Dear Charles and Xplor-NIH team, I am a beginner in learning Xplor-NIH and I have a few questions.
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://doi.org/10.1021/jacs.3c04355). 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). 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? 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? Best regards, Suze Ma Graduate Student in Chemistry, Fudan University ######################################################################## To unsubscribe from the XPLOR-NIH list, click the following link: http://list.nih.gov/cgi-bin/wa.exe?SUBED1=XPLOR-NIH&A=1
