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Author Topic: Water molecules in DSSR  (Read 4720 times)

Offline Luigi

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Water molecules in DSSR
« 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

Offline xiangjun

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Re: Water molecules in DSSR
« Reply #1 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
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

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Offline Luigi

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Re: Water molecules in DSSR
« Reply #2 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


Offline xiangjun

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Re: Water molecules in DSSR
« Reply #3 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
« Last Edit: August 19, 2015, 11:02:37 am by xiangjun »
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

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* Original Poster, please provide a summary
* DSSR 2.0 has superseded the 3DNA v2.4 suite

 

Created and maintained by Dr. Xiang-Jun Lu [律祥俊], Principal Investigator of the NIH grant R01GM096889
Dr. Lu is currently affiliated with the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.