5 files changed, 283 insertions, 362 deletions

diff --git a/biology/pymol/Makefile b/biology/pymol/Makefile
index 267c761a5647..6af4fd3c6fab 100644
--- a/biology/pymol/Makefile
+++ b/biology/pymol/Makefile
@@ -5,8 +5,7 @@
 # $FreeBSD$
 
 PORTNAME=	pymol
-PORTVERSION=	0.82
-PORTREVISION=	3
+PORTVERSION=	0.86
 CATEGORIES=	biology python
 MASTER_SITES=	${MASTER_SITE_SOURCEFORGE}
 MASTER_SITE_SUBDIR=	pymol
diff --git a/biology/pymol/distinfo b/biology/pymol/distinfo
index fd4363004806..eb546ea16d68 100644
--- a/biology/pymol/distinfo
+++ b/biology/pymol/distinfo
@@ -1 +1 @@
-MD5 (pymol-0_82-src.tgz) = d01bf39dbaa3ada27809a0ba013a162a
+MD5 (pymol-0_86-src.tgz) = 7610bb7689230eff2ec945236fdce0b8
diff --git a/biology/pymol/files/patch-aa b/biology/pymol/files/patch-Rules.make
index cd49db0abc36..ead488b0a7d9 100644
--- a/biology/pymol/files/patch-aa
+++ b/biology/pymol/files/patch-Rules.make
@@ -1,5 +1,5 @@
---- Rules.make.orig	Thu Jul 11 08:11:51 2002
-+++ Rules.make	Thu Jul 11 08:23:03 2002
+--- Rules.make.orig	Wed Apr 30 11:42:37 2003
++++ Rules.make	Wed Apr 30 11:52:50 2003
 @@ -4,42 +4,42 @@
  #
  #- Building ----------------------------------------------------------
@@ -40,11 +40,12 @@
  #--- How we build shared libraries
  BUILD = -shared 
  #--- What are we trying to build?
- DEST = -o modules/_cmd.so
+-DEST = -o modules/pymol/_cmd.so
 -#--- Gcc Options for Linux
--CCOPT1 = -m486 -D__i686__ -ffast-math -Wall -ansi -Wmissing-prototypes
+-CCOPT1 = -march=i486 -D__i686__ -ffast-math -Wall -ansi -Wmissing-prototypes
++DEST = -o modules/_cmd.so
 +#--- Gcc Options for FreeBSD
-+CCOPT1 = #-m486 -D__i686__ -ffast-math -Wall -ansi -Wmissing-prototypes
++CCOPT1 = #-march=i486 -D__i686__ -ffast-math -Wall -ansi -Wmissing-prototypes
  #--- libraries for PyOpenGL 
  PYOGL_LIB =  -lglut -lGL -lGLU -lXmu -lXi
  #---------------------------------------------------------------------
diff --git a/biology/pymol/files/patch-ab b/biology/pymol/files/patch-setup+pymol+com+linux-rh7x
index 07ae40a91fc9..07ae40a91fc9 100644
--- a/biology/pymol/files/patch-ab
+++ b/biology/pymol/files/patch-setup+pymol+com+linux-rh7x
diff --git a/biology/pymol/pkg-plist b/biology/pymol/pkg-plist
index 56e793c8072e..843bbcdc555a 100644
--- a/biology/pymol/pkg-plist
+++ b/biology/pymol/pkg-plist
@@ -14,481 +14,395 @@ bin/pymol
 %%PORTDOCS%%share/examples/pymol/devel/cgo03.py
 %%PORTDOCS%%share/examples/pymol/devel/cgo_3Dtext01.py
 %%PORTDOCS%%share/examples/pymol/devel/cgo_label_hack.py
+%%PORTDOCS%%share/examples/pymol/devel/chempy_model01.py
+%%PORTDOCS%%share/examples/pymol/devel/chempy_model02.py
+%%PORTDOCS%%share/examples/pymol/devel/chempy_model03.py
 %%PORTDOCS%%share/examples/pymol/devel/gl01.py
 %%PORTDOCS%%share/examples/pymol/devel/gl02.py
 %%PORTDOCS%%share/examples/pymol/devel/gl03.py
 %%PORTDOCS%%share/examples/pymol/devel/povray01.py
