Water molecules in DSSR

[Luigi]

Hi Xiang-Jun,

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

Best regards,

Luigi

[xiangjun]

Hi Luigi,

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

Xiang-Jun

[Luigi]

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

[xiangjun]

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