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: http://list.nih.gov/cgi-bin/wa.exe?SUBED1=XPLOR-NIH&A=1