+%%PORTDOCS%%share/examples/pymol/devel/sele_wiz.py
 %%PORTDOCS%%share/examples/pymol/devel/start_pymol.py
-share/pymol/modules/ExtensionClass.so
-share/pymol/modules/_cmd.so
-share/pymol/modules/_glu_nummodule.so
-share/pymol/modules/_glumodule.so
-share/pymol/modules/_glutmodule.so
-share/pymol/modules/_opengl_nummodule.so
-share/pymol/modules/_openglmodule.so
-share/pymol/modules/chempy/__init__.py
-share/pymol/modules/chempy/__init__.pyc
-share/pymol/modules/chempy/__init__.pyo
-share/pymol/modules/chempy/arc.py
-share/pymol/modules/chempy/arc.pyc
-share/pymol/modules/chempy/arc.pyo
+%%PORTDOCS%%share/examples/pymol/devel/xmlrpc01.py
 share/pymol/modules/chempy/bmin/__init__.py
-share/pymol/modules/chempy/bmin/__init__.pyc
-share/pymol/modules/chempy/bmin/__init__.pyo
 share/pymol/modules/chempy/bmin/commands.py
-share/pymol/modules/chempy/bmin/commands.pyc
-share/pymol/modules/chempy/bmin/commands.pyo
 share/pymol/modules/chempy/bmin/realtime.py
-share/pymol/modules/chempy/bmin/realtime.pyc
-share/pymol/modules/chempy/bmin/realtime.pyo
 share/pymol/modules/chempy/bmin/state.py
-share/pymol/modules/chempy/bmin/state.pyc
-share/pymol/modules/chempy/bmin/state.pyo
 share/pymol/modules/chempy/bmin/util.py
+share/pymol/modules/chempy/bmin/__init__.pyc
+share/pymol/modules/chempy/bmin/commands.pyc
+share/pymol/modules/chempy/bmin/realtime.pyc
+share/pymol/modules/chempy/bmin/state.pyc
 share/pymol/modules/chempy/bmin/util.pyc
+share/pymol/modules/chempy/bmin/__init__.pyo
+share/pymol/modules/chempy/bmin/commands.pyo
+share/pymol/modules/chempy/bmin/realtime.pyo
+share/pymol/modules/chempy/bmin/state.pyo
 share/pymol/modules/chempy/bmin/util.pyo
+share/pymol/modules/chempy/fast/__init__.py
+share/pymol/modules/chempy/fast/__init__.pyc
+share/pymol/modules/chempy/fast/__init__.pyo
+share/pymol/modules/chempy/__init__.py
+share/pymol/modules/chempy/arc.py
 share/pymol/modules/chempy/bond_amber.py
-share/pymol/modules/chempy/bond_amber.pyc
-share/pymol/modules/chempy/bond_amber.pyo
 share/pymol/modules/chempy/bond_mmff.py
-share/pymol/modules/chempy/bond_mmff.pyc
-share/pymol/modules/chempy/bond_mmff.pyo
 share/pymol/modules/chempy/bonds.py
-share/pymol/modules/chempy/bonds.pyc
-share/pymol/modules/chempy/bonds.pyo
 share/pymol/modules/chempy/brick.py
-share/pymol/modules/chempy/brick.pyc
-share/pymol/modules/chempy/brick.pyo
 share/pymol/modules/chempy/cc1.py
-share/pymol/modules/chempy/cc1.pyc
-share/pymol/modules/chempy/cc1.pyo
-share/pymol/modules/chempy/champ/__init__.py
-share/pymol/modules/chempy/champ/__init__.pyc
-share/pymol/modules/chempy/champ/__init__.pyo
+share/pymol/modules/chempy/cex.py
 share/pymol/modules/chempy/charge.py
-share/pymol/modules/chempy/charge.pyc
-share/pymol/modules/chempy/charge.pyo
 share/pymol/modules/chempy/cpv.py
-share/pymol/modules/chempy/cpv.pyc
