Software Programs Installed on Local Machines
|
Program Name |
Version |
Description |
Workstation |
Directory |
Alias |
|
CCP4 |
4.2.2 4.2.2 |
CCP4 processing suite |
xray bragg dots |
/usr/local/apps/ccp4-4.2.2/ /opt/ccp4-4.2.2/bin/ /opt/ccp4-4.2.2/bin/ |
ccp4i |
|
CNS |
1.1 1.0 1.1 |
data processing |
xray viewer bragg |
/usr/local/apps/cns_solve_1.1/ /capps/cns_solve_1.0/bin/ /usr/local/cns_solve/bin/ |
cns_web |
|
Crave |
1.2 |
auto-generate a C-shell script to do N cycles of averaging over M crystal forms |
xray |
/usr/local/apps/o7.0/rave_alpha/ |
crave |
|
Ct2het |
1.3 |
to find hetero compounds in the PDB using only atom type and connectivity information |
xray |
/usr/local/apps/o7.0/xutil_alpha/ |
ct2het |
|
Curve |
|
|
xray |
/usr/local/apps/surfnetv16/source/ |
curve |
|
Cutsrf |
|
|
xray |
/usr/local/apps/surfnetv16/source/ |
cutsrf |
|
Dataman |
6.0 |
manipulate reflection datasets |
xray |
/usr/local/apps/o7.0/rave_alpha/ |
dataman |
|
Denzo |
1.97.2 1.97.2 1.97.2 |
data processing |
xray bragg dots |
/usr/local/apps/HKLv1.97.2/ /usr/local/apps/HKLv1.97.2/ /usr/local/apps/HKLv1.97.2/ |
denzo |
|
Denzo2merlot |
? |
|
viewer |
/cruncher/myoder/source/bin |
denzo2merlot |
|
Denzo2xplor |
? |
|
viewer |
/cruncher/myoder/source/bin |
denzo2xplor |
|
Empty |
|
|
xray |
/usr/local/apps/o7.0/xutil_alpha/ |
empty |
|
Essens |
3.03 |
real-space searches for fragments (e.g., helices) or molecules |
xray |
/usr/local/apps/o7.0/rave_alpha/ |
essens |
|
Genbox |
|
|
xray |
/usr/local/apps/surfnetv16/source/ |
genbox |
|
Hetze |
0.4 |
real-space searches for fragments (e.g., helices) or molecules |
xray |
/usr/local/apps/o7.0/xutil_alpha/ |
hetze |
|
Imp |
3.0 |
improve NCS operators |
xray |
/usr/local/apps/o7.0/rave_alpha/ |
imp |
|
Mama |
6.0 |
manipulate masks |
xray |
/usr/local/apps/o7.0/rave_alpha/ |
mama |
|
Mapdiff |
16 |
|
xray |
/usr/local/apps/surfnetv16/source/ |
mapdiff |
|
Mapfix |
3.0 |
add spacegroup and symmetry operators to a CCP4 map |
xray |
/usr/local/apps/o7.0/rave_alpha/ |
mapfix |
|
Mapman |
7.2.1 |
manipulate maps |
xray |
/usr/local/apps/o7.0/rave_alpha/ |
mapman |
|
Mappage |
1.0 |
obsolete, use Mapman instead |
xray |
/usr/local/apps/o7.0/rave_alpha/ |
mappage |
|
Mapsphere |
|
|
xray |
/usr/local/apps/surfnetv16/source/ |
mapsphere |
|
Mask |
|
|
xray |
/usr/local/apps/surfnetv16/source/ |
mask |
|
Maskit |
1.0 |
find cross-crystal averaging mask using local correlation maps |
xray |
/usr/local/apps/o7.0/rave_alpha/ |
maskit |
|
Mave |
4.1 |
|
xray |
/usr/local/apps/o7.0/rave_alpha/ |
mave |
|
Molauto |
2.1.2 |
|
viewer |
/cruncher/local/apps/molscript_2.1.2/ |
molauto |
|
Moleman |
7.3.2 |
use MOLEMAN2 instead |
xray |
/usr/local/apps/o7.0/xutil_alpha/ |
moleman |
|
Moleman2 |
2.8.2 |
pdb manipulation |
xray |
/usr/local/apps/o7.0/xutil_alpha/ |
moleman2 |
|
Molscript |
2.1.2 2.1.2 |
|
xray viewer |
/usr/local/apps/molscript-2.1.2/ /vdsk1/local/apps/molscript-2.1.2/ |
ms |
|
Mosflm |
6.01 |
|
bragg |
