servalcat 0.4.72__cp38-cp38-macosx_11_0_arm64.whl → 0.4.99__cp38-cp38-macosx_11_0_arm64.whl

servalcat/refine/refine_spa.py

@@ -14,12 +14,12 @@ from servalcat import utils
 from servalcat.spa.run_refmac import check_args, process_input, calc_fsc, calc_fofc
 from servalcat.spa import fofc
 from servalcat.refine import spa
-from servalcat.refine.refine import Geom, Refine
+from servalcat.refine.refine import Geom, Refine, update_meta, print_h_options
 from servalcat.refmac import refmac_keywords
 b_to_u = utils.model.b_to_u
 
 def add_arguments(parser):
-    parser.description = "EXPERIMENTAL program to refine cryo-EM SPA structures"
+    parser.description = "program to refine cryo-EM SPA structures"
     group = parser.add_mutually_exclusive_group(required=True)
     group.add_argument("--halfmaps", nargs=2, help="Input half map files")
     group.add_argument("--map", help="Use this only if you really do not have half maps.")
@@ -53,8 +53,10 @@ def add_arguments(parser):
                         help="Monomer library path. Default: $CLIBD_MON")
     parser.add_argument('--ligand', nargs="*", action="append",
                         help="restraint dictionary cif file(s)")
+    parser.add_argument('--newligand_continue', action='store_true',
+                        help="Make ad-hoc restraints for unknown ligands (not recommended)")
     parser.add_argument('--hydrogen', default="all", choices=["all", "yes", "no"],
-                        help="all: add riding hydrogen atoms, yes: use hydrogen atoms if present, no: remove hydrogen atoms in input. "
+                        help="all: (re)generate hydrogen atoms, yes: use hydrogen atoms if present, no: remove hydrogen atoms in input. "
                         "Default: %(default)s")
     parser.add_argument('--hout', action='store_true', help="write hydrogen atoms in the output model")
     parser.add_argument('--jellybody', action='store_true',
@@ -65,15 +67,15 @@ def add_arguments(parser):
     parser.add_argument('--jellyonly', action='store_true',
                         help="Jelly body only (experimental, may not be useful)")
     utils.symmetry.add_symmetry_args(parser) # add --pg etc
-    parser.add_argument('--contacting_only', action="store_true", help="Filter out non-contacting NCS")
-    parser.add_argument('--ignore_symmetry',
+    parser.add_argument('--contacting_only', action="store_true", help="Filter out non-contacting strict NCS copies")
+    parser.add_argument('--ignore_symmetry', action='store_true',
                         help='Ignore symmetry information (MTRIX/_struct_ncs_oper) in the model file')
     parser.add_argument('--find_links', action='store_true', 
                         help='Automatically add links')
     parser.add_argument('--no_check_ncs_overlaps', action='store_true', 
-                        help='Disable model overlap (e.g. expanded model is used with --pg) test')
+                        help='Disable model overlap test due to strict NCS')
     parser.add_argument('--no_check_ncs_map', action='store_true', 
-                        help='Disable map NCS consistency test')
+                        help='Disable map symmetry test due to strict NCS')
     parser.add_argument('--no_check_mask_with_model', action='store_true', 
                         help='Disable mask test using model')
     parser.add_argument('--keywords', nargs='+', action="append",
@@ -81,7 +83,7 @@ def add_arguments(parser):
     parser.add_argument('--keyword_file', nargs='+', action="append",
                         help="refmac keyword file(s)")
     parser.add_argument('--randomize', type=float, default=0,
-                        help='Shake coordinates with specified rmsd')
+                        help='Shake coordinates with the specified rmsd value')
     parser.add_argument('--ncycle', type=int, default=10,
                         help="number of CG cycles (default: %(default)d)")
     parser.add_argument('--weight', type=float,
@@ -91,21 +93,26 @@ def add_arguments(parser):
     parser.add_argument('--target_bond_rmsz_range', nargs=2, type=float, default=[0.5, 1.],
                         help='Bond rmsz range for weight adjustment (default: %(default)s)')
     parser.add_argument('--adpr_weight', type=float, default=1.,
-                        help="ADP restraint weight in B (default: %(default)f)")
+                        help="ADP restraint weight (default: %(default)f)")
+    parser.add_argument('--occr_weight', type=float, default=1.,
+                        help="Occupancy restraint weight (default: %(default)f)")
     parser.add_argument('--ncsr', action='store_true', 
                         help='Use local NCS restraints')
     parser.add_argument('--bfactor', type=float,
-                        help="reset all atomic B values to specified value")
-    parser.add_argument('--fix_xyz', action="store_true")
-    parser.add_argument('--adp',  choices=["fix", "iso", "aniso"], default="iso")
+                        help="reset all atomic B values to the specified value")
+    parser.add_argument('--fix_xyz', action="store_true",
+                        help="Fix atomic coordinates")
+    parser.add_argument('--adp',  choices=["fix", "iso", "aniso"], default="iso",
+                        help="ADP parameterization")
     parser.add_argument('--refine_all_occ', action="store_true")
     parser.add_argument('--max_dist_for_adp_restraint', type=float, default=4.)
     parser.add_argument('--adp_restraint_power', type=float)
     parser.add_argument('--adp_restraint_exp_fac', type=float)
     parser.add_argument('--adp_restraint_no_long_range', action='store_true')
     parser.add_argument('--adp_restraint_mode', choices=["diff", "kldiv"], default="diff")
-    parser.add_argument('--refine_h', action="store_true", help="Refine hydrogen (default: restraints only)")
-    parser.add_argument("--source", choices=["electron", "xray", "neutron"], default="electron")
+    parser.add_argument('--unrestrained',  action='store_true', help="No positional restraints")
+    parser.add_argument('--refine_h', action="store_true", help="Refine hydrogen against data (default: only restraints apply)")
+    parser.add_argument("-s", "--source", choices=["electron", "xray", "neutron"], default="electron")
     parser.add_argument('-o','--output_prefix', default="refined")
     parser.add_argument('--cross_validation', action='store_true',
                         help='Run cross validation. Only "throughout" mode is available (no "shake" mode)')
@@ -138,11 +145,23 @@ def main(args):
     params["write_trajectory"] = args.write_trajectory
 
