atom-base capping

[Mohit Chawla]

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

[xiangjun]

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

[Mohit Chawla]

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

[xiangjun]

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

[Mohit Chawla]

Dear Xiang-Jun,

It is working now. Thanks very much.

Regards,
Mohit

[Mohit Chawla]

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

[xiangjun]

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

Xiang-Jun

[Mohit Chawla]

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