/usr/local/apps/mosflm601/bin |
mosflm |
|
Mosflm611 |
6.11 |
|
bragg |
/usr/local/apps/mosflm611/bin |
mosflm611 |
|
Mtzdump2dgn |
? |
|
viewer |
/usr/local/bin/ |
mtzdump2dgn |
|
Multiflex |
1.1.8 |
|
xray |
/usr/local/apps/MEAD/MEADexe-alphaOSF1V4/ |
multiflex |
|
My_datdifdel |
? |
|
viewer |
/capps/calc/ |
my_datdifdel |
|
NCS6D |
3.1 |
find NCS operators |
xray |
/usr/local/apps/o7.0/rave_alpha/ |
ncs6d |
|
O |
7 7.01 8.0 |
modelling |
xray viewer bragg |
/usr/local/apps/o7.0/ /usr/local/apps/o701/ /usr/local/apps/ov8/ |
runo |
|
O2D |
5.3.1 |
make 2D plots |
xray |
/usr/local/apps/o7.0/xutil_alpha/ |
o2d |
|
O2mol |
? |
|
viewer |
/vdsk1/local/apps/o/omac/ |
o2mol |
|
ODBM |
1.3.1 |
analyse O datablocks, use ODBMAN instead |
xray |
/usr/local/apps/o7.0/xutil_alpha/ |
odbm |
|
ODBMAN |
2.1.3 |
analyse O datablocks |
xray |
/usr/local/apps/o7.0/xutil_alpha/ |
odbman |
|
ODLEDIT |
0.7 |
? |
xray |
/usr/local/apps/o7.0/xutil_alpha/ |
|
|
OOPS |
5.3.3 |
obsolete, use OOPS2 instead |
xray |
/usr/local/apps/o7.0/xutil_alpha/ |
oops |
|
PACMAN |
0.6 |
check packing after Molecular Replacement |
xray |
/usr/local/apps/o7.0/xutil_alpha/ |
pacman |
|
PDB2CT |
12 |
? |
xray |
/usr/local/apps/o7.0/xutil_alpha/ |
pdb2ct |
|
Plane |
1.6 |
surfnet component |
xray |
/usr/local/apps/surfnetv16/source/ |
plane |
|
Potential |
|
|
xray |
/usr/local/apps/MEAD/MEADexe-alphaOSF1V4/ |
potential |
|
Pretty |
? |
|
xray |
/usr/local/apps/o7.0/xutil_alpha/ |
pretty |
|
Princip |
1.6 |
surfnet component |
xray |
/usr/local/apps/surfnetv16/source/ |
princip |
|
Rasmol |
2.6 |
molecular visualization |
xray viewer |
/usr/local/bin/rasmol/ /cruncher/local/bin/ |
rasmol |
|
Raster3d |
2.5f |
|
xray |
/usr/local/apps/Raster3d_2.5f.tar |
|
|
Redti |
4 |
|
xray |
/usr/local/apps/MEAD/MEADexe-alphaOSF1V4/ |
redti |
|
Render |
? |
|
viewer |
/cruncher/local/bin/raster3d/ |
render |
|
Resolve_giant |
2.05 |
|
xray |
/usr/local/bin/solve205/ |
resolve_giant |
|
Resolve_huge |
2.05 |
|
xray |
/usr/local/bin/solve205/ |
resolve_huge |
|
Resolve_pattern |
2.05 |
|
xray |
/usr/local/bin/solve205/ |
resolve_pattern |
|
Resolve_pattern_giant |
2.05 |
|
xray |
/usr/local/bin/solve205/ |
resolve_pattern_giant |
|
Resolve_pattern_huge |
2.05 |
|
xray |
/usr/local/bin/solve205/ |
resolve_pattern_huge |
|
Ribbon |
? |
|
viewer |
/cruncher/local/bin/raster3d/ |
ribbon |
|
RMSPDB |
1.3 |
analyse multiple models , use LSQMAN instead |
xray |
/usr/local/apps/o7.0/xutil_alpha/ |
rmspdb |
|
Rods |
? |
|
viewer |
/cruncher/local/bin/raster3d/ |
rods |
|
Rotma2rotsym |
1.0 |
|
viewer |
/capps/myoder/bin |
roma2rotsym |
|
Run_diffs |
1.1 1.0 1.1 |
|
xray viewer bragg |
/usr/local/apps/cns_solve_1.1/bin /capps/cns_solve_1.0/bin /usr/local/cns_solve/bin |
run_diffs |
|
Run_tests |
1.1 1.0 1.1 |
|
xray viewer bragg |
/usr/local/apps/cns_solve_1.1/bin /capps/cns_solve_1.0/bin /usr/local/cns_solve/bin |
run_tests |
|
Sav-driver |
4 |
|
xray |
/usr/local/apps/MEAD/MEADexe-alphaOSF1V4/ |
sav-driver |
|
Scalepack |