     st = utils.fileio.read_structure(args.model)
-    try:
-        monlib = utils.restraints.load_monomer_library(st, monomer_dir=args.monlib, cif_files=args.ligand,
-                                                       stop_for_unknowns=True, params=params)
-    except RuntimeError as e:
-        raise SystemExit("Error: {}".format(e))
+    if args.unrestrained:
+        monlib = gemmi.MonLib()
+        topo = None
+        if args.hydrogen == "all":
+            logger.writeln("\nWARNING: in unrestrained refinement hydrogen atoms are not generated.\n")
+            args.hydrogen = "yes"
+        elif args.hydrogen == "no":
+            st.remove_hydrogens()
+        for i, cra in enumerate(st[0].all()):
+            cra.atom.serial = i + 1
+    else:
+        try:
+            monlib = utils.restraints.load_monomer_library(st, monomer_dir=args.monlib, cif_files=args.ligand,
+                                                           stop_for_unknowns=not args.newligand_continue,
+                                                           params=params)
+        except RuntimeError as e:
+            raise SystemExit("Error: {}".format(e))
     if not args.keep_entities:
         utils.model.setup_entities(st, clear=True, force_subchain_names=True, overwrite_entity_type=True)
     if not args.keep_charges:
@@ -161,7 +180,8 @@ def main(args):
         st.spacegroup_hm = hkldata.sg.xhm()
         st.setup_cell_images()
         info = {}
-        utils.restraints.find_and_fix_links(st, monlib, add_found=args.find_links)
+        utils.restraints.find_and_fix_links(st, monlib, find_metal_links=args.find_links,
+                                            add_found=args.find_links)
     else:
         if args.halfmaps:
             maps = utils.fileio.read_halfmaps(args.halfmaps, pixel_size=args.pixel_size)
@@ -180,6 +200,8 @@ def main(args):
     except RuntimeError as e:
         raise SystemExit("Error: {}".format(e))
 
+    print_h_options(h_change, st[0].has_hydrogen(), args.refine_h, args.hout, geom_only=False)
+
     # initialize ADP
     utils.model.reset_adp(st[0], args.bfactor, args.adp)
 
