servalcat 0.4.99__tar.gz → 0.4.105__tar.gz

{servalcat-0.4.99 → servalcat-0.4.105}/CMakeLists.txt

@@ -91,7 +91,7 @@ else()
     FetchContent_Declare(
       gemmi
       GIT_REPOSITORY https://github.com/project-gemmi/gemmi.git
-      GIT_TAG        v0.7.0
+      GIT_TAG        v0.7.1
     )
     FetchContent_GetProperties(gemmi)
     if (NOT gemmi_POPULATED)

{servalcat-0.4.99 → servalcat-0.4.105}/PKG-INFO

@@ -1,16 +1,16 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.2
 Name: servalcat
-Version: 0.4.99
+Version: 0.4.105
 Summary: Structure refinement and validation for crystallography and single particle analysis
 Author: Keitaro Yamashita, Garib N. Murshudov
 License: MPL-2.0
-Project-URL: Repository, https://github.com/keitaroyam/servalcat
+Project-URL: repository, https://github.com/keitaroyam/servalcat
 Requires-Python: >=3.8
 Requires-Dist: packaging
 Requires-Dist: numpy>=1.15
 Requires-Dist: scipy
 Requires-Dist: pandas>=1.1.0
-Requires-Dist: gemmi==0.7.0
+Requires-Dist: gemmi==0.7.1
 Description-Content-Type: text/markdown
 
 # Servalcat
@@ -40,7 +40,7 @@ pip install servalcat
 ```
 will install the stable version.
 
-The required GEMMI version is now [v0.7.0](https://github.com/project-gemmi/gemmi/releases/tag/v0.7.0). It may not work with the latest gemmi code from the github. The policy is in the main branch I only push the code that works with the latest package of GEMMI.
+The required GEMMI version is now [v0.7.1](https://github.com/project-gemmi/gemmi/releases/tag/v0.7.1). It may not work with the latest gemmi code from the github. The policy is in the main branch I only push the code that works with the latest package of GEMMI.
 
 To use the Refmac5 related commands, you also need to install [CCP4](https://www.ccp4.ac.uk/). For "No Refmac5" commands, you may just need [the monomer library](https://github.com/MonomerLibrary/monomers) if CCP4 is not installed.
 

{servalcat-0.4.99 → servalcat-0.4.105}/README.md

@@ -25,7 +25,7 @@ pip install servalcat
 ```
 will install the stable version.
 
-The required GEMMI version is now [v0.7.0](https://github.com/project-gemmi/gemmi/releases/tag/v0.7.0). It may not work with the latest gemmi code from the github. The policy is in the main branch I only push the code that works with the latest package of GEMMI.
+The required GEMMI version is now [v0.7.1](https://github.com/project-gemmi/gemmi/releases/tag/v0.7.1). It may not work with the latest gemmi code from the github. The policy is in the main branch I only push the code that works with the latest package of GEMMI.
 
 To use the Refmac5 related commands, you also need to install [CCP4](https://www.ccp4.ac.uk/). For "No Refmac5" commands, you may just need [the monomer library](https://github.com/MonomerLibrary/monomers) if CCP4 is not installed.
 

{servalcat-0.4.99 → servalcat-0.4.105}/pyproject.toml

@@ -1,5 +1,5 @@
 [build-system]
-requires = ["scikit-build-core~=0.10.7", "nanobind >=2.2"]
+requires = ["scikit-build-core ~=0.11.1", "nanobind >=2.2"]
 build-backend = "scikit_build_core.build"
 
 # https://packaging.python.org/en/latest/specifications/declaring-project-metadata/
@@ -7,7 +7,7 @@ build-backend = "scikit_build_core.build"
 name = "servalcat"
 dynamic = ["version"]
 requires-python = ">=3.8"
-dependencies = ['packaging', 'numpy>=1.15', 'scipy', 'pandas>=1.1.0', 'gemmi==0.7.0']
+dependencies = ['packaging', 'numpy>=1.15', 'scipy', 'pandas>=1.1.0', 'gemmi==0.7.1']
 description="Structure refinement and validation for crystallography and single particle analysis"
 readme = "README.md"
 authors = [

