From 24e6557939ed885f5292e0fb7dfc4a23f4d04a57 Mon Sep 17 00:00:00 2001
From: "UENO, M." <eunosium-1128@live.jp>
Date: Wed, 9 Oct 2024 09:30:58 +0000
Subject: [PATCH 1/5] Update coot.desktop considering flatpak package

---
 coot.desktop | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/coot.desktop b/coot.desktop
index 10f1efac8..164d2282f 100644
--- a/coot.desktop
+++ b/coot.desktop
@@ -1,9 +1,10 @@
 [Desktop Entry]
 Type=Application
 Name=Coot
+GenericName=Crystallographic Object-Oriented Toolkit
 Comment=Macromolecular model builder
 Exec=coot %f
-Icon=coot
+Icon=io.github.pemsley.coot
 Terminal=true
-Categories=Science;Chemistry;
+Categories=Science;Chemistry;Biology;GTK;
 MimeType=chemical/x-pdb;chemical/x-mmcif;chemical/x-mdl-molfile;

From 42b31217403fbdb50d8b9bd26dc5654da8c091a0 Mon Sep 17 00:00:00 2001
From: "UENO, M." <eunosium-1128@live.jp>
Date: Wed, 9 Oct 2024 09:31:23 +0000
Subject: [PATCH 2/5] Update coot.appdata.xml considering flatpak package

---
 coot.appdata.xml | 15 +++++++++++----
 1 file changed, 11 insertions(+), 4 deletions(-)

diff --git a/coot.appdata.xml b/coot.appdata.xml
index 19bccb947..340ac666a 100644
--- a/coot.appdata.xml
+++ b/coot.appdata.xml
@@ -1,7 +1,7 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<!-- Copyright 2014 Paul Emsley <pemsley at mrc dash lmb dot cam dot ac dot uk> -->
+<!-- Copyright 2024 Paul Emsley <pemsley at mrc dash lmb dot cam dot ac dot uk> -->
 <component type="desktop">
- <id>org.emsley.coot</id>
+ <id>io.github.pemsley.coot</id>
  <metadata_license>GFDL-1.3</metadata_license>
  <project_license>GPL-2.0+ and GPL-3.0+ and LGPL-3.0+</project_license>
  <name>Coot</name>
@@ -16,7 +16,7 @@
      refinement.
   </p>
   <p>
-     Coot is used by scientists using X-ray crystallography for
+     Coot is used by scientists using X-ray crystallography or cryo-EM for
      analysis of proteins, electron density maps, protein interactions
      and drug design.
   </p>
@@ -31,6 +31,13 @@
     <caption>Coot can be used to convert from 2D ligands to 3D and from 3D to 2D</caption>
   </screenshot>
  </screenshots>
- <url type="homepage">http://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/</url>
+ <url type="homepage">https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/</url>
+ <url type="help">https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/web/docs</url>
+ <url type="bugtracker">https://github.com/pemsley/coot/issues</url>
+ <developer_name>Paul Emsley</developer_name>
  <updatecontact>pemsley _at_ mrc dash lmb.cam.ac.uk</updatecontact>
+ <content_rating type="oars-1.1" />
+<releases>
+    <release version="1.1.10" date="2024-07-21"></release>
+</releases>
 </component>

From 1106feceda38fe45e3732e923d287f09682b8711 Mon Sep 17 00:00:00 2001
From: "UENO, M." <eunosium-1128@live.jp>
Date: Wed, 9 Oct 2024 09:55:35 +0000
Subject: [PATCH 3/5] Update copyright span and icon name

---
 coot.appdata.xml | 2 +-
 coot.desktop     | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/coot.appdata.xml b/coot.appdata.xml
index 340ac666a..aaee84696 100644
--- a/coot.appdata.xml
+++ b/coot.appdata.xml
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<!-- Copyright 2024 Paul Emsley <pemsley at mrc dash lmb dot cam dot ac dot uk> -->
+<!-- Copyright 2014-2024 Paul Emsley <pemsley at mrc dash lmb dot cam dot ac dot uk> -->
 <component type="desktop">
  <id>io.github.pemsley.coot</id>
  <metadata_license>GFDL-1.3</metadata_license>
diff --git a/coot.desktop b/coot.desktop
index 164d2282f..5b854ad6e 100644
--- a/coot.desktop
+++ b/coot.desktop
@@ -4,7 +4,7 @@ Name=Coot
 GenericName=Crystallographic Object-Oriented Toolkit
 Comment=Macromolecular model builder
 Exec=coot %f
-Icon=io.github.pemsley.coot
+Icon=coot
 Terminal=true
 Categories=Science;Chemistry;Biology;GTK;
 MimeType=chemical/x-pdb;chemical/x-mmcif;chemical/x-mdl-molfile;

From 0e2e93936d0ebf4206e1f17b657d283b8f4fecfa Mon Sep 17 00:00:00 2001
From: "UENO, M." <eunosium-1128@live.jp>
Date: Wed, 9 Oct 2024 11:26:16 +0000
Subject: [PATCH 4/5] Update coot.appdata.xml

---
 coot.appdata.xml | 10 +++++++---
 1 file changed, 7 insertions(+), 3 deletions(-)

diff --git a/coot.appdata.xml b/coot.appdata.xml
index aaee84696..0c0606703 100644
--- a/coot.appdata.xml
+++ b/coot.appdata.xml
@@ -1,7 +1,8 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<!-- Copyright 2014-2024 Paul Emsley <pemsley at mrc dash lmb dot cam dot ac dot uk> -->
+<!-- Copyright 2014-2024 Paul Emsley <pemsley@mrc-lmb.cam.ac.uk> -->
 <component type="desktop">
  <id>io.github.pemsley.coot</id>
+ <launchable type="desktop-id">io.github.pemsley.coot.desktop</launchable>
  <metadata_license>GFDL-1.3</metadata_license>
  <project_license>GPL-2.0+ and GPL-3.0+ and LGPL-3.0+</project_license>
  <name>Coot</name>
@@ -34,8 +35,11 @@
  <url type="homepage">https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/</url>
  <url type="help">https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/web/docs</url>
  <url type="bugtracker">https://github.com/pemsley/coot/issues</url>
- <developer_name>Paul Emsley</developer_name>
- <updatecontact>pemsley _at_ mrc dash lmb.cam.ac.uk</updatecontact>
+ <developer>
+  <developer-id>pemsley</developer-id>
+  <developer-name>Paul Emsley</developer-name>
+</developer>
+ <contact>pemsley@mrc-lmb.cam.ac.uk</contact>
  <content_rating type="oars-1.1" />
 <releases>
     <release version="1.1.10" date="2024-07-21"></release>

From f46c10daa3d2ef120fd105d4056338e7acd1fa08 Mon Sep 17 00:00:00 2001
From: "UENO, M." <eunosium-1128@live.jp>
Date: Wed, 9 Oct 2024 21:40:58 +0900
Subject: [PATCH 5/5] Update coot.appdata.xml

---
 coot.appdata.xml | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/coot.appdata.xml b/coot.appdata.xml
index 0c0606703..52580bb62 100644
--- a/coot.appdata.xml
+++ b/coot.appdata.xml
@@ -24,22 +24,24 @@
  </description>
  <screenshots>
   <screenshot type="default">
-    <image type="source">http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/web/screenshots/other/coot-viagra-1.png</image>
+    <image type="source">https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/web/screenshots/other/coot-viagra-1.png</image>
     <caption>Coot is typically used to view protein models and electron density</caption>
   </screenshot>
   <screenshot>
-    <image type="source">http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/web/screenshots/other/coot-ligand-builder.png</image>
+    <image type="source">https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/web/screenshots/other/coot-ligand-builder.png</image>
     <caption>Coot can be used to convert from 2D ligands to 3D and from 3D to 2D</caption>
   </screenshot>
+  <screenshot>
+    <image type="source">https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/web/screenshots/apoferritin/sapphires-and-emeralds.png</image>
+  </screenshot>
  </screenshots>
  <url type="homepage">https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/</url>
  <url type="help">https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/web/docs</url>
  <url type="bugtracker">https://github.com/pemsley/coot/issues</url>
  <developer>
-  <developer-id>pemsley</developer-id>
   <developer-name>Paul Emsley</developer-name>
+  <url type="contact">mailto:pemsley@mrc-lmb.cam.ac.uk</url>
 </developer>
- <contact>pemsley@mrc-lmb.cam.ac.uk</contact>
  <content_rating type="oars-1.1" />
 <releases>
     <release version="1.1.10" date="2024-07-21"></release>