-share/pymol/modules/chempy/cpv.pyo
 share/pymol/modules/chempy/dictdb.py
-share/pymol/modules/chempy/dictdb.pyc
-share/pymol/modules/chempy/dictdb.pyo
-share/pymol/modules/chempy/fast/__init__.py
-share/pymol/modules/chempy/fast/__init__.pyc
-share/pymol/modules/chempy/fast/__init__.pyo
-share/pymol/modules/chempy/fragments/__init__.py
-share/pymol/modules/chempy/fragments/__init__.pyc
-share/pymol/modules/chempy/fragments/__init__.pyo
-share/pymol/modules/chempy/fragments/ace.pkl
-share/pymol/modules/chempy/fragments/acetylene.pkl
-share/pymol/modules/chempy/fragments/ala.pkl
-share/pymol/modules/chempy/fragments/arg.pkl
-share/pymol/modules/chempy/fragments/asn.pkl
-share/pymol/modules/chempy/fragments/asp.pkl
-share/pymol/modules/chempy/fragments/benzene.pkl
-share/pymol/modules/chempy/fragments/butane.pkl
-share/pymol/modules/chempy/fragments/ct_ala.pkl
-share/pymol/modules/chempy/fragments/ct_arg.pkl
-share/pymol/modules/chempy/fragments/ct_asn.pkl
-share/pymol/modules/chempy/fragments/ct_asp.pkl
-share/pymol/modules/chempy/fragments/ct_cys.pkl
-share/pymol/modules/chempy/fragments/ct_gln.pkl
-share/pymol/modules/chempy/fragments/ct_glu.pkl
-share/pymol/modules/chempy/fragments/ct_gly.pkl
-share/pymol/modules/chempy/fragments/ct_hid.pkl
-share/pymol/modules/chempy/fragments/ct_hie.pkl
-share/pymol/modules/chempy/fragments/ct_hip.pkl
-share/pymol/modules/chempy/fragments/ct_his.pkl
-share/pymol/modules/chempy/fragments/ct_ile.pkl
-share/pymol/modules/chempy/fragments/ct_leu.pkl
-share/pymol/modules/chempy/fragments/ct_lys.pkl
-share/pymol/modules/chempy/fragments/ct_met.pkl
-share/pymol/modules/chempy/fragments/ct_phe.pkl
-share/pymol/modules/chempy/fragments/ct_pro.pkl
-share/pymol/modules/chempy/fragments/ct_ser.pkl
-share/pymol/modules/chempy/fragments/ct_thr.pkl
-share/pymol/modules/chempy/fragments/ct_trp.pkl
-share/pymol/modules/chempy/fragments/ct_tyr.pkl
-share/pymol/modules/chempy/fragments/ct_val.pkl
-share/pymol/modules/chempy/fragments/cyclobutane.pkl
-share/pymol/modules/chempy/fragments/cycloheptane.pkl
-share/pymol/modules/chempy/fragments/cyclohexane.pkl
-share/pymol/modules/chempy/fragments/cyclopentadiene.pkl
-share/pymol/modules/chempy/fragments/cyclopentane.pkl
-share/pymol/modules/chempy/fragments/cys.pkl
-share/pymol/modules/chempy/fragments/formaldehyde.pkl
-share/pymol/modules/chempy/fragments/formamide.pkl
-share/pymol/modules/chempy/fragments/gln.pkl
-share/pymol/modules/chempy/fragments/glu.pkl
-share/pymol/modules/chempy/fragments/gly.pkl
-share/pymol/modules/chempy/fragments/hid.pkl
-share/pymol/modules/chempy/fragments/hie.pkl
-share/pymol/modules/chempy/fragments/hip.pkl
-share/pymol/modules/chempy/fragments/his.pkl
-share/pymol/modules/chempy/fragments/ile.pkl
-share/pymol/modules/chempy/fragments/leu.pkl
-share/pymol/modules/chempy/fragments/lys.pkl