{servalcat-0.4.99 → servalcat-0.4.105}/servalcat/__init__.py

@@ -6,5 +6,5 @@ This software is released under the
 Mozilla Public License, version 2.0; see LICENSE.
 """
 
-__version__ = '0.4.99'
-__date__ = '2024-12-04'
+__version__ = '0.4.105'
+__date__ = '2025-03-26'

{servalcat-0.4.99 → servalcat-0.4.105}/servalcat/refine/refine.py

@@ -7,6 +7,7 @@ Mozilla Public License, version 2.0; see LICENSE.
 """
 from __future__ import absolute_import, division, print_function, generators
 import os
+import time
 import re
 import gemmi
 import numpy
@@ -221,7 +222,16 @@ def write_stats_json_safe(stats, json_out):
     out_tmp = json_out + ".part"
     with open(out_tmp, "w") as ofs:
         json.dump(tmp, ofs, indent=2)
-    os.replace(out_tmp, json_out)
+    for i in range(10):
+        try:
+            # On Windows, this fails when another process open the file
+            os.replace(out_tmp, json_out)
+            break
+        except PermissionError:
+            logger.writeln(f"{json_out} locked. retrying..")
+            time.sleep(0.5)
+    else:
+        raise RuntimeError(f"Cannot write {json_out}")
     logger.writeln(f"Refinement statistics saved: {json_out}")
 # write_stats_json_safe()
 

{servalcat-0.4.99 → servalcat-0.4.105}/servalcat/refine/refine_spa.py

@@ -150,8 +150,8 @@ def main(args):
         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":
+        if args.hydrogen != "yes":
+            args.hydrogen = "no"
             st.remove_hydrogens()
         for i, cra in enumerate(st[0].all()):
             cra.atom.serial = i + 1
@@ -271,7 +271,6 @@ def main(args):
     st_expanded = refiner.st.clone()
     if not all(op.given for op in st.ncs):
         utils.model.expand_ncs(st_expanded)
-        utils.fileio.write_model(st_expanded, args.output_prefix+"_expanded", pdb=True, cif=True, hout=args.hout)
 
     # Calc FSC
     if args.hklin: # cannot update a mask
@@ -294,11 +293,14 @@ def main(args):
     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 not all(op.given for op in st.ncs): # to apply updated metadata
+        st_expanded = refiner.st.clone()
+        utils.model.expand_ncs(st_expanded)
+        utils.fileio.write_model(st_expanded, args.output_prefix+"_expanded", 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)
+    calc_fofc(refiner.st, st_expanded, maps, monlib, ".mmcif", args, diffmap_prefix=args.output_prefix)
     
     # Final summary
     adpstats_txt = ""
@@ -317,8 +319,8 @@ def main(args):
     if args.mask_for_fofc:
         map_peaks_str = """\
 List Fo-Fc map peaks in the ASU:
-servalcat util map_peaks --map {diffmap_prefix}_normalized_fofc.mrc --model {prefix}.pdb --abs_level 4.0 \
-""".format(prefix=args.output_prefix, diffmap_prefix=diffmap_prefix)
+servalcat util map_peaks --map {prefix}_normalized_fofc.mrc --model {prefix}.pdb --abs_level 4.0 \
+""".format(prefix=args.output_prefix)
     else:
         map_peaks_str = "WARNING: --mask_for_fofc was not given, so the Fo-Fc map was not normalized."
 
@@ -340,7 +342,7 @@ Weight used: {final_weight:.3e}
              If you want to change the weight, give larger (looser restraints)
              or smaller (tighter) value to --weight=.
              
-Open refined model and {diffmap_prefix}.mtz with COOT:
+Open refined model and {prefix}_maps.mtz with COOT:
 coot --script {prefix}_coot.py
 
 Open refined model, map and difference map with ChimeraX/ISOLDE:
@@ -355,7 +357,6 @@ chimerax {prefix}_chimerax.cxc
            adpstats=adpstats_txt.rstrip(),
            final_weight=args.weight,
            prefix=args.output_prefix,
-           diffmap_prefix=diffmap_prefix,
            map_peaks_msg=map_peaks_str))
 
