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Questions and answers => w3DNA -- web interface to 3DNA => Topic started by: sowmya on October 19, 2022, 07:54:02 am

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Title: can't open the baselist file error for 2 PDB IDs
Post by: sowmya on October 19, 2022, 07:54:02 am

Dear Dr. Xiang,

I was trying to calculate the base pair and base step parameters for PDB IDs - 7E9E and 7E9I by uploading the PDB files to the web interface of 3DNA. I am getting a "can't open the baselist file error" for these 2 IDs. I am yet to come across this error for other PDB IDs - I have calculated for around 20 other PDB IDs (deposited after 2019) in the web interface and they were parsed fine. Requesting your suggestions to resolve this error in the web interface.

With regards,
Sowmya

Title: Re: can't open the baselist file error for 2 PDB IDs
Post by: xiangjun on December 25, 2022, 11:49:24 am

The modified nucleotide J0C in 7E9E and 7E9I does not follow the naming convention of canonical bases. 3DNA can not handle it and thus the error message you reported.

DSSR can run successfully on these two PDB entries.

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.