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Questions and answers => RNA structures (DSSR) => Topic started by: Mohit Chawla on December 11, 2016, 09:43:12 am

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Title: atom-base capping
Post by: Mohit Chawla on December 11, 2016, 09:43:12 am

Hi,
In the atom-base capping interactions, is it possible to also search for oxygen(water) to base contacts. For instance, in PDB id: 3d0u, HOH 213 makes a capping contact with G77, which we can not detect in the current version of dssr or may be I am missing with some option. Kindly suggest.
Thanks,
Mohit

Title: Re: atom-base capping
Post by: xiangjun on December 11, 2016, 11:00:19 am

Hi Mohit,

The functionality is certainly implemented (but undocumented) in DSSR. I just cannot remember exactly what it is right now. Try to add the --water (or --h2o) option to DSSR, and report back if that does the trick.

Best regards,

Xiang-Jun

Title: Re: atom-base capping
Post by: Mohit Chawla on December 12, 2016, 04:57:30 am

Dear Xiang-Jun,
Thanks for the reply. I tried to add --water ( or --h20) option, but it does not return the water-base contact.

Regards,
Mohit

Title: Re: atom-base capping
Post by: xiangjun on December 12, 2016, 08:16:28 am

I made slight changes to DSSR after my previous response -- download it again and now the --water option should output the expected water-base capping interactions. Please confirm.

Xiang-Jun

Title: Re: atom-base capping
Post by: Mohit Chawla on December 12, 2016, 02:43:44 pm

Dear Xiang-Jun,

It is working now. Thanks very much.

Regards,
Mohit

Title: Re: atom-base capping
Post by: Mohit Chawla on April 04, 2017, 12:07:26 am

Dear Xiang-Jun,
Related to the atom-base capping interactions, I can see that such an interaction is detected with the distance of atom with the base plane of <= 3.5 A. However, if I want to detect such an interaction with distance > 3.5A, is it possible by the DSSR? If yes, please suggest me the option.
regards,
Mohit

Title: Re: atom-base capping
Post by: xiangjun on April 04, 2017, 10:06:24 am

Try --a2base-vd=4, for example.

Xiang-Jun

Title: Re: atom-base capping
Post by: Mohit Chawla on April 04, 2017, 10:27:34 am

Thanks Xiang-Jun.
It is working.
Regards,
Mohit

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