,
> Yes, exactly! But the numbering is:
>
>
> 1-214: first chain
> 215-442: second chain
>
>
> However, for the secondary structure codes:
>
>
> 214th:
> "TTSTSSSTSSSTTSTSS~SSSTTTTTTTTSSTTTTTTTTTTTTSTSSSTSTTTTTTTTTTTTTTTTTTTTTTTSTTTTTSTSTTTTTTTTTTTTTTTTTT~SS~SSSTSTTTSSSSSSTTTSSSSSSTSSTTTSTTTTTTTTTTTTTTTTSGSTTSTSTTTTSSSSSSTTTTSSSSTSSTTTTTSTTTTTTTTTTTTSTTSSSSSSTSTTSSSTSSTTSSSSTTTEEBSSESSSSBSSTSSTSEESTSSSSSTSTSTSTTTSSSTTTSTTTTTSTSSTSTTTTTTSSTTTTTTTTSTTTESET~~~SSS~SSS~~S~",
>
>
> 215th:
> "TTST~~~TSSSTTST~~~~SSTTTTTTTTSSTTTTTTTTTTTTSTSSSTSTTTTTTTTTTTTTTTTTTTTTTTSTTTTTSTSTTTTTTTTTTTTTTTTTT~~SSSS~TSTTTSSSS~STTTSSSSSSTSSTTTSTTTTTTTTTTTTTTTTSGSTTSTSTTTT~~~~~STTTT~SSSTSSTTTTTSTTTTTTTTSTTTSTTSSSSSSTSTTSSSTSSTTSSSSTTTSSSSSSSSSSSSSTSSTSSSSTSSSSSTSTSTSTTTSSSTTTSTTTTTSTSSTSTTTTTTSSTTTTTTTTSTTT~SSS~S~~~~~~~~~~~~",
>
>
> 442th:
> "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~BBBBB~~BBB~BB~~~~~BBB~B~~~B~~B~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~T~~~~~~~~~~~~~~~~~~~~~B~B~~~~~~B~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~",
>
>
> 443th: "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
>
>
>
>
> Do you think the 443th line is the separator? So ignore the 443th line?

No, the output is in the order of the coordinates: 1-214, chain 
separator, then 215-442.

-Justin

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Justin A. Lemkul, Ph.D.
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