@@ -208,8 +230,8 @@ def main(args):
         ncslist = utils.restraints.prepare_ncs_restraints(st)
     else:
         ncslist = False
-    geom = Geom(st, topo, monlib, shake_rms=args.randomize, adpr_w=args.adpr_weight,
-                params=params, unrestrained=args.jellyonly,
+    geom = Geom(st, topo, monlib, shake_rms=args.randomize, adpr_w=args.adpr_weight, occr_w=args.occr_weight,
+                params=params, unrestrained=args.unrestrained or args.jellyonly,
                 ncslist=ncslist)
     ll = spa.LL_SPA(hkldata, st, monlib,
                     lab_obs="F_map1" if args.cross_validation else "FP",
@@ -218,6 +240,7 @@ def main(args):
                      refine_xyz=not args.fix_xyz,
                      adp_mode=dict(fix=0, iso=1, aniso=2)[args.adp],
                      refine_h=args.refine_h,
+                     unrestrained=args.unrestrained,
                      params=params,
                      refine_occ=args.refine_all_occ)
 
@@ -241,12 +264,8 @@ def main(args):
         refiner.st.cell = maps[0][0].unit_cell
         refiner.st.setup_cell_images()
 
-    refiner.st.name = args.output_prefix
-    utils.fileio.write_model(refiner.st, args.output_prefix, pdb=True, cif=True, hout=args.hout)
     if params["write_trajectory"]:
         utils.fileio.write_model(refiner.st_traj, args.output_prefix + "_traj", cif=True)
-    if args.hklin:
-        return
         
     # Expand sym here
     st_expanded = refiner.st.clone()
@@ -255,20 +274,28 @@ def main(args):
         utils.fileio.write_model(st_expanded, args.output_prefix+"_expanded", pdb=True, cif=True, hout=args.hout)
 
     # Calc FSC
-    mask = utils.fileio.read_ccp4_map(args.mask)[0] if args.mask else None
-    fscavg_text = calc_fsc(st_expanded, args.output_prefix, maps,
-                           args.resolution, mask=mask, mask_radius=args.mask_radius if not args.no_mask else None,
-                           soft_edge=args.mask_soft_edge,
-                           b_before_mask=args.b_before_mask,
-                           no_sharpen_before_mask=args.no_sharpen_before_mask,
-                           make_hydrogen="yes", # no change needed in the model
-                           monlib=monlib, 
-                           blur=args.blur,
-                           d_min_fsc=args.fsc_resolution,
-                           cross_validation=args.cross_validation,
-                           cross_validation_method=args.cross_validation_method
-                           )
-    
+    if args.hklin: # cannot update a mask
+        stats_for_meta = stats[-1]
+    else:
+        mask = utils.fileio.read_ccp4_map(args.mask)[0] if args.mask else None
+        fscavg_text, stats2 = calc_fsc(st_expanded, args.output_prefix, maps,
+                                       args.resolution, mask=mask, mask_radius=args.mask_radius if not args.no_mask else None,
+                                       soft_edge=args.mask_soft_edge,
+                                       b_before_mask=args.b_before_mask,
+                                       no_sharpen_before_mask=args.no_sharpen_before_mask,
+                                       make_hydrogen="yes", # no change needed in the model
+                                       monlib=monlib,
+                                       blur=args.blur,
+                                       d_min_fsc=args.fsc_resolution,
+                                       cross_validation=args.cross_validation,
+                                       cross_validation_method=args.cross_validation_method
+                                       )
+        stats_for_meta = {"geom": stats[-1]["geom"], "data": stats2}
+    update_meta(refiner.st, stats_for_meta, ll)
+    refiner.st.name = args.output_prefix
+    utils.fileio.write_model(refiner.st, args.output_prefix, pdb=True, cif=True, hout=args.hout)
+    if args.hklin:
+        return
     # Calc Fo-Fc (and updated) maps
     diffmap_prefix = "{}_diffmap".format(args.output_prefix)
     calc_fofc(refiner.st, st_expanded, maps, monlib, ".mmcif", args, diffmap_prefix=diffmap_prefix)
@@ -316,6 +343,9 @@ Weight used: {final_weight:.3e}
 Open refined model and {diffmap_prefix}.mtz with COOT:
 coot --script {prefix}_coot.py
 