 # main()

{servalcat-0.4.99 → servalcat-0.4.105}/servalcat/refine/refine_xtal.py

@@ -24,11 +24,15 @@ b_to_u = utils.model.b_to_u
 def add_arguments(parser):
     parser.description = "program to refine crystallographic structures"
     parser.add_argument("--hklin", required=True)
+    parser.add_argument('--hklin_free',
+                        help='Input MTZ file for test flags')
     parser.add_argument("-d", '--d_min', type=float)
     parser.add_argument('--d_max', type=float)
     parser.add_argument('--nbins', type=int, 
                         help="Number of bins (default: auto)")
     parser.add_argument("--labin", help="F,SIGF,FREE input")
+    parser.add_argument('--labin_free',
+                        help='MTZ column of --hklin_free')
     parser.add_argument('--free', type=int,
                         help='flag number for test set')
     parser.add_argument('--model', required=True,
@@ -128,20 +132,7 @@ def main(args):
     elif utils.fileio.is_mmhkl_file(hklin):
         hklin = utils.fileio.read_mmhkl(hklin)
         labin = decide_mtz_labels(hklin)
-        
-    if labin and len(labin) == 3: # with test flags
-        use_in_target = "work"
-        if args.use_work_in_est:
-            use_in_est = "work"
-            n_per_bin = 100
-        else:
-            use_in_est = "test"
-            n_per_bin = 50
-    else:
-        use_in_est = "all"
-        use_in_target = "all"
-        n_per_bin = 100
-
+    software_items = utils.fileio.software_items_from_mtz(hklin)
     try:
         hkldata, sts, fc_labs, centric_and_selections, args.free = process_input(hklin=hklin,
                                                                                  labin=labin,
@@ -151,26 +142,39 @@ def main(args):
                                                                                  source=args.source,
                                                                                  d_max=args.d_max,
                                                                                  d_min=args.d_min,
-                                                                                 n_per_bin=n_per_bin,
-                                                                                 use=use_in_est,
+                                                                                 use="work" if args.use_work_in_est else "test",
                                                                                  max_bins=30,
                                                                                  keep_charges=args.keep_charges,
-                                                                                 allow_unusual_occupancies=args.allow_unusual_occupancies)
+                                                                                 allow_unusual_occupancies=args.allow_unusual_occupancies,
+                                                                                 hklin_free=args.hklin_free,
+                                                                                 labin_free=args.labin_free)
+
     except RuntimeError as e:
         raise SystemExit("Error: {}".format(e))
 
+    if "FREE" in hkldata.df:
+        use_in_target = "work"
+        if args.use_work_in_est:
+            use_in_est = "work"
+        else:
+            use_in_est = "test"
+    else:
+        use_in_est = "all"
+        use_in_target = "all"
+
     is_int = "I" in hkldata.df
     st = sts[0]
     utils.model.fix_deuterium_residues(st)
     if args.unrestrained:
         monlib = gemmi.MonLib()
         topo = None
-        h_change = gemmi.HydrogenChange.NoChange
-        if args.hydrogen == "all":
-            logger.writeln("\nWARNING: in unrestrained refinement hydrogen atoms are not generated.\n")
-        elif args.hydrogen == "no":
-            st.remove_hydrogens()
+        if args.hydrogen == "yes":
+            h_change = gemmi.HydrogenChange.NoChange
+        else:
             h_change = gemmi.HydrogenChange.Remove
+            st.remove_hydrogens()
+            if args.hydrogen == "all":
+                logger.writeln("\nWARNING: in unrestrained refinement hydrogen atoms are not generated.\n")
         for i, cra in enumerate(st[0].all()):
             cra.atom.serial = i + 1
     else:
@@ -239,6 +243,7 @@ def main(args):
                                weight_adjust_bond_rmsz_range=args.target_bond_rmsz_range,
                                stats_json_out=args.output_prefix + "_stats.json")
     update_meta(st, stats[-1], ll)
+    st.meta.software = software_items + st.meta.software
     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"]:
@@ -257,12 +262,12 @@ def main(args):
 
