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Author Topic: atom-base capping  (Read 913 times)

Offline Mohit Chawla

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atom-base capping
« 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

Offline xiangjun

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Re: atom-base capping
« Reply #1 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
« Last Edit: December 11, 2016, 01:54:01 pm by xiangjun »
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

Offline Mohit Chawla

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Re: atom-base capping
« Reply #2 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

Offline xiangjun

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Re: atom-base capping
« Reply #3 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
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

Offline Mohit Chawla

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Re: atom-base capping
« Reply #4 on: December 12, 2016, 02:43:44 pm »
Dear Xiang-Jun,

It is working now. Thanks very much.

Regards,
Mohit

Offline Mohit Chawla

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Re: atom-base capping
« Reply #5 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

Offline xiangjun

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Re: atom-base capping
« Reply #6 on: April 04, 2017, 10:06:24 am »
Try --a2base-vd=4, for example.

Xiang-Jun
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

Offline Mohit Chawla

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Re: atom-base capping
« Reply #7 on: April 04, 2017, 10:27:34 am »
Thanks Xiang-Jun.
It is working.
Regards,
Mohit

 

Created and maintained by Dr. Xiang-Jun Lu[律祥俊]· Supported by the NIH grant R01GM096889 · Dr. Lu is currently a member of the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University. The project is in collabration with the Olson Laborarory at Rutgers where 3DNA got started.