From 1261fd469d8557eec2f4803a629bb8eedbeb6f59 Mon Sep 17 00:00:00 2001 From: "Yu-Yuan (Stuart) Yang - from connectin, AFLab" Date: Sat, 12 Apr 2025 10:42:48 +0100 Subject: [PATCH 1/7] update PDB format --- doc/source/formats/reference/pdb.rst | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/doc/source/formats/reference/pdb.rst b/doc/source/formats/reference/pdb.rst index 2250ebc4a..e690aca57 100644 --- a/doc/source/formats/reference/pdb.rst +++ b/doc/source/formats/reference/pdb.rst @@ -98,7 +98,13 @@ PDB specification 47 - 54 Real(8.3) z Orthogonal coordinates for Z in Angstroms. 55 - 60 Real(6.2) occupancy Occupancy. 61 - 66 Real(6.2) tempFactor Temperature factor. - 67 - 76 String segID (unofficial CHARMM extension ?) + 67 - 72 (not used in the official PDB format) + 73 - 76 String segID (unofficial PDB format*) 77 - 78 LString(2) element Element symbol, right-justified. 79 - 80 LString(2) charge Charge on the atom. ============= ============ =========== ============================================= + +*(version change since 2.10.0) The columns 73-76 are not part of the official PDB format but are used by some programs to store/operate the segment ID. For instance, Chimera_ assigns it as the attribute `pdbSegment` to allow command-line specification. + +.. _Chimera: + https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/pdbintro.html#note6 From 63eee24ba9f34499faac1aee3917f022b68bd5f5 Mon Sep 17 00:00:00 2001 From: "Yu-Yuan (Stuart) Yang - from connectin, AFLab" Date: Sat, 12 Apr 2025 10:51:26 +0100 Subject: [PATCH 2/7] more clear --- doc/source/formats/reference/pdb.rst | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/doc/source/formats/reference/pdb.rst b/doc/source/formats/reference/pdb.rst index e690aca57..7c45ca3b3 100644 --- a/doc/source/formats/reference/pdb.rst +++ b/doc/source/formats/reference/pdb.rst @@ -98,13 +98,15 @@ PDB specification 47 - 54 Real(8.3) z Orthogonal coordinates for Z in Angstroms. 55 - 60 Real(6.2) occupancy Occupancy. 61 - 66 Real(6.2) tempFactor Temperature factor. - 67 - 72 (not used in the official PDB format) - 73 - 76 String segID (unofficial PDB format*) + 67 - 72 (not used in the official PDB format*1) + 73 - 76 String segID (unofficial PDB format*2) 77 - 78 LString(2) element Element symbol, right-justified. 79 - 80 LString(2) charge Charge on the atom. ============= ============ =========== ============================================= -*(version change since 2.10.0) The columns 73-76 are not part of the official PDB format but are used by some programs to store/operate the segment ID. For instance, Chimera_ assigns it as the attribute `pdbSegment` to allow command-line specification. +*1(version change since 2.10.0) The columns 67-72 are not used by MDAnalysis since version 2.10.0. + +*2(version change since 2.10.0) The columns 73-76 are not part of the official PDB format but are used by some programs to store/operate the segment ID. For instance, Chimera_ assigns it as the attribute `pdbSegment` to allow command-line specification. .. _Chimera: https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/pdbintro.html#note6 From bfc3fa7e60bcd860e91b432463f070377588d940 Mon Sep 17 00:00:00 2001 From: Oliver Beckstein Date: Thu, 10 Jul 2025 14:40:17 -0700 Subject: [PATCH 3/7] Update pdb.rst --- doc/source/formats/reference/pdb.rst | 11 +++++++---- 1 file changed, 7 insertions(+), 4 deletions(-) diff --git a/doc/source/formats/reference/pdb.rst b/doc/source/formats/reference/pdb.rst index 7c45ca3b3..237500dfc 100644 --- a/doc/source/formats/reference/pdb.rst +++ b/doc/source/formats/reference/pdb.rst @@ -98,15 +98,18 @@ PDB specification 47 - 54 Real(8.3) z Orthogonal coordinates for Z in Angstroms. 55 - 60 Real(6.2) occupancy Occupancy. 61 - 66 Real(6.2) tempFactor Temperature factor. - 67 - 72 (not used in the official PDB format*1) - 73 - 76 String segID (unofficial PDB format*2) + 67 - 72 (not used in the official PDB format) + 73 - 76 String segID (unofficial PDB format) 77 - 78 LString(2) element Element symbol, right-justified. 