     # Write mtz file
     if ll.twin_data:
-        labs = ["F_est", "F_exp", "FOM"]
+        labs = ["F_est", "F_exp"]
     elif is_int:
-        labs = ["I", "SIGI", "FOM"]
+        labs = ["I", "SIGI", "F_est"]
     else:
-        labs = ["FP", "SIGFP", "FOM"]
-    labs.extend(["FWT", "DELFWT", "FC"])
+        labs = ["FP", "SIGFP"]
+    labs.extend(["FOM", "FWT", "DELFWT", "FC"])
     if "FAN" in hkldata.df:
         labs.append("FAN")
     if not args.no_solvent:

{servalcat-0.4.99 → servalcat-0.4.105}/servalcat/refine/xtal.py

@@ -45,7 +45,7 @@ class LL_Xtal:
         self.ll = None
         self.scaling = sigmaa.LsqScale()
         if twin:
-            self.twin_data = find_twin_domains_from_data(self.hkldata)
+            self.twin_data, _ = find_twin_domains_from_data(self.hkldata)
         else:
             self.twin_data = None
         if self.twin_data:
@@ -94,7 +94,7 @@ class LL_Xtal:
                 fc_sum = self.hkldata.df[self.fc_labs[:-1]].sum(axis=1).to_numpy()
             fc_list = [fc_sum, Fmask]
         else:
-            if twin_data:
+            if self.twin_data:
                 fc_list = [self.twin_data.f_calc.sum(axis=1)]
             else:
                 fc_list = [self.hkldata.df[self.fc_labs].sum(axis=1).to_numpy()]
@@ -235,11 +235,11 @@ class LL_Xtal:
                             m = numpy.tanh(X)
                             g = (Fc_abs - m * Fo) / Sigma * Ds[:,0]
                             dll_dab[cidxes] = g * expip
-                            d2ll_dab2[cidxes] = (1. / Sigma - (Fo / (Sigma * numpy.cosh(X)))**2) * Ds[:,0]**2
+                            d2ll_dab2[cidxes] = (1. / Sigma - (Fo / Sigma)**2 * (1. - m**2)) * Ds[:,0]**2
             dll_dab *= self.hkldata.debye_waller_factors(b_iso=-blur)
 
         if self.mott_bethe:
-            d2 = 1 / self.twin_data.s2_array if self.twin_data else self.hkldata.d_spacings()**2
+            d2 = numpy.reciprocal(self.twin_data.s2_array) if self.twin_data else self.hkldata.d_spacings()**2
             dll_dab *= d2 * gemmi.mott_bethe_const()
             d2ll_dab2 *= gemmi.mott_bethe_const()**2
 

{servalcat-0.4.99 → servalcat-0.4.105}/servalcat/refmac/refmac_wrapper.py

@@ -33,6 +33,8 @@ def add_arguments(parser):
     parser.add_argument('--keep_original_output', action='store_true', help="with .org extension")
     parser.add_argument("--keep_entities", action='store_true',
                         help="Do not override entities")
+    parser.add_argument("--tls_addu", action='store_true',
+                        help="Write prefix_addu.mmcif where TLS contribution is added to aniso U. Don't use this with 'tlso addu' keyword.")
     parser.add_argument('--prefix', help="output prefix")
     parser.add_argument("-v", "--version", action="version",
                         version=logger.versions_str())
@@ -222,7 +224,7 @@ def get_output_model_names(xyzout):
     return pdb, mmcif
 # get_output_model_names()
 
-def modify_output(pdbout, cifout, fixes, hout, cispeps, keep_original_output=False):
+def modify_output(pdbout, cifout, fixes, hout, cispeps, software_items, keep_original_output=False, tls_addu=False):
     st = utils.fileio.read_structure(cifout)
     st.cispeps = cispeps
     if os.path.exists(pdbout):
@@ -256,11 +258,37 @@ def modify_output(pdbout, cifout, fixes, hout, cispeps, keep_original_output=Fal
     # add servalcat version
     if len(st.meta.software) > 0 and st.meta.software[-1].name == "refmac":
         st.meta.software[-1].version += f" (refmacat {servalcat.__version__})"
+    st.meta.software = software_items + st.meta.software
     
     suffix = ".org"
     os.rename(cifout, cifout + suffix)
     utils.fileio.write_mmcif(st, cifout, cifout + suffix)
 