+Open refined model, map and difference map with ChimeraX/ISOLDE:
+chimerax {prefix}_chimerax.cxc
+
 {map_peaks_msg}
 =============================================================================
 """.format(rmsbond=rmsbond,

servalcat/refine/refine_xtal.py

@@ -8,19 +8,21 @@ Mozilla Public License, version 2.0; see LICENSE.
 from __future__ import absolute_import, division, print_function, generators
 import gemmi
 import numpy
+import pandas
 import os
 import shutil
 import argparse
 from servalcat.utils import logger
 from servalcat import utils
-from servalcat.xtal.sigmaa import decide_mtz_labels, process_input, calculate_maps, calculate_maps_int
+from servalcat.xtal.sigmaa import decide_mtz_labels, process_input, calculate_maps, calculate_maps_int, calculate_maps_twin
 from servalcat.refine.xtal import LL_Xtal
-from servalcat.refine.refine import Geom, Refine
+from servalcat.refine.refine import Geom, Refine, update_meta, print_h_options
 from servalcat.refmac import refmac_keywords
+from servalcat import ext
 b_to_u = utils.model.b_to_u
 
 def add_arguments(parser):
-    parser.description = "EXPERIMENTAL program to refine crystallographic structures"
+    parser.description = "program to refine crystallographic structures"
     parser.add_argument("--hklin", required=True)
     parser.add_argument("-d", '--d_min', type=float)
     parser.add_argument('--d_max', type=float)
@@ -35,6 +37,8 @@ def add_arguments(parser):
                         help="Monomer library path. Default: $CLIBD_MON")
     parser.add_argument('--ligand', nargs="*", action="append",
                         help="restraint dictionary cif file(s)")
+    parser.add_argument('--newligand_continue', action='store_true',
+                        help="Make ad-hoc restraints for unknown ligands (not recommended)")
     parser.add_argument('--hydrogen', default="all", choices=["all", "yes", "no"],
                         help="all: add riding hydrogen atoms, yes: use hydrogen atoms if present, no: remove hydrogen atoms in input. "
                         "Default: %(default)s")
@@ -60,10 +64,14 @@ def add_arguments(parser):
                         help="refinement weight (default: auto)")
     parser.add_argument('--no_weight_adjust', action='store_true', 
                         help='Do not adjust weight during refinement')
+    parser.add_argument('--target_bond_rmsz_range', nargs=2, type=float, default=[0.5, 1.],
+                        help='Bond rmsz range for weight adjustment (default: %(default)s)')
     parser.add_argument('--ncsr', action='store_true', 
                         help='Use local NCS restraints')
     parser.add_argument('--adpr_weight', type=float, default=1.,
                         help="ADP restraint weight (default: %(default)f)")
+    parser.add_argument('--occr_weight', type=float, default=1.,
+                        help="Occupancy restraint weight (default: %(default)f)")
     parser.add_argument('--bfactor', type=float,
                         help="reset all atomic B values to specified value")
     parser.add_argument('--fix_xyz', action="store_true")
@@ -76,6 +84,7 @@ def add_arguments(parser):
     parser.add_argument('--adp_restraint_mode', choices=["diff", "kldiv"], default="kldiv")
     parser.add_argument('--unrestrained',  action='store_true', help="No positional restraints")
     parser.add_argument('--refine_h', action="store_true", help="Refine hydrogen (default: restraints only)")
+    parser.add_argument('--twin', action="store_true", help="Turn on twin refinement")
     parser.add_argument("-s", "--source", choices=["electron", "xray", "neutron"], required=True)
     parser.add_argument('--no_solvent',  action='store_true',
                         help="Do not consider bulk solvent contribution")
@@ -83,9 +92,14 @@ def add_arguments(parser):
                         help="Use work reflections in ML parameter estimates")
     parser.add_argument('--keep_charges',  action='store_true',
                         help="Use scattering factor for charged atoms. Use it with care.")
+    parser.add_argument("--keep_entities", action='store_true',
+                        help="Do not override entities")
+    parser.add_argument('--allow_unusual_occupancies', action="store_true", help="Allow negative or more than one occupancies")
     parser.add_argument('-o','--output_prefix')
     parser.add_argument("--write_trajectory", action='store_true',
                         help="Write all output from cycles")
+    parser.add_argument("--vonmises", action='store_true',
+                        help="Experimental: von Mises type restraint for angles")
 # add_arguments()
 
 def parse_args(arg_list):
@@ -140,7 +154,8 @@ def main(args):
                                                                                  n_per_bin=n_per_bin,
                                                                                  use=use_in_est,
                                                                                  max_bins=30,
-                                                                                 keep_charges=args.keep_charges)
+                                                                                 keep_charges=args.keep_charges,
+                                                                                 allow_unusual_occupancies=args.allow_unusual_occupancies)
     except RuntimeError as e:
         raise SystemExit("Error: {}".format(e))
 
