nucleic acid secondary structure restraint sigmas
Hi, Does anyone one whether is it possible (and if so how) to change the target sigmas of the H-bonds restraining base pairs? It seems that base pair restraints can do several things: base_pair { enabled = True base1 = chain 'C' and resid 21 base2 = chain 'D' and resid 5 saenger_class = 19 restrain_planarity = False planarity_sigma = 0.176 restrain_hbonds = True restrain_hb_angles = True restrain_parallelity = True parallelity_target = 0 parallelity_sigma = 0.0335 What I'd like to know whether the restrain_hbonds and restrain_hb_angles sigmas can be adjusted. Or is it the case that parallelity_sigma is doing what I'm looking for? Thanks! Fred [32m******************************************************************************* Fred Dyda, Ph.D. Phone:301-402-4496 Laboratory of Molecular Biology Fax: 301-496-0201 DHHS/NIH/NIDDK e-mail:[email protected] Bldg. 5. Room 303 Bethesda, MD 20892-0560 URGENT message e-mail: [email protected] Google maps coords: 39.000597, -77.102102 http://www2.niddk.nih.gov/NIDDKLabs/IntramuralFaculty/DydaFred *******************************************************************************[m
Hi Fred, Does anyone one whether is it possible (and if so how)
to change the target sigmas of the H-bonds restraining base pairs?
It is not possible to change target or sigma values for H-bonds or H-bond angles. The values are picked individually depending on atoms involved and Saenger class of a base pair. It could be instructive for us to know why do you want to change them? Do you have any particular scenario where the standard sigmas do not work as you are expecting?
Or is it the case that parallelity_sigma is doing what I'm looking for?
parallelity_sigma is a sigma for separate restraint (parallelity) which has no influence on H-bond restraints. Best regards, Oleg Sobolev.
participants (2)
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Dyda
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Oleg Sobolev