+    if tls_addu:
+        doc_ref = gemmi.cif.read(cifout + suffix)
+        tls_groups = {int(x.id): x for x in st.meta.refinement[0].tls_groups}
+        tls_details = doc_ref[0].find_value("_ccp4_refine_tls.details")
+        if tls_groups and gemmi.cif.as_string(tls_details) == "U values: residual only":
+            st2 = st.clone()
+            for cra in st2[0].all():
+                tlsgr = tls_groups.get(cra.atom.tls_group_id)
+                if cra.atom.tls_group_id > 0 and tlsgr is not None:
+                    if not cra.atom.aniso.nonzero():
+                        u = cra.atom.b_iso * utils.model.b_to_u
+                        cra.atom.aniso = gemmi.SMat33f(u, u, u, 0, 0, 0)
+                    u_from_tls = gemmi.calculate_u_from_tls(tlsgr, cra.atom.pos)
+                    cra.atom.aniso += gemmi.SMat33f(*u_from_tls.elements_pdb())
+                    cra.atom.b_iso = cra.atom.aniso.trace() / 3. * utils.model.u_to_b
+            cifout2 = cifout[:cifout.rindex(".")] + "_addu" + cifout[cifout.rindex("."):]
+            doc_ref[0].set_pair("_ccp4_refine_tls.details", gemmi.cif.quote("U values: with tls added"))
+            utils.fileio.write_mmcif(st2, cifout2, cif_ref_doc=doc_ref)
+        else:
+            if not tls_groups:
+                msg = "TLS group definition not found in the model"
+            else:
+                msg = "TLS already applied to the U values"
+            logger.writeln(f"Error: --tls_addu requested, but {msg}.")
+
     if st.has_d_fraction:
         st.store_deuterium_as_fraction(False) # also useful for pdb
         logger.writeln("will write a H/D expanded mmcif file")
@@ -313,6 +341,11 @@ def main(args):
     # TODO what if restin is given or make cr prepared is given?
     # TODO check make pept/link/suga/ss/conn/symm/chain
 
+    if "hklin" in opts: # for history
+        software_items = utils.fileio.software_items_from_mtz(opts["hklin"])
+    else:
+        software_items = []
+    
     # Process model
     crdout = None
     refmac_fixes = None
@@ -380,7 +413,8 @@ def main(args):
     if xyzin is not None:
         pdbout, cifout = get_output_model_names(opts.get("xyzout"))
         if os.path.exists(cifout):
-            modify_output(pdbout, cifout, refmac_fixes, keywords["make"].get("hout"), cispeps, args.keep_original_output)
+            modify_output(pdbout, cifout, refmac_fixes, keywords["make"].get("hout"), cispeps,
+                          software_items, args.keep_original_output, args.tls_addu)
 # main()
 
 def command_line():

{servalcat-0.4.99 → servalcat-0.4.105}/servalcat/spa/fofc.py

@@ -357,7 +357,7 @@ def write_files(hkldata, map_labs, grid_start, stats_str,
             hkldata2.translate(lab, -shifts)
         hkldata = hkldata2
         
-    dump_to_mtz(hkldata, map_labs, "{}.mtz".format(output_prefix))
+    dump_to_mtz(hkldata, map_labs, "{}_maps.mtz".format(output_prefix))
     if stats_str: open("{}_Fstats.log".format(output_prefix), "w").write(stats_str)
 # write_files()
 
@@ -458,15 +458,15 @@ def main(args):
 
     py_out = "{}_coot.py".format(args.output_prefix)
     write_coot_script(py_out, model_file=args.model,
-                      mtz_file=args.output_prefix+".mtz",
+                      mtz_file=args.output_prefix+"_maps.mtz",
                       contour_fo=None if mask is None else 1.2,
                       contour_fofc=None if mask is None else 3.0,
                       ncs_ops=ncs_org)
-    logger.writeln("\nOpen model and diffmap.mtz with COOT:")
+    logger.writeln("\nOpen model and diffmap mtz with COOT:")
     logger.writeln("coot --script " + py_out)
     if mask is not None:
         logger.writeln("\nWant to list Fo-Fc map peaks? Try:")
-        if omit_h_electron:
+        if args.omit_h_electron:
             logger.writeln("servalcat util map_peaks --map {}_normalized_fofc_flipsign.mrc --model {} --abs_level 4.0".format(args.output_prefix, args.model))
         else:
             logger.writeln("servalcat util map_peaks --map {}_normalized_fofc.mrc --model {} --abs_level 4.0".format(args.output_prefix, args.model))