79 - 80 LString(2) charge Charge on the atom. ============= ============ =========== ============================================= -*1(version change since 2.10.0) The columns 67-72 are not used by MDAnalysis since version 2.10.0. +.. versionchanged:: 2.10.0 + The columns 67-72 are not read by MDAnalysis since version 2.10.0. -*2(version change since 2.10.0) The columns 73-76 are not part of the official PDB format but are used by some programs to store/operate the segment ID. For instance, Chimera_ assigns it as the attribute `pdbSegment` to allow command-line specification. +.. note:: + The columns 73-76 are not part of the official PDB format but are used by some programs to store/operate + the segment ID. For instance, Chimera_ assigns it as the attribute *pdbSegment*. .. _Chimera: https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/pdbintro.html#note6 From 1468c43ddf9132167f075c18ee0715aaabf79d99 Mon Sep 17 00:00:00 2001 From: Oliver Beckstein Date: Thu, 10 Jul 2025 14:44:22 -0700 Subject: [PATCH 4/7] make pre-commit happy --- doc/source/formats/reference/pdb.rst | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/doc/source/formats/reference/pdb.rst b/doc/source/formats/reference/pdb.rst index 237500dfc..c1fbdf901 100644 --- a/doc/source/formats/reference/pdb.rst +++ b/doc/source/formats/reference/pdb.rst @@ -105,11 +105,12 @@ PDB specification ============= ============ =========== ============================================= .. versionchanged:: 2.10.0 - The columns 67-72 are not read by MDAnalysis since version 2.10.0. + The columns 67-72 are not read by MDAnalysis since version 2.10.0. .. note:: - The columns 73-76 are not part of the official PDB format but are used by some programs to store/operate - the segment ID. For instance, Chimera_ assigns it as the attribute *pdbSegment*. + The columns 73-76 are not part of the official PDB format but are used by some programs to store/operate + the segment ID. For instance, Chimera_ assigns it as the attribute *pdbSegment*. + .. _Chimera: https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/pdbintro.html#note6 From 0cf9c7259db649a2a58ddd3e6ef004913e64d227 Mon Sep 17 00:00:00 2001 From: Oliver Beckstein Date: Thu, 10 Jul 2025 14:44:49 -0700 Subject: [PATCH 5/7] Update pdb.rst --- doc/source/formats/reference/pdb.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/source/formats/reference/pdb.rst b/doc/source/formats/reference/pdb.rst index c1fbdf901..9cc91d12c 100644 --- a/doc/source/formats/reference/pdb.rst +++ b/doc/source/formats/reference/pdb.rst @@ -105,7 +105,7 @@ PDB specification ============= ============ =========== ============================================= .. versionchanged:: 2.10.0 - The columns 67-72 are not read by MDAnalysis since version 2.10.0. + The columns 67-72 are not read by MDAnalysis since version 2.10.0. .. note:: The columns 73-76 are not part of the official PDB format but are used by some programs to store/operate From 726f83649798f793666a40154927113b073ad626 Mon Sep 17 00:00:00 2001 From: Oliver Beckstein Date: Mon, 14 Jul 2025 10:16:33 -0700 Subject: [PATCH 6/7] Update pdb.rst with Rocco's suggestion --- doc/source/formats/reference/pdb.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/source/formats/reference/pdb.rst b/doc/source/formats/reference/pdb.rst index 9cc91d12c..a5ca8129d 100644 --- a/doc/source/formats/reference/pdb.rst +++ b/doc/source/formats/reference/pdb.rst @@ -105,7 +105,7 @@ PDB specification ============= ============ =========== ============================================= .. versionchanged:: 2.10.0 - The columns 67-72 are not read by MDAnalysis since version 2.10.0. + The columns 67-72 are not read by MDAnalysis any more. .. note:: The columns 73-76 are not part of the official PDB format but are used by some programs to store/operate From 4c1603ed2be319bb7da7eda5607e55ede251d666 Mon Sep 17 00:00:00 2001 From: "Yu-Yuan (Stuart) Yang - from connectin, AFLab" Date: Mon, 14 Jul 2025 23:03:23 +0100 Subject: [PATCH 7/7] add myself in author list --- doc/source/AUTHORS | 2 ++ 1 file changed, 2 insertions(+) diff --git a/doc/source/AUTHORS b/doc/source/AUTHORS index 782d78b6e..caa629e0b 100644 --- a/doc/source/AUTHORS +++ b/doc/source/AUTHORS @@ -44,3 +44,5 @@ Chronological list of authors 2024 - Mahfuza Humayra Mohona - Rubén Chaves +2025 + - Yu-Yuan (Stuart) Yang \ No newline at end of file