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Questions and answers => RNA structures (DSSR) => Topic started by: Luigi on August 17, 2015, 01:09:41 pm

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Title: Water molecules in DSSR
Post by: Luigi on August 17, 2015, 01:09:41 pm

Hi Xiang-Jun,

is there an option in DSSR to obtain hydrogen bonds with nucleic acid atoms for crystallographic water molecules?

Best regards,

Luigi

Title: Re: Water molecules in DSSR
Post by: xiangjun on August 17, 2015, 01:30:29 pm

Hi Luigi,

Try the DSSR --water option, and report back if that fits your needs.

Xiang-Jun

Title: Re: Water molecules in DSSR
Post by: Luigi on August 18, 2015, 01:09:28 pm

Hello Xiang-Jun,

I tried running DSSR on tRNAPhe 1EHZ and ribosome 1VQ8 with the option --water and I do not see differences from the standard DSSR output.
Just for information I used the command: x3dna-dssr --water --i=1EHZ.py.pdb -o=1EHZ.py.dssr.out.
I do not attach the output file as it is the same of a run without the --water option.

Luigi

Title: Re: Water molecules in DSSR
Post by: xiangjun on August 18, 2015, 01:21:59 pm

Hi Luigi,

With the --water option, you can get more H-bonds involving waters (e.g., together with the --get-hbond  option). As to the default DSSR output, please use 1ehz as an example to show me what difference you want to see with the --water option.

Xiang-Jun

Funded by the NIH R24GM153869 grant on X3DNA-DSSR, an NIGMS National Resource for Structural Bioinformatics of Nucleic Acids

Created and maintained by Dr. Xiang-Jun Lu, Department of Biological Sciences, Columbia University