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Re: [ccp4bb] Alternate Ligand Conformations |
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CCP4bb navigationCCP4bb <-- 2008 <-- May 2008 <-- 14 May 2008Subject: Re: Alternate Ligand Conformations From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK Date: 2008-05-14 > Hello. > > I am trying to refine a structure that has 2 ligand conformations as seen in > the electron density. I tried to put both conformations in Coot and format > the PDB similar to a residue alternate conformation and changing the > occupancies to 0.50 for each conformation. This formatting did not work when > I ran Refmac5 for the Refinement. Has anyone had this issue before? And can > anyone suggest a PDB format that will work in Refmac5? > > Thanks, > Kathleen > > Well - if you have done what you say it should work.. Here is an example output from coot I think.. ATOM 367 N AASN A 47 100.099 30.157 38.611 0.50 35.38 N ATOM 368 N BASN A 47 100.071 30.021 38.850 0.50 34.89 N ATOM 369 CA AASN A 47 100.973 30.544 39.734 0.50 34.32 C ATOM 370 CA BASN A 47 100.652 30.686 40.048 0.50 33.18 C ATOM 371 CB AASN A 47 102.212 29.645 39.706 0.50 34.37 C ATOM 372 CB BASN A 47 101.486 29.746 40.934 0.50 32.39 C ATOM 373 CG AASN A 47 101.906 28.258 39.171 0.50 32.80 C ATOM 374 CG BASN A 47 101.766 30.345 42.310 0.50 29.44 C ATOM 375 OD1AASN A 47 101.360 27.422 39.882 0.50 30.40 O ATOM 376 OD1BASN A 47 101.480 31.531 42.576 0.50 23.45 O ATOM 377 ND2AASN A 47 102.256 28.010 37.902 0.50 32.31 N ATOM 378 ND2BASN A 47 102.316 29.526 43.195 0.50 24.43 N and so on eleanor You must have all the residue number together but it doesnt really matter if you have all A then all B conformers.. CCP4bb navigationCCP4bb <-- 2008 <-- May 2008 <-- 14 May 2008 |
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