@@ -150,20 +165,25 @@ def main(args):
     if args.unrestrained:
         monlib = gemmi.MonLib()
         topo = None
+        h_change = gemmi.HydrogenChange.NoChange
         if args.hydrogen == "all":
-            logger.writeln("WARNING: in unrestrained refinement hydrogen atoms are not generated.")
+            logger.writeln("\nWARNING: in unrestrained refinement hydrogen atoms are not generated.\n")
         elif args.hydrogen == "no":
             st.remove_hydrogens()
+            h_change = gemmi.HydrogenChange.Remove
         for i, cra in enumerate(st[0].all()):
             cra.atom.serial = i + 1
     else:
         try:
             monlib = utils.restraints.load_monomer_library(st, monomer_dir=args.monlib, cif_files=args.ligand,
-                                                           stop_for_unknowns=True, params=params)
+                                                           stop_for_unknowns=not args.newligand_continue,
+                                                           params=params)
         except RuntimeError as e:
             raise SystemExit("Error: {}".format(e))
-        utils.model.setup_entities(st, clear=True, force_subchain_names=True, overwrite_entity_type=True)
-        utils.restraints.find_and_fix_links(st, monlib, add_found=args.find_links)
+        if not args.keep_entities:
+            utils.model.setup_entities(st, clear=True, force_subchain_names=True, overwrite_entity_type=True)
+        utils.restraints.find_and_fix_links(st, monlib, find_metal_links=args.find_links,
+                                            add_found=args.find_links)
         h_change = {"all":gemmi.HydrogenChange.ReAddKnown,
                     "yes":gemmi.HydrogenChange.NoChange,
                     "no":gemmi.HydrogenChange.Remove}[args.hydrogen]
@@ -174,6 +194,8 @@ def main(args):
         except RuntimeError as e:
             raise SystemExit("Error: {}".format(e))
 
+    print_h_options(h_change, st[0].has_hydrogen(), args.refine_h, args.hout, geom_only=False)
+    
     # initialize ADP
     utils.model.reset_adp(st[0], args.bfactor, args.adp)
         
@@ -188,9 +210,10 @@ def main(args):
         ncslist = utils.restraints.prepare_ncs_restraints(st)
     else:
         ncslist = False
-    geom = Geom(st, topo, monlib, shake_rms=args.randomize, adpr_w=args.adpr_weight, params=params,
+    geom = Geom(st, topo, monlib, shake_rms=args.randomize, adpr_w=args.adpr_weight, occr_w=args.occr_weight, params=params,
                 unrestrained=args.unrestrained or args.jellyonly, use_nucleus=(args.source=="neutron"),
                 ncslist=ncslist)
+    geom.geom.angle_von_mises = args.vonmises
     geom.geom.adpr_max_dist = args.max_dist_for_adp_restraint
     if args.adp_restraint_power is not None: geom.geom.adpr_d_power = args.adp_restraint_power
     if args.adp_restraint_exp_fac is not None: geom.geom.adpr_exp_fac = args.adp_restraint_exp_fac
@@ -201,7 +224,8 @@ def main(args):
     if args.jellyonly: geom.geom.ridge_exclude_short_dist = False
 
     ll = LL_Xtal(hkldata, centric_and_selections, args.free, st, monlib, source=args.source,
-                 use_solvent=not args.no_solvent, use_in_est=use_in_est, use_in_target=use_in_target)
+                 use_solvent=not args.no_solvent, use_in_est=use_in_est, use_in_target=use_in_target,
+                 twin=args.twin)
     refiner = Refine(st, geom, ll=ll,
                      refine_xyz=not args.fix_xyz,
                      adp_mode=dict(fix=0, iso=1, aniso=2)[args.adp],
@@ -212,13 +236,19 @@ def main(args):
 
     stats = refiner.run_cycles(args.ncycle, weight=args.weight,
                                weight_adjust=not args.no_weight_adjust,
+                               weight_adjust_bond_rmsz_range=args.target_bond_rmsz_range,
                                stats_json_out=args.output_prefix + "_stats.json")
+    update_meta(st, stats[-1], ll)
     refiner.st.name = args.output_prefix
     utils.fileio.write_model(refiner.st, args.output_prefix, pdb=True, cif=True, hout=args.hout)
     if params["write_trajectory"]:
         utils.fileio.write_model(refiner.st_traj, args.output_prefix + "_traj", cif=True)
 
