Dear Charles, Thanks you very much for your kindness! I am now sending you several files including seq, pdb, upl of the cluster which I used in Cyana2.1 (i.e. connectivity between Cd and SG). The protein is actually the alpha-domain of Metallothionein3, and the structure was formed mainly through the Cd4-Cys11 cluster with each Cd binding to four SG from cysteins and some sulfur bridged between Cd. A few more questions here. When using eginput/gb1_rdc/refine.py, do I also need to use noe constrains or just rdc constraints since I will start from my initial structures? How to get a good set of Da and Rh? I tried to run grid_search.py but always get error with input pdb possibly due to wrong format? I also tried fitting RDC data using MODULE and get Aa and Ar but not sure how to convert into Da (Rh=Ar/Aa). I have tested another protein using eginput/protG/anneal.py script to refine my structure with RDC and NOE constrains, should the result similar to that from eginput/gb1_rdc/refine.py. I will try later. Sorry for so many questions!
Looking forward to your suggestion! Best wishes, Hongyan Quoting Charles at Schwieters.org: > -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > > > Hello Hongyan-- > > > I am a new user for Xplor-nih, and have used Cyana and Aria to > > determine protein structures. Since I need to use RDC to refine the > > structures so I am planning to use xplor-nih to do refinement. I > > wonder if the eginput/protG/anneal.py is suitable for this. > > It is better to use eginput/gb1_rdc/refine.py. > > > In the > > mean time, I need to add metal cluster into PSF file. My protein > > contains a Cd4Cys11 cluster, different from sample script > > (generatmetal.inp that FeS cluster with 4Fe and 4S was constructed > > into one residue). I wonder if any person knows how to generate .psf > > file with the metal cluster in it and how to incorporate into > > anneal.py script. > > I can help with this, but we will need the structure of the cluster > before attempting this. A few extra statements will also be necessary in > the .py script to hold the cluster rigid. > > best regards-- > Charles Dr. Hongyan Li Department of Chemistry The University of Hong Kong Pokfulam Road Hong Kong -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: CD.upl Url: http://dcb.cit.nih.gov/pipermail/xplor-nih/attachments/20070307/88f75268/attachment-0002.pl -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: MT3.seq Url: http://dcb.cit.nih.gov/pipermail/xplor-nih/attachments/20070307/88f75268/attachment-0003.pl -------------- next part -------------- A non-text attachment was scrubbed... Name: Mt3.pdb Type: application/vnd.palm Size: 51667 bytes Desc: not available Url : http://dcb.cit.nih.gov/pipermail/xplor-nih/attachments/20070307/88f75268/attachment-0001.bin
