Hi Gary-- This service may be helpful in this case- I encourage users to try it out.
Charles On Tue, 04 Jun 2024 11:32:31 -0400, Gary Thompson wrote: > > [1 <text/plain; utf-8 (base64)>] > [2 <text/html; utf-8 (base64)>] > Hi Charles > > Would https://atb.uq.edu.au/ help you here, I am planning to do similar things > and was planning to use it… > > regards > Gary > > Dr Gary S Thompson NMR Facility Manager > CCPN CoI & Working Group Member > Wellcome Trust Biomolecular NMR Facility > School of Biosciences, Division of Natural Sciences > University of Kent, Canterbury, Kent, England, CT2 7NZ > > ☎:01227 82 7117 > ✉️: [email protected] > orchid: orcid.org/0000-0001-9399-7636 > > On 4 Jun 2024, at 16:28, Charles Schwieters <[email protected]> > wrote: > > CAUTION: This email originated from outside of the organisation. Do not > click links or open attachments unless you recognise the sender and know > the content is safe. > > Hello Suze Ma-- > > 1. I intend to calculate the solution 3D structures of two peptide > macrocycles based on their 1H-1H NOESY data. The first one contains > an ether crosslink (from an exogenous oxygen atom) inserted between > the Trp1-C7 and the Phe3-Cβ while the second one contains a > carbon-carbon crosslink derived from Trp1-C7 and Lys3-Cβ. (for both > structures, see ref: > > https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdoi.org%2F10.1021%2Fjacs.3c04355&data=05%7C02%7CG.S.Thompson%40kent.ac.uk%7C004d4f2097b34693a64808dc84ab194b%7C51a9fa563f32449aa7213e3f49aa5e9a%7C0%7C0%7C638531117717912748%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=6NlDB%2FwAT6jU1%2FZjG3b%2BfY9OyFKFbFJJUkrsoq02mxs%3D&reserved=0). > I am > wondering if there are patches to add these two types of > modifications to the structures. I guess addAtom.py is not suitable > for these cases. In addition, I am not sure how to generate the > parameters (e.g. bond, angle, etc) associated with these > intramolecular crosslinks (I understand that the original protein > topology file, e.g. protein-1.0.top, does not contain such > information). > > You will need patches along the lines of those used in > eginput/PSF_generation/gen*CircPep.py in the Xplor-NIH distribution. > I can help with the required patches. But particularly for the ether > case, parameters are required - we might borrow those of anisole, if > you can find the atomic coordinates of that molecule. For the > carbon-carbon crosslink, we can make a decent educated guess. > > 2. To generate distance restraints, I use sparky to assign the NOESY > spectrum and obtain the intensity of NOE signals, which, upon > calibrated by a known interprotein distance (e.g. Thr-HA to Thr-HN, > 2.51 angstrom) and its NOE intensity in my spectrum, only results in > a single list of distances, referred to as d. However, I'm not sure > how to generate the dminus and dplus to define the distance > restraint bounds (d-dminus, d-dplus). I know there are other > methods, such as MARDIGRAS, to generate the bounds. However, I don't > find an available access to these algorithms. Thus, I am asking if > there are other methods to overcome or circumvent the problem in > generating distance restraints bounds for calculations? > > Usually, the intensity-derived distances are rather qualitative, so > that distance bounds would be at least +/- 1 Angstrom, so unless you > know otherwise, you might use this value. > > 3. I am wondering is it possible to only rely on the NOE restraints > (and not dihedral restraints or others) to model the structures of > the small peptide macrocycles in my case? If it is theoretically > feasible, how to calculate only with distance restraints and not > other restraints by using fold.py, anneal.py, etc? Simply by > deleting the contents regarding other restraints while only > maintaining the contents regarding distance restraints? > > Of course, more data is better, but distance-only information can be > used by commenting-out or removing sections of the scripts which > involve other restraints. > > best regards-- > Charles > > ######################################################################## > > To unsubscribe from the XPLOR-NIH list, click the following link: > Bad URL Removed - see why - > > https://ees.sps.nih.gov/services/Pages/Anti-Virus.aspx%3FSUBED1%3DXPLOR-NIH%26A%3D1&data=05%7C02%7CG.S.Thompson%40kent.ac.uk%7C004d4f2097b34693a64808dc84ab194b%7C51a9fa563f32449aa7213e3f49aa5e9a%7C0%7C0%7C638531117717923308%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=ZjQCxbbsn0uyB9o2F%2FAH5%2F9g7z88Bk45cBsd0mgb1lA%3D&reserved=0 > > > ------------------------------------------------------------------------------- > > To unsubscribe from the XPLOR-NIH list, click the following link: > Bad URL Removed - see why - > https://ees.sps.nih.gov/services/Pages/Anti-Virus.aspx?SUBED1=XPLOR-NIH&A=1 ######################################################################## To unsubscribe from the XPLOR-NIH list, click the following link: http://list.nih.gov/cgi-bin/wa.exe?SUBED1=XPLOR-NIH&A=1