-    if is_int:
+    if ll.twin_data:
+        # replace hkldata
+        hkldata = calculate_maps_twin(ll.hkldata, ll.b_aniso, ll.fc_labs, ll.D_labs, ll.twin_data,
+                                      centric_and_selections, use=use_in_target)
+    elif is_int:
         calculate_maps_int(ll.hkldata, ll.b_aniso, ll.fc_labs, ll.D_labs, centric_and_selections,
                            use=use_in_target)
     else:
@@ -226,7 +256,9 @@ def main(args):
                        use=use_in_target)
 
     # Write mtz file
-    if is_int:
+    if ll.twin_data:
+        labs = ["F_est", "F_exp", "FOM"]
+    elif is_int:
         labs = ["I", "SIGI", "FOM"]
     else:
         labs = ["FP", "SIGFP", "FOM"]
@@ -239,7 +271,7 @@ def main(args):
         labs.append("FREE")
     labs += ll.D_labs + ["S"] # for debugging, for now
     mtz_out = args.output_prefix+".mtz"
-    hkldata.write_mtz(mtz_out, labs=labs, types={"FOM": "W", "FP":"F", "SIGFP":"Q", "I":"J", "SIGI":"Q"})
+    hkldata.write_mtz(mtz_out, labs=labs, types={"FOM": "W", "FP":"F", "SIGFP":"Q", "I":"J", "SIGI":"Q", "F_est": "F", "F_exp": "F"})
 
 # main()
 

servalcat/refine/spa.py

@@ -38,8 +38,14 @@ class LL_SPA:
         self.lab_obs = lab_obs
         self.st = st
         self.monlib = monlib
-        self.d_min = hkldata.d_min_max()[0]
+        self.d_min_max = hkldata.d_min_max()
         self.ll = None
+        self.b_aniso = None
+
+    def refine_id(self):
+        if self.source == "electron":
+            return "ELECTRON MICROSCOPY"
+        return "NON-EM SPA" # does not happen, I guess
 
     def update_ml_params(self):
         # FIXME make sure D > 0
@@ -52,12 +58,15 @@ class LL_SPA:
         else:
             st = self.st
 
-        self.hkldata.df["FC"] = utils.model.calc_fc_fft(st, self.d_min - 1e-6,
+        self.hkldata.df["FC"] = utils.model.calc_fc_fft(st, self.d_min_max[0] - 1e-6,
                                                         monlib=self.monlib,
                                                         source=self.source,
                                                         mott_bethe=self.mott_bethe,
                                                         miller_array=self.hkldata.miller_array())
 
+    def prepare_target(self):
+        pass
+
     def overall_scale(self, min_b=0.5):
         k, b = self.hkldata.scale_k_and_b(lab_ref=self.lab_obs, lab_scaled="FC")
         min_b_iso = self.st[0].calculate_b_aniso_range()[0] # actually min of aniso too
@@ -89,15 +98,17 @@ class LL_SPA:
         stats = fsc.calc_fsc_all(self.hkldata, labs_fc=["FC"], lab_f=self.lab_obs)
         fsca = fsc.fsc_average(stats.ncoeffs, stats.fsc_FC_full)
         logger.writeln("FSCaverage = {:.4f}".format(fsca))
+        ret = {"summary": {"FSCaverage": fsca, "-LL": self.calc_target()}}
         # XXX in fsc object, _full is misleading - it's not full in cross validation mode
         if "D" in self.hkldata.binned_df and "S" in self.hkldata.binned_df:
             stats[["D", "S"]] = self.hkldata.binned_df[["D", "S"]]
-        return {"bin_stats": stats, "summary": {"FSCaverage": fsca, "-LL": self.calc_target()}}
+        ret["bin_stats"] = stats
+        return ret
 
     def calc_grad(self, atom_pos, refine_xyz, adp_mode, refine_occ, refine_h, specs):
         dll_dab = numpy.empty_like(self.hkldata.df[self.lab_obs])
         d2ll_dab2 = numpy.zeros(len(self.hkldata.df.index))
-        blur = utils.model.determine_blur_for_dencalc(self.st, self.d_min / 3) # TODO need more work
+        blur = utils.model.determine_blur_for_dencalc(self.st, self.d_min_max[0] / 3) # TODO need more work
         logger.writeln("blur for deriv= {:.2f}".format(blur))
         for i_bin, idxes in self.hkldata.binned():
             D = self.hkldata.binned_df.D[i_bin]