-share/pymol/modules/chempy/fragments/met.pkl
-share/pymol/modules/chempy/fragments/methane.pkl
-share/pymol/modules/chempy/fragments/nme.pkl
-share/pymol/modules/chempy/fragments/nt_ala.pkl
-share/pymol/modules/chempy/fragments/nt_arg.pkl
-share/pymol/modules/chempy/fragments/nt_asn.pkl
-share/pymol/modules/chempy/fragments/nt_asp.pkl
-share/pymol/modules/chempy/fragments/nt_cys.pkl
-share/pymol/modules/chempy/fragments/nt_gln.pkl
-share/pymol/modules/chempy/fragments/nt_glu.pkl
-share/pymol/modules/chempy/fragments/nt_gly.pkl
-share/pymol/modules/chempy/fragments/nt_hid.pkl
-share/pymol/modules/chempy/fragments/nt_hie.pkl
-share/pymol/modules/chempy/fragments/nt_hip.pkl
-share/pymol/modules/chempy/fragments/nt_his.pkl
-share/pymol/modules/chempy/fragments/nt_ile.pkl
-share/pymol/modules/chempy/fragments/nt_leu.pkl
-share/pymol/modules/chempy/fragments/nt_lys.pkl
-share/pymol/modules/chempy/fragments/nt_met.pkl
-share/pymol/modules/chempy/fragments/nt_phe.pkl
-share/pymol/modules/chempy/fragments/nt_pro.pkl
-share/pymol/modules/chempy/fragments/nt_ser.pkl
-share/pymol/modules/chempy/fragments/nt_thr.pkl
-share/pymol/modules/chempy/fragments/nt_trp.pkl
-share/pymol/modules/chempy/fragments/nt_tyr.pkl
-share/pymol/modules/chempy/fragments/nt_val.pkl
-share/pymol/modules/chempy/fragments/peptide.pkl
-share/pymol/modules/chempy/fragments/phe.pkl
-share/pymol/modules/chempy/fragments/pro.pkl
-share/pymol/modules/chempy/fragments/realtime.pkl
-share/pymol/modules/chempy/fragments/ser.pkl
-share/pymol/modules/chempy/fragments/sulfone.pkl
-share/pymol/modules/chempy/fragments/thr.pkl
-share/pymol/modules/chempy/fragments/trp.pkl
-share/pymol/modules/chempy/fragments/tyr.pkl
-share/pymol/modules/chempy/fragments/val.pkl
 share/pymol/modules/chempy/gamess1.py
-share/pymol/modules/chempy/gamess1.pyc
-share/pymol/modules/chempy/gamess1.pyo
 share/pymol/modules/chempy/gms.py
-share/pymol/modules/chempy/gms.pyc
-share/pymol/modules/chempy/gms.pyo
 share/pymol/modules/chempy/hetatm.py
-share/pymol/modules/chempy/hetatm.pyc
-share/pymol/modules/chempy/hetatm.pyo
 share/pymol/modules/chempy/io.py
-share/pymol/modules/chempy/io.pyc
-share/pymol/modules/chempy/io.pyo
 share/pymol/modules/chempy/lst.py
-share/pymol/modules/chempy/lst.pyc
-share/pymol/modules/chempy/lst.pyo
 share/pymol/modules/chempy/mae.py
-share/pymol/modules/chempy/mae.pyc
-share/pymol/modules/chempy/mae.pyo
 share/pymol/modules/chempy/map.py
-share/pymol/modules/chempy/map.pyc
-share/pymol/modules/chempy/map.pyo
+share/pymol/modules/chempy/mass.py
 share/pymol/modules/chempy/mmd.py
-share/pymol/modules/chempy/mmd.pyc
-share/pymol/modules/chempy/mmd.pyo
 share/pymol/modules/chempy/models.py
-share/pymol/modules/chempy/models.pyc
-share/pymol/modules/chempy/models.pyo
 share/pymol/modules/chempy/mol.py
-share/pymol/modules/chempy/mol.pyc
-share/pymol/modules/chempy/mol.pyo
