version 1.0
- auxiliary/ncs.def
- Skew matrix incorrectly applied
- xtal_refine/composite_omit_map.inp
- Map made over most of unit cell instead of around selected atoms
- xtal_refine/refine.inp
- Atom-based parameter corrections were not applied hence cis-peptides were not correctly handled
- xtal_refine/*.inp
- Anisotropic scaling incorrectly applied to intensities for the MLI target
version 0.9a
- xtal_twin/*.inp
- Incorrect number of reflections selected in some spacegroups
version 0.9
- general/generate_seq.inp
- Incorrect renumbering of protein chains.
- xtal_mr/cross_rotation.inp
- Incorrect rotation results for fastdirect option.
- xtal_refine/refine.inp
- Output coordinate file incorrectly named when user provides an
input MTF file.
- xtal_twin/detect_twinning.inp
- Crashes if the input amplitude data is of type complex.
- xtal_twin/detwin_partial.inp
- Crashes if no input or output test set array is selected.
- xtal_twin/detwin_perfect.inp
- Crashes if no input or output test set array is selected.
version 0.5
- general/generate.inp
- Incorrect patching of RNA to DNA with multiple segids.
- general/generate_seq.inp
- Incorrect patching of RNA to DNA with multiple segids.
- general/generate_easy.inp
- There is no option to patch RNA to DNA.
- auxiliary/ncs.def
- Calling script terminates if all NCS restraint slots are used
in a restraint group.
- xtal_mmcif/deposit_mmcif.inp
- Anomalous data treated incorrectly.
- xtal_mr/cross_rotation.inp
- For the realspace rotation search the size of the model P1 box
is incorrectly calculated if only a subset of the structure read
in is used as the search model.
- xtal_patterson/patterson_map.inp
- The 3-d Patterson map only covers the asymmetric unit even
when the Harker sections are plotted over the extent of the unit
cell.
- xtal_patterson/predict_patterson.inp
- The 3-d Patterson map only covers the asymmetric unit even
when the Harker sections are plotted over the extent of the unit
cell.
- xtal_phase/ir_phase.inp
- The script aborts if the derivative name is lower case in the
site database file.
- xtal_phase/mad_phase.inp
- The script aborts if the derivative name is lower case in the
site database file.
- xtal_refine/composite_omit_map.inp
- Incorrect FOM weighting using the "observed" map type option.
Inconsistant resolution limits map and refinement result in
incorrect maps.
- xtal_refine/model_map.inp
- Incorrect FOM weighting using the "observed" map type option.
Fill-in option does not use the calculated data for missing
reflections.
- xtal_refine/ncs_average_map.inp
- Incorrect FOM weighting using the "observed" map type option.
- xtal_refine/sa_omit_map.inp
- Incorrect FOM weighting using the "observed" map type option.
- xtal_util/fourier_map.inp
- When a model has been read in around which the map will be
calculated, picked peaks are not mapped as close as possible to
the molecule.
- xtal_util/scale.inp
- The script terminates when trying to applying Wilson scaling
with more than approximately 2000 residues.
- nmr_calc/anneal_cv.inp
- Script aborts if complete cross-validation is turned off
without setting all complete cross-validation flags to false.
- nmr_calc/ensemble_cv.inp
- Script aborts if complete cross-validation is turned off
without setting all complete cross-validation flags to false.
version 0.4a
- BREAK card ignored
- During MTF generation a BREAK card in a PDB file was not
recognized, resulting in a link between the residues either side of the
break.
version 0.4
- xtal_refine/composite_omit_map.inp
- Maps made using the "combined" option were heavily biased
towards the model.
- xtal_phase/mad_refine.inp
- Minor typo caused the script to abort.
- xtal_phase/mad_phase.inp
- Minor typo caused the script to abort.
- xtal_refine/water_pick.inp
- Atoms with unknown coordinates could cause the script to crash
during refinement of newly picked waters.
version 0.3 patch level c
- xtal_mr/translation.inp
- Incorrect results using a fixed part of a structure.
- xtal_phase/density_modify.inp
- Merging input and output reciprocal space arrays writes out
temporary arrays also.
- xtal_phase/wang_mask.inp
- Job aborts if array FOM is not declared in input reflection file.
- xtal_refine/bdomain.inp
- Job aborts if there are any atoms with unknown coordinates.
- xtal_refine/bgroup.inp
- Job aborts if there are any atoms with unknown coordinates.
- xtal_refine/bindividual.inp
- Job aborts if there are any atoms with unknown coordinates.
- xtal_refine/composite_omit_map.inp
- Job aborts if the map types "standard" or "observed" are used.
- xtal_refine/optimize_rweight.inp
- Job aborts if there are any atoms with unknown coordinates.
- xtal_refine/optimize_wa.inp
- Small errors in sigmaa estimates for maximum likelihood targets.
- xtal_refine/qgroup.inp
- Job aborts if there are any atoms with unknown coordinates.
- xtal_refine/qindividual.inp
- Job aborts if there are any atoms with unknown coordinates.
- xtal_refine/rigid.inp
- Job aborts if there are any atoms with unknown coordinates.
- xtal_refine/optimize_rweight.inp
- Job aborts if there are any atoms with unknown coordinates.
- xtal_util/model_stats.inp
- Estimation of coordinate error by sigmaa uses all data
regardless of low resolution limit given for error estimate.