[ccp4bb] refmac low resolution REMARK
Dear Developers, it seems to me that at least Refmac 5.6.0117 does not report the actual lowest resolution used in refinement, but instead the lowest resolution of the hkl index range generated by the default cif import script instead. REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.99 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.63 <--- The data go only to 28.66 A according to mtzdump as well as xprep as far as I can tell, cif2mtz does it right and reports * Cell Dimensions : (obsolete - refer to dataset cell dimensions above) 33.1300 57.2300 38.6500 90. 91.9400 90. * Resolution Range : 0.001220.25305 ( 28.660 - 1.988 A ) < - then the script calls unique which pads the reflections up * Cell Dimensions : (obsolete - refer to dataset cell dimensions above) 33.1300 57.2300 38.6500 90. 91.9400 90. * Resolution Range : 0.000670.25302 ( 38.628 - 1.988 A ) <- which then propagates to CAD and FREEFLAG into the MTZ header where it is picked up by refmac. OVERALL FILE STATISTICS for resolution range 0.001 - 0.253 === Col SortMinMaxNum % Mean Mean Resolution Type Column num order Missing complete abs. LowHigh label 1 ASC-16 16 0 100.00 0.1 6.3 38.63 1.99 H H 2 NONE 0 28 0 100.00 10.5 10.5 38.63 1.99 H K 3 NONE 0 19 0 100.00 7.3 7.3 38.63 1.99 H L 4 NONE0.0 9.0 0 100.00 4.50 4.50 38.63 1.99 I FREE 5 NONE7.7 707.8 361 96.40 102.76 102.76 28.66 1.99 F FP <- this is the right number! 6 NONE1.637.3 361 96.40 8.84 8.84 28.66 1.99 Q SIGFP I have noticed that other PDB/sf file sets (not mine) seem to be affected as well. Best regards, BR - Bernhard Rupp 001 (925) 209-7429 +43 (676) 571-0536 b...@ruppweb.org hofkristall...@gmail.com http://www.ruppweb.org/ - No animals were hurt or killed during the production of this email. -
Re: [ccp4bb] Refmac and metal on a two-fold?
On Sun, 2012-01-01 at 12:14 -0600, Dima Klenchin wrote: > With Garib's help, I have forced the atom into its position by using > external distance restrains of zero length against the same > symmetry-related atom. The cause is unclear because the same program > handles special positions in another structure just fine. Thanks - good to know. Perhaps a good practice is to take care of special positions manually every time just in case. >From what I understand, the way refinement software generally treats special positions (other than automatically resetting occupancy to 1/z) is to exclude vdw repulsion to symmetry-related atom which in this case would always push the atom out of position. Exclusion is usually applied to the atom when it is within the cutoff distance (0.1A?) from the corresponding symmetry element. If for whatever reason the atom shifts, the vdw will push it out. Why would such atoms shift varies - I suspect in some cases it is due to hydrogen bonding restraints, in others it could be due to noisy density. -- Oh, suddenly throwing a giraffe into a volcano to make water is crazy? Julian, King of Lemurs
Re: [ccp4bb] Refmac and metal on a two-fold?
Good to know, thanks. I was actually wondering about this recently. On Sun, Jan 1, 2012 at 1:14 PM, Dima Klenchin wrote: > I've seen this happening to water molecules as well (in a somewhat >> unpredictable fashion). In the latest refmac versions, you can try >> harmonic restraints, although these will only slow down the atom drift, >> as the target position is updated every cycle. >> >> Perhaps you can use distance restraints against a dummy atom to fix the >> metal ion in place. >> > > Thanks, Ed! > > Just in case anyone else has the same issue: > > With Garib's help, I have forced the atom into its position by using > external distance restrains of zero length against the same > symmetry-related atom. The cause is unclear because the same program > handles special positions in another structure just fine. Here is the exact > command I used: > > EXTERNAL DISTANCE first chain M residue 3 atom MN - > second chain M residue 3 atom MN value 0.0 sigma 0.00 symm Y > > Occupancy set manually to 0.5. > > - Dima >
Re: [ccp4bb] Refmac and metal on a two-fold?
I've seen this happening to water molecules as well (in a somewhat unpredictable fashion). In the latest refmac versions, you can try harmonic restraints, although these will only slow down the atom drift, as the target position is updated every cycle. Perhaps you can use distance restraints against a dummy atom to fix the metal ion in place. Thanks, Ed! Just in case anyone else has the same issue: With Garib's help, I have forced the atom into its position by using external distance restrains of zero length against the same symmetry-related atom. The cause is unclear because the same program handles special positions in another structure just fine. Here is the exact command I used: EXTERNAL DISTANCE first chain M residue 3 atom MN - second chain M residue 3 atom MN value 0.0 sigma 0.00 symm Y Occupancy set manually to 0.5. - Dima
Re: [ccp4bb] Refmac and metal on a two-fold?
I've seen this happening to water molecules as well (in a somewhat unpredictable fashion). In the latest refmac versions, you can try harmonic restraints, although these will only slow down the atom drift, as the target position is updated every cycle. Perhaps you can use distance restraints against a dummy atom to fix the metal ion in place. Another remedy might be to manually place the metal ion in position followed by zero cycles of refinement to get the final R-values. There is some evidence that excluding isolated atoms from refinement may introduce some systematic error on the rest of the structure, but it is likely very small. Cheers, Ed. On Wed, 2011-12-28 at 13:29 -0600, Dima Klenchin wrote: > Hello, > > I have a metal ion sitting on a two-fold. I assigned it an occupancy of 0.5 > but Refmac keeps refining it away from that position so that in the end > there is a symmetry-related ion 1.6A away. I thought that this problem has > been rectified long ago? Certainly I had several occasions where Refmac > would automatically recognize special position and automatically assigned > proper occupancy (1/n). Not sure why this particular case is different... > > This behavior is the same in: > > Refmac 5.5.0088 (Windows) > Refmac 5.5.0102 (Windows) > Refmac 5.6.0117 (Windows) > Refmac 5.5.0109 (Linux) > > I also tried leaving it at occupancy 1.0 and also tried renaming MN2+ to > water at occupancies of 0.5 and 1.0. All to no avail - the atom is always > shifted away from the density. > > Anything I can do to force Refmac to keep it nice and tidy? > > Thanks and Happy New Year! > > - Dima