 share/pymol/modules/chempy/neighbor.py
-share/pymol/modules/chempy/neighbor.pyc
-share/pymol/modules/chempy/neighbor.pyo
 share/pymol/modules/chempy/pdb.py
-share/pymol/modules/chempy/pdb.pyc
-share/pymol/modules/chempy/pdb.pyo
 share/pymol/modules/chempy/pkl.py
-share/pymol/modules/chempy/pkl.pyc
-share/pymol/modules/chempy/pkl.pyo
 share/pymol/modules/chempy/place.py
-share/pymol/modules/chempy/place.pyc
-share/pymol/modules/chempy/place.pyo
 share/pymol/modules/chempy/protein.py
-share/pymol/modules/chempy/protein.pyc
-share/pymol/modules/chempy/protein.pyo
 share/pymol/modules/chempy/protein_amber.py
-share/pymol/modules/chempy/protein_amber.pyc
-share/pymol/modules/chempy/protein_amber.pyo
 share/pymol/modules/chempy/protein_amber99.py
-share/pymol/modules/chempy/protein_amber99.pyc
-share/pymol/modules/chempy/protein_amber99.pyo
 share/pymol/modules/chempy/protein_mmff.py
-share/pymol/modules/chempy/protein_mmff.pyc
-share/pymol/modules/chempy/protein_mmff.pyo
 share/pymol/modules/chempy/protein_residues.py
-share/pymol/modules/chempy/protein_residues.pyc
-share/pymol/modules/chempy/protein_residues.pyo
 share/pymol/modules/chempy/sdf.py
-share/pymol/modules/chempy/sdf.pyc
-share/pymol/modules/chempy/sdf.pyo
-share/pymol/modules/chempy/sidechains/generate1.py
-share/pymol/modules/chempy/sidechains/generate1.pyc
-share/pymol/modules/chempy/sidechains/generate1.pyo
-share/pymol/modules/chempy/sidechains/generate2.py
-share/pymol/modules/chempy/sidechains/generate2.pyc
-share/pymol/modules/chempy/sidechains/generate2.pyo
-share/pymol/modules/chempy/sidechains/sc_library.pkl
 share/pymol/modules/chempy/solvate.py
-share/pymol/modules/chempy/solvate.pyc
-share/pymol/modules/chempy/solvate.pyo
-share/pymol/modules/chempy/tinker/Makefile
+share/pymol/modules/chempy/water_amber.py
+share/pymol/modules/chempy/water_residues.py
+share/pymol/modules/chempy/xyz.py
+share/pymol/modules/chempy/champ/__init__.py
+share/pymol/modules/chempy/champ/__init__.pyc
+share/pymol/modules/chempy/champ/__init__.pyo
+share/pymol/modules/chempy/fragments/__init__.py
+share/pymol/modules/chempy/fragments/__init__.pyc
+share/pymol/modules/chempy/fragments/__init__.pyo
 share/pymol/modules/chempy/tinker/__init__.py
-share/pymol/modules/chempy/tinker/__init__.pyc
-share/pymol/modules/chempy/tinker/__init__.pyo
 share/pymol/modules/chempy/tinker/amber.py
-share/pymol/modules/chempy/tinker/amber.pyc
-share/pymol/modules/chempy/tinker/amber.pyo
-share/pymol/modules/chempy/tinker/chempy.prm
 share/pymol/modules/chempy/tinker/keyword.py
-share/pymol/modules/chempy/tinker/keyword.pyc
-share/pymol/modules/chempy/tinker/keyword.pyo
-share/pymol/modules/chempy/tinker/make99_simple.py
-share/pymol/modules/chempy/tinker/make99_simple.pyc
-share/pymol/modules/chempy/tinker/make99_simple.pyo
-share/pymol/modules/chempy/tinker/make_simple.py
