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Dear Lu Yu, SHELXL is usually very stable so there must be an error in your .ins file, but it is difficult fo us to guess what it is without seeing the full file. A common error that can cause such instability is caused by a long-standing bug in Coot, which sets some occupancies in the .ins file to 1.0 (meaning that they can be refined freely starting at 1.0) rather than the usual 11.0 (which means that they should be fixed at 1.0; you can add 10 to a parameter to fix it). Another possibility is that Coot has not understood a 'free variable' that has been used for e.g. occupancy refinement. The small molecule people use other graphical GUIs for SHELXL (shelXle, WinGX, Olex2, System-S, XSEED, Oscail, XSHELL etc.) that make far fewer mistakes. The .ins files written by Coot should always be checked carefully and if necessary edited before running SHELXL. Best wishes, George On 03/19/2012 05:00 PM, Lu Yu wrote: > Hi all, > > I was using SHELXL for the refinement of a small peptide molecule (6-7 > residues), and it was working for the first round. But then it gave me > an error message. I don't know what's going on and have you had the > same problems? Can you give me some suggestions? > > _For more information_: > I was using coot to read in .fcf and .res file, and after model > building, coot can generate an .ins file. I was using this .ins file > and the original .hkl for the next round of SHELXL, except I added one > line "ANIS" in the .ins file: > > "DEFS 0.02 0.1 0.01 0.04 > CGLS 10 -1 > SHEL 10 0.1 > FMAP 2 > PLAN 200 2.3 > LIST 6 > WPDB 2 > *ANIS*" > > I checked the working .ins and not-working (generated from coot) .ins > files, > 1)*the working .ins* (generated from .res file at the very beginning) > has: > > "WGHT 0.100000 > SWAT 1.352762 2.1931 > FVAR 2.6206 0.5 0.5 0.5 0.5" > > 2) *the not-workind(generated from coot) .ins* has: > > "WGHT 0.1 > FVAR 1.00000" > > *The refinement is shown as follows:* > "Read instructions and data > ** Warning: unusual EXTI or SWAT parameter ** > ** Warning: 8 bad CHIV instructions ignored ** > Data: 6342 unique, 0 suppressed R(int) = 0.0000 R(sigma) > = 0.0615 > Systematic absence violations: 0 Bad equivalents: 0 > wR2 = 0.4370 before cycle 1 for 6058 data and 1690 / 1690 > parameters > GooF = S = 4.279; Restrained GooF = 5.862 for 2243 > restraints > Max. shift = 0.259 A for O_1131b Max. dU =-0.409 for O_1131b at > 06:08:24 > wR2 = 0.7365 before cycle 2 for 6058 data and 1690 / 1690 > parameters > GooF = S = 12.229; Restrained GooF = 12.221 for 2243 > restraints > Max. shift = 0.175 A for O_2131a Max. dU =-0.157 for O_5017 at > 06:08:25 > > ** REFINEMENT UNSTABLE **" > > > > The other peptide dataset also has similar problem: > I was using coot-SHELXL, model building - refinement cycle > *successfully for the first 3 rounds*, but then, it gave me an error > message: > > "Read instructions and data > ** Warning: unusual EXTI or SWAT parameter ** > ** Warning: no match for 1 atoms in CONN ** > > ** CANNOT RESOLVE ISOR .. O > LAST **" > > I checked the working .ins and not-working .ins files (both generated > from coot this case), > 1) the *working .ins*: > "WGHT 0.100000 > SWAT 1.288932 3.0398 > FVAR 2.6472 0.5 0.5" > > 2) the*not-working .ins*: > "WGHT 0.100000 > SWAT 1.344708 3.0452 > FVAR 2.731 0.54231 0.5409" > > I was really confused, since I was using coot for model building for > other datasets, and the .ins file generated from coot is good for > SHELXL, but it didn't work all the time, eg. it work for the first few > rounds, then there is a problem. > > Can you give me some suggestions about what I should do to get the > SHELXL running again? > > Thanks, > Lu > -- Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-22582