{servalcat-0.4.99 → servalcat-0.4.105}/servalcat/spa/run_refmac.py

@@ -125,7 +125,7 @@ def add_arguments(parser):
     group = parser.add_mutually_exclusive_group()
     group.add_argument('--mask_for_fofc', help="Mask file for Fo-Fc map calculation")
     group.add_argument('--mask_radius_for_fofc', type=float, help="Mask radius for Fo-Fc map calculation")
-    parser.add_argument('--trim_fofc_mtz', action="store_true", help="diffmap.mtz will have smaller cell (if --mask_for_fofc is given)")
+    parser.add_argument('--trim_fofc_mtz', action="store_true", help="maps mtz will have smaller cell (if --mask_for_fofc is given)")
     parser.add_argument("--fsc_resolution", type=float,
                         help="High resolution limit for FSC calculation. Default: Nyquist")
 
@@ -312,7 +312,7 @@ def calc_fofc(st, st_expanded, maps, monlib, model_format, args, diffmap_prefix=
     # Create Coot script
     spa.fofc.write_coot_script("{}_coot.py".format(args.output_prefix),
                                model_file="{}.pdb".format(args.output_prefix), # as Coot is not good at mmcif file..
-                               mtz_file="{}.mtz".format(diffmap_prefix),
+                               mtz_file="{}_maps.mtz".format(diffmap_prefix),
                                contour_fo=None if mask is None else 1.2,
                                contour_fofc=None if mask is None else 3.0,
                                ncs_ops=st.ncs)
@@ -364,7 +364,7 @@ Weight used: {final_weight}
              If you want to change the weight, give larger (looser restraints)
              or smaller (tighter) value to --weight_auto_scale=.
              
-Open refined model and diffmap.mtz with COOT:
+Open refined model and maps mtz with COOT:
 coot --script {prefix}_coot.py
 
 Open refined model, map and difference map with ChimeraX/ISOLDE:

{servalcat-0.4.99 → servalcat-0.4.105}/servalcat/utils/commands.py

@@ -330,7 +330,7 @@ def symmodel(args):
     map_and_start = None
     if args.map:
         logger.writeln("Reading cell from map")
-        map_and_start = fileio.read_ccp4_map(args.map)
+        map_and_start = fileio.read_ccp4_map(args.map, header_only=True)
         st.cell = map_and_start[0].unit_cell
     elif args.cell:
         st.cell = gemmi.UnitCell(*args.cell)
@@ -388,7 +388,7 @@ def helical_biomt(args):
     map_and_start = None
     if args.map:
         logger.writeln("Reading cell from map")
-        map_and_start = fileio.read_ccp4_map(args.map)
+        map_and_start = fileio.read_ccp4_map(args.map, header_only=True)
         st.cell = map_and_start[0].unit_cell
     elif args.cell:
         st.cell = gemmi.UnitCell(*args.cell)
@@ -1307,7 +1307,7 @@ def mask_from_model(args):
     st = fileio.read_structure(args.model) # TODO option to (or not to) expand NCS
     if args.selection:
         gemmi.Selection(args.selection).remove_not_selected(st)
-    gr, grid_start, _ = fileio.read_ccp4_map(args.map)
+    gr, grid_start, _ = fileio.read_ccp4_map(args.map, header_only=True)
     mask = maps.mask_from_model(st, args.radius, soft_edge=args.soft_edge, grid=gr)
     maps.write_ccp4_map(args.output, mask, grid_start=grid_start)
 # mask_from_model()
@@ -1367,7 +1367,7 @@ def map2mtz(args):
 
 def sm2mm(args):
     if args.output_prefix is None:
-        args.output_prefix = fileio.splitext(args.files[0])[0]
+        args.output_prefix = os.path.basename(fileio.splitext(args.files[0])[0])
     st, mtz = fileio.read_small_molecule_files(args.files)
     if st is not None:
         fileio.write_model(st, prefix=args.output_prefix, pdb=True, cif=True)