From e6be592bc8d0fe49f9378bdaa36c8cb0d4f37078 Mon Sep 17 00:00:00 2001 From: John LaGrone Date: Tue, 23 Jun 2026 10:58:22 -0500 Subject: [PATCH 1/6] add phenix --- modules/m3/applications/phenix/2.1-6048.lua | 12 ++++++++++++ 1 file changed, 12 insertions(+) create mode 100644 modules/m3/applications/phenix/2.1-6048.lua diff --git a/modules/m3/applications/phenix/2.1-6048.lua b/modules/m3/applications/phenix/2.1-6048.lua new file mode 100644 index 00000000..8648a72b --- /dev/null +++ b/modules/m3/applications/phenix/2.1-6048.lua @@ -0,0 +1,12 @@ +whatis("Phenix) +family("phenix") + +source_sh('bash', '/hpc/m3/apps/phenix/2.1-6048/phenix_env.sh') + +help([[Name: Phenix +Version: 2.1-6048 +Website: https://phenix-online.org/ +License Owners: John LaGrone / requested by Zoltowski / Approved by Dr. Hites + +A comprehensive software package for macromolecular structure determination using crystallographic (X-ray, neutron and electron) and electron cryo-microscopy data. +]]) \ No newline at end of file From 6155211a20b440b0ae5c203107e28978cf50d30e Mon Sep 17 00:00:00 2001 From: John LaGrone Date: Tue, 23 Jun 2026 11:26:35 -0500 Subject: [PATCH 2/6] load miniforge for conda commands --- modules/m3/applications/phenix/2.1-6048.lua | 1 + 1 file changed, 1 insertion(+) diff --git a/modules/m3/applications/phenix/2.1-6048.lua b/modules/m3/applications/phenix/2.1-6048.lua index 8648a72b..92ff13e6 100644 --- a/modules/m3/applications/phenix/2.1-6048.lua +++ b/modules/m3/applications/phenix/2.1-6048.lua @@ -1,6 +1,7 @@ whatis("Phenix) family("phenix") +load("miniforge") source_sh('bash', '/hpc/m3/apps/phenix/2.1-6048/phenix_env.sh') help([[Name: Phenix From 93e4c92a02b1ba7402de5ffeaec52f8ac53dce52 Mon Sep 17 00:00:00 2001 From: John LaGrone Date: Tue, 23 Jun 2026 11:27:14 -0500 Subject: [PATCH 3/6] add Xtrapol8 module --- modules/m3/applications/xtrapol8/1.2.9.lua | 14 ++++++++++++++ 1 file changed, 14 insertions(+) create mode 100644 modules/m3/applications/xtrapol8/1.2.9.lua diff --git a/modules/m3/applications/xtrapol8/1.2.9.lua b/modules/m3/applications/xtrapol8/1.2.9.lua new file mode 100644 index 00000000..3f64822e --- /dev/null +++ b/modules/m3/applications/xtrapol8/1.2.9.lua @@ -0,0 +1,14 @@ +whatis("Xtrapol8) +family("xtrapol8") + +load("phenix/2.1-6048") +load("ccp4/9.0.015) + +set_alias("X8", "phenix.python /hpc/m3/apps/xtrapol8/1.2.9/Fextr.py") + +help([[Name: Xtrapol8 +Version: 1.2.9 +Website: https://github.com/ElkeDeZitter/Xtrapol8 + +Xtrapol8 is software for the calculation of Fourier difference maps, extrapolated structure factor ampltiudes (ESFAs) and estimation of the occupancy of at triggered state that occupies the crystal at low occupancy. +]]) \ No newline at end of file From f7683c530b6c525dca435e1e9b71bb294721eb0e Mon Sep 17 00:00:00 2001 From: John LaGrone Date: Tue, 23 Jun 2026 11:33:54 -0500 Subject: [PATCH 4/6] fix missing quote --- modules/m3/applications/xtrapol8/1.2.9.lua | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/m3/applications/xtrapol8/1.2.9.lua b/modules/m3/applications/xtrapol8/1.2.9.lua index 3f64822e..2285d259 100644 --- a/modules/m3/applications/xtrapol8/1.2.9.lua +++ b/modules/m3/applications/xtrapol8/1.2.9.lua @@ -1,4 +1,4 @@ -whatis("Xtrapol8) +whatis("Xtrapol8") family("xtrapol8") load("phenix/2.1-6048") From 3a3f54a0fbb6cba53b5f5723a2c11ac786313a82 Mon Sep 17 00:00:00 2001 From: John LaGrone Date: Tue, 23 Jun 2026 11:37:11 -0500 Subject: [PATCH 5/6] fix another missing quote --- modules/m3/applications/xtrapol8/1.2.9.lua | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/m3/applications/xtrapol8/1.2.9.lua b/modules/m3/applications/xtrapol8/1.2.9.lua index 2285d259..cdb1a224 100644 --- a/modules/m3/applications/xtrapol8/1.2.9.lua +++ b/modules/m3/applications/xtrapol8/1.2.9.lua @@ -2,7 +2,7 @@ whatis("Xtrapol8") family("xtrapol8") load("phenix/2.1-6048") -load("ccp4/9.0.015) +load("ccp4/9.0.015") set_alias("X8", "phenix.python /hpc/m3/apps/xtrapol8/1.2.9/Fextr.py") From 574756aba87622174de803ef8d13cf95744f29b8 Mon Sep 17 00:00:00 2001 From: John LaGrone Date: Tue, 23 Jun 2026 11:40:09 -0500 Subject: [PATCH 6/6] fix another missing quote --- modules/m3/applications/phenix/2.1-6048.lua | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/m3/applications/phenix/2.1-6048.lua b/modules/m3/applications/phenix/2.1-6048.lua index 92ff13e6..e87cf04e 100644 --- a/modules/m3/applications/phenix/2.1-6048.lua +++ b/modules/m3/applications/phenix/2.1-6048.lua @@ -1,4 +1,4 @@ -whatis("Phenix) +whatis("Phenix") family("phenix") load("miniforge")