-share/pymol/modules/chempy/tinker/make_simple.pyc
-share/pymol/modules/chempy/tinker/make_simple.pyo
-share/pymol/modules/chempy/tinker/parm94.dat
-share/pymol/modules/chempy/tinker/parm94_rsm.dat
-share/pymol/modules/chempy/tinker/parm96.dat
-share/pymol/modules/chempy/tinker/parm96_rsm.dat
-share/pymol/modules/chempy/tinker/parm99.dat
-share/pymol/modules/chempy/tinker/parm99_simple.dat
-share/pymol/modules/chempy/tinker/parm99_wld.dat
-share/pymol/modules/chempy/tinker/parm_simple.dat
-share/pymol/modules/chempy/tinker/parm_simple.inp
 share/pymol/modules/chempy/tinker/realtime.py
-share/pymol/modules/chempy/tinker/realtime.pyc
-share/pymol/modules/chempy/tinker/realtime.pyo
 share/pymol/modules/chempy/tinker/state.py
+share/pymol/modules/chempy/tinker/__init__.pyc
+share/pymol/modules/chempy/tinker/amber.pyc
+share/pymol/modules/chempy/tinker/keyword.pyc
+share/pymol/modules/chempy/tinker/realtime.pyc
 share/pymol/modules/chempy/tinker/state.pyc
+share/pymol/modules/chempy/tinker/__init__.pyo
+share/pymol/modules/chempy/tinker/amber.pyo
+share/pymol/modules/chempy/tinker/keyword.pyo
+share/pymol/modules/chempy/tinker/realtime.pyo
 share/pymol/modules/chempy/tinker/state.pyo
-share/pymol/modules/chempy/water.pdb
-share/pymol/modules/chempy/water_amber.py
+share/pymol/modules/chempy/__init__.pyc
+share/pymol/modules/chempy/arc.pyc
+share/pymol/modules/chempy/bond_amber.pyc
+share/pymol/modules/chempy/bond_mmff.pyc
+share/pymol/modules/chempy/bonds.pyc
+share/pymol/modules/chempy/brick.pyc
+share/pymol/modules/chempy/cc1.pyc
+share/pymol/modules/chempy/cex.pyc
+share/pymol/modules/chempy/charge.pyc
+share/pymol/modules/chempy/cpv.pyc
+share/pymol/modules/chempy/dictdb.pyc
+share/pymol/modules/chempy/gamess1.pyc
+share/pymol/modules/chempy/gms.pyc
+share/pymol/modules/chempy/hetatm.pyc
+share/pymol/modules/chempy/io.pyc
+share/pymol/modules/chempy/lst.pyc
+share/pymol/modules/chempy/mae.pyc
+share/pymol/modules/chempy/map.pyc
+share/pymol/modules/chempy/mass.pyc
+share/pymol/modules/chempy/mmd.pyc
+share/pymol/modules/chempy/models.pyc
+share/pymol/modules/chempy/mol.pyc
+share/pymol/modules/chempy/neighbor.pyc
+share/pymol/modules/chempy/pdb.pyc
+share/pymol/modules/chempy/pkl.pyc
+share/pymol/modules/chempy/place.pyc
+share/pymol/modules/chempy/protein.pyc
+share/pymol/modules/chempy/protein_amber.pyc
+share/pymol/modules/chempy/protein_amber99.pyc
+share/pymol/modules/chempy/protein_mmff.pyc
+share/pymol/modules/chempy/protein_residues.pyc
+share/pymol/modules/chempy/sdf.pyc
+share/pymol/modules/chempy/solvate.pyc
 share/pymol/modules/chempy/water_amber.pyc
-share/pymol/modules/chempy/water_amber.pyo
-share/pymol/modules/chempy/water_residues.py
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+share/pymol/test/win.py
+share/pymol/test/inp/C0020pdb.pml
 share/pymol/test/inp/B01.py
