If *overlapping nucleotides* no contacts are computed

[vreinharz]

In the file: zGetNTData, the warning has overlapping nucleotides and should be used with caution is produced when the array d, the atom distances has the condition
if d(min(10, length(d))) < 1
but in that case the base pairs are never computed!
In particular 1S72 fails with that condition.
Closing the if condition instead of the else
fixed the problem as here zGetNTData.txt.

I am not sure if side effects are produced.

[clzirbel]

Thanks for the note. The problem seems to be that in certain PDB files, nucleotides have 3D coordinates that are literally right on top of other nucleotides. This can result in many spurious basepairs, which we are reluctant to annotate. But I have never seen this cause trouble with 1S72. Could you tell me more about the 1S72 file you are using?

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On 2/8/2017 1:38 PM, Vladimir Reinharz wrote: In the file: /zGetNTData/, the warning *has overlapping nucleotides and should be used with caution* is produced when the array |d|, the atom distances has the condition if d(min(10, length(d))) < 1 but in that case the base pairs are never computed! In particular 1S72 fails with that condition. Closing the |if| condition instead of the else fixed the problem as here zGetNTData.txt <https://github.com/BGSU-RNA/FR3D/files/761598/zGetNTData.txt>. I am not sure if side effects are produced. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#11>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AA8PkzGFGC-wflPmp0q_U8qxIIFcEGY5ks5ragu7gaJpZM4L7Mo2>.

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______________________________________________________________________ *Craig L. Zirbel* Professor and Graduate Coordinator Department of Mathematics and Statistics BGSU | Bowling Green State University Bowling Green, OH 43403 +1-419-372-7466; zirbel@bgsu.edu <mailto:zirbel@bgsu.edu> http://www-math.bgsu.edu/~zirbel <http://www-math.bgsu.edu/%7Ezirbel>

______________________________________________________________________

[vreinharz]

Hi Craig, Both the latest .cif from the PDB and the .pdb file you provide with the repositor. Thye thing is that 1S72 has already in the repository the PrecomputeData, so the error doesn't show unless you erase it first. Best, -- Vladimir Reinharz

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On Feb 8, 2017, at 9:46 PM, Craig L. Zirbel ***@***.***> wrote: Thanks for the note. The problem seems to be that in certain PDB files, nucleotides have 3D coordinates that are literally right on top of other nucleotides. This can result in many spurious basepairs, which we are reluctant to annotate. But I have never seen this cause trouble with 1S72. Could you tell me more about the 1S72 file you are using? On 2/8/2017 1:38 PM, Vladimir Reinharz wrote: > > In the file: /zGetNTData/, the warning *has overlapping nucleotides > and should be used with caution* is produced when the array |d|, the > atom distances has the condition > if d(min(10, length(d))) < 1 > but in that case the base pairs are never computed! > In particular 1S72 fails with that condition. > Closing the |if| condition instead of the else > fixed the problem as here zGetNTData.txt > <https://github.com/BGSU-RNA/FR3D/files/761598/zGetNTData.txt>. > > I am not sure if side effects are produced. > > — > You are receiving this because you are subscribed to this thread. > Reply to this email directly, view it on GitHub > <#11>, or mute the thread > <https://github.com/notifications/unsubscribe-auth/AA8PkzGFGC-wflPmp0q_U8qxIIFcEGY5ks5ragu7gaJpZM4L7Mo2>. > -- ______________________________________________________________________ *Craig L. Zirbel* Professor and Graduate Coordinator Department of Mathematics and Statistics BGSU | Bowling Green State University Bowling Green, OH 43403 +1-419-372-7466; ***@***.*** ***@***.***> http://www-math.bgsu.edu/~zirbel <http://www-math.bgsu.edu/%7Ezirbel> ______________________________________________________________________ — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#11 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAj8xM56RwR5MYrTnDTzNIskV7RZbR_cks5rahuLgaJpZM4L7Mo2>.

[vreinharz]

Oh, and I am using the script annotate_pdb.m from Anton https://gist.github.com/AntonPetrov/4108400 <https://gist.github.com/AntonPetrov/4108400> -- Vladimir Reinharz

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On Feb 8, 2017, at 9:46 PM, Craig L. Zirbel ***@***.***> wrote: Thanks for the note. The problem seems to be that in certain PDB files, nucleotides have 3D coordinates that are literally right on top of other nucleotides. This can result in many spurious basepairs, which we are reluctant to annotate. But I have never seen this cause trouble with 1S72. Could you tell me more about the 1S72 file you are using? On 2/8/2017 1:38 PM, Vladimir Reinharz wrote: > > In the file: /zGetNTData/, the warning *has overlapping nucleotides > and should be used with caution* is produced when the array |d|, the > atom distances has the condition > if d(min(10, length(d))) < 1 > but in that case the base pairs are never computed! > In particular 1S72 fails with that condition. > Closing the |if| condition instead of the else > fixed the problem as here zGetNTData.txt > <https://github.com/BGSU-RNA/FR3D/files/761598/zGetNTData.txt>. > > I am not sure if side effects are produced. > > — > You are receiving this because you are subscribed to this thread. > Reply to this email directly, view it on GitHub > <#11>, or mute the thread > <https://github.com/notifications/unsubscribe-auth/AA8PkzGFGC-wflPmp0q_U8qxIIFcEGY5ks5ragu7gaJpZM4L7Mo2>. > -- ______________________________________________________________________ *Craig L. Zirbel* Professor and Graduate Coordinator Department of Mathematics and Statistics BGSU | Bowling Green State University Bowling Green, OH 43403 +1-419-372-7466; ***@***.*** ***@***.***> http://www-math.bgsu.edu/~zirbel <http://www-math.bgsu.edu/%7Ezirbel> ______________________________________________________________________ — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#11 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAj8xM56RwR5MYrTnDTzNIskV7RZbR_cks5rahuLgaJpZM4L7Mo2>.