crash on biolip web site and a site at position 0

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morgannprice
Posts: 1
Joined: Fri Feb 03, 2023 12:18 am

crash on biolip web site and a site at position 0

Post by morgannprice »

Hi,

I was wondering how to interpret the BioLiP download file for 8gwo:G, so I looked it up in the BioLip web site, but it crashed

https://zhanggroup.org/BioLiP2/pdb.cgi? ... =G&bs=BS01

The position information in the download table is odd -- it includes "u0" and there is a lower-case character at the beginning of the sequence. I'm wondering what position 0 means and why there is a lower-case character in the sequence.

Also, the readme link on the biolip download page
https://seq2fun.dcmb.med.umich.edu//Bio ... nload.html
points at
https://seq2fun.dcmb.med.umich.edu//BioLiP/readme.txt
which does not work.

Thanks,
Morgan Price
Lawrence Berkeley Lab
jlspzw
Posts: 124
Joined: Tue May 04, 2021 5:04 pm

Re: crash on biolip web site and a site at position 0

Post by jlspzw »

Dear user,

Which link on the download page did you open?

I check the readme link at https://zhanggroup.org/BioLiP/download.html

It seems I didn't get any problem. The link is https://zhanggroup.org/BioLiP/download/readme.txt

Let me know if you find any issues.

Thank you.

Best
IT Team
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zcx@umich.edu
Posts: 40
Joined: Wed Nov 03, 2021 5:59 pm

Re: crash on biolip web site and a site at position 0

Post by zcx@umich.edu »

We have fixed the issue for 8gwo:G. The webpage you mention should now work. u0 is not a mistake. If you check line 22085 to line 22104 of the PDB format file for 8gwo at https://files.rcsb.org/view/8GWO.pdb, you will notice that residue 0 of chain G is ribonucleotide U, while the remaining residues are all amino acid. Lower case means this is a nucleotide rather than amino acid. Position 0 is literally what it mean (residue sequence number 0 in the original PDB entry).

We have also updated https://seq2fun.dcmb.med.umich.edu//Bio ... nload.html with the correct readme.txt link. You will need to refresh browser to reload the new download page.
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