1.97.2 1.97.2 1.97.2 |
data processing |
xray bragg dots |
/usr/local/apps/HKLv1.97.2/ /usr/local/apps/HKLv1.97.2/ /usr/local/apps/HKLv1.97.2/ |
sp |
|
Seaman |
1.4 |
generate search models for Molecular Replacement |
xray |
/usr/local/apps/o7.0/xutil_alpha/ |
seaman |
|
Shelxa |
97-2 |
Post-absorption corrections (for emergency use only) |
xray |
/usr/local/apps/shelx/dig_unix/ |
shelxa |
|
Shelxd |
97-2 |
Structure solution for difficult problems (and location of heavy atom sites) |
xray |
/usr/local/apps/shelx/dig_unix/ |
shelxd |
|
Shelxe |
97-2 |
Phases from SHELXD heavy atom sites (and density modification) |
xray |
/usr/local/apps/shelx/dig_unix/ |
shelxe |
|
Shelxh |
97-2 |
Large Structure refinement |
xray |
/usr/local/apps/shelx/dig_unix/ |
shelxh |
|
Shelxl |
97-2 |
Structure refinement |
xray |
/usr/local/apps/shelx/dig_unix/ |
shelxl |
|
Shelxpro |
97-2 |
Protein interface to SHELX |
xray |
/usr/local/apps/shelx/dig_unix/ |
shelxpro |
|
Shelxs |
97-2 |
Structure solution by Patterson and direct methods |
xray |
/usr/local/apps/shelx/dig_unix/ |
shelxs |
|
Shelxwat |
97-2 |
Automatic water divining for macromolecules |
xray |
/usr/local/apps/shelx/dig_unix/ |
shelxwat |
|
Site2rt |
0.3 |
find RT-operators between (heavy atom or selenium) sites in different crystal forms |
xray |
/usr/local/apps/o7.0/rave_alpha/ |
site2rt |
|
Sod |
0.7 |
generate O datablocks from (aligned) sequences |
xray |
/usr/local/apps/o7.0/xutil_alpha/ |
sod |
|
Solex |
2.0 |
extract the best solutions from ESSENS runs (and to attempt to auto-trace helices and strands) |
xray |
/usr/local/apps/o7.0/rave_alpha/ |
solex |
|
Solvate |
4 |
MEAD program |
xray |
/usr/local/apps/MEAD/MEADexe-alphaOSF1V4/ |
solvate |
|
Solve |
2.05 |
|
xray |
/usr/local/bin/solve205/ |
solve |
|
Solve_giant |
2.05 |
|
xray |
/usr/local/bin/solve205/ |
solve_giant |
|
Solve_huge |
2.05 |
|
xray |
/usr/local/bin/solve205/ |
solve_huge |
|
Spancsi |
1.0 |
investigate if your NCS-related molecules have very different average temperature factors |
xray |
/usr/local/apps/o7.0/rave_alpha/ |
spancsi |
|
Surface |
1.6 |
|
xray |
/usr/local/apps/surfnetv16/source |
|
|
Surfnet |
1.6 |
|
xray |
/usr/local/apps/surfnetv16/source |
|
|
Theta2euler |
? |
|
viewer |
/cruncher/myoder/source/bin |
theta2euler |
|
Transform |
1.6 |
|
xray |
/usr/local/apps/surfnetv16/source |
|
|
Xdispmar |
1.97.2 1.97.2 1.97.2 |
data processing |
xray bragg dots |
/usr/local/apps/HKLv1.97.2/ /usr/local/apps/HKLv1.97.2/ /usr/local/apps/HKLv1.97.2/ |
xdispmar |
|
Xpand |
1.3.1 |
expand molecules under NCS and/or spacegroup symmetry |
xray |
/usr/local/apps/o7.0/xutil_alpha/ |
xpand |
|
Xplo2d |
2.8.9 |
does "stuff" to X-PLOR input or output files |
xray |
/usr/local/apps/o7.0/xutil_alpha/ |
xplo2d |
|
Xplor2rotmat |
? |
|
viewer |
/capps/myoder/bin/ |
xplor2rotmat |
|
Xtalview |
4 |
|
xray |
/usr/local/apps/Xtalview_v4 |
|
|
Xvrml |
0.7 |
generate VRML files from PDB files |
xray |
/usr/local/apps/o7.0/xutil_alpha/ |
xvrml |