 share/pymol/test/inp/B02.py
 share/pymol/test/inp/C0001quit.pml
 share/pymol/test/inp/C0010hello.pml
-share/pymol/test/inp/C0020pdb.pml
 share/pymol/test/inp/C0025mol.pml
 share/pymol/test/inp/C0030pkl.pml
 share/pymol/test/inp/C0050multi.pml
@@ -496,6 +410,7 @@ share/pymol/test/inp/C0060delete.pml
 share/pymol/test/inp/C0070rep.pml
 share/pymol/test/inp/C0080create.pml
 share/pymol/test/inp/C0100select.pml
+share/pymol/test/inp/C0105names.pml
 share/pymol/test/inp/C0140iterate.pml
 share/pymol/test/inp/C0150alter.pml
 share/pymol/test/inp/C0500misc.pml
@@ -508,6 +423,11 @@ share/pymol/test/inp/C1040editing.pml
 share/pymol/test/inp/C1050fitting.py
 share/pymol/test/inp/C1060controlling.py
 share/pymol/test/inp/C1070exporting.pml
+share/pymol/test/inp/L0010ccp4read.pml
+share/pymol/test/inp/L0020xplorread.pml
+share/pymol/test/inp/L0030isomesh.pml
+share/pymol/test/inp/L0040isomesh2.pml
+share/pymol/test/inp/L0100isomisc.pml
 share/pymol/test/inp/T01.py
 share/pymol/test/inp/T02.py
 share/pymol/test/inp/T03.py
@@ -526,10 +446,12 @@ share/pymol/test/ref/C0080create.1.pdb
 share/pymol/test/ref/C0080create.2.pdb
 share/pymol/test/ref/C0080create.log
 share/pymol/test/ref/C0100select.log
+share/pymol/test/ref/C0105names.log
 share/pymol/test/ref/C0140iterate.log
 share/pymol/test/ref/C0150alter.1.pdb
 share/pymol/test/ref/C0150alter.log
 share/pymol/test/ref/C0500misc.log
+share/pymol/test/ref/T01.log
 share/pymol/test/ref/C0600util.log
 share/pymol/test/ref/C1000viewing.log
 share/pymol/test/ref/C1010helping.log
@@ -539,13 +461,12 @@ share/pymol/test/ref/C1040editing.log
 share/pymol/test/ref/C1050fitting.log
 share/pymol/test/ref/C1060controlling.log
 share/pymol/test/ref/C1070exporting.log
-share/pymol/test/ref/T01.log
+share/pymol/test/ref/L0010ccp4read.log
+share/pymol/test/ref/L0020xplorread.log
+share/pymol/test/ref/L0030isomesh.log
+share/pymol/test/ref/L0040isomesh2.log
+share/pymol/test/ref/L0100isomisc.log
 share/pymol/test/ref/U01.log
-share/pymol/test/run
-share/pymol/test/show
-share/pymol/test/trim.py
-share/pymol/test/vdiff
-share/pymol/test/win.py
 @dirrm share/pymol/test/ref
 @dirrm share/pymol/test/inp
 @dirrm share/pymol/test/dat
@@ -555,13 +476,13 @@ share/pymol/test/win.py
 @dirrm share/pymol/modules/pymol/opengl/glu
 @dirrm share/pymol/modules/pymol/opengl/gl
 @dirrm share/pymol/modules/pymol/opengl
-@dirrm share/pymol/modules/pymol/matrices
+@dirrm share/pymol/modules/pymol/embed/wxpymol
+@dirrm share/pymol/modules/pymol/embed
 @dirrm share/pymol/modules/pymol
 @dirrm share/pymol/modules/pmg_wx
 @dirrm share/pymol/modules/pmg_tk/startup
 @dirrm share/pymol/modules/pmg_tk
 @dirrm share/pymol/modules/chempy/tinker
-@dirrm share/pymol/modules/chempy/sidechains
 @dirrm share/pymol/modules/chempy/fragments
 @dirrm share/pymol/modules/chempy/fast
 @dirrm share/pymol/modules/chempy/champ