Document figures for part 3 and 4 are updated

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@501 a2be9bc6-48de-4e38-9406-05402d4bc13c

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diff --git a/Documents/src/doc_source.html b/Documents/src/doc_source.html
index 701765d..e28dc82 100644 (file)
--- a/Documents/src/doc_source.html
+++ b/Documents/src/doc_source.html
@@ -627,57 +627,57 @@ Like any other decent "editing" applications, Molby has a capability of cut/copy
 <p>
 We start from the toluene molecule again. Select the methyl group and do copy.
 </p>
-<p><img src="../etc/tutorial_25.png" /></p>
+<p><img src="../etc/copy_01.png" /></p>
 <p>
 Unselect the methyl group, and do paste. Another methyl group appears, with no connection to the existing atoms. This is how "paste" works when nothing is selected beforehand.
 </p>
-<p><img src="../etc/tutorial_26.png" /></p>
+<p><img src="../etc/copy_02.png" /></p>
 <p>
 Now we will see what happens when something is selected before pasting. As described above, start with the toluene molecule, select the methyl group, and copy it. Unselect the methyl group, and this time select the hydrogen atom that is "ortho" to the methyl group.
 </p>
-<p><img src="../etc/tutorial_27.png" /></p>
+<p><img src="../etc/copy_03.png" /></p>
 <p>
 Do paste. The selected hydrogen atom is replaced with the pasted methyl group. Note that a new bond is created between the pasted methyl carbon and the ortho carbon, with an acceptable bond length and angles. 
 </p>
-<p><img src="../etc/tutorial_28.png" /></p>
 <p class="note">
 The dihedral angle may not be acceptable. In that case, you can rotate the pasted fragment by use of the left rotation bar until the dihedral angle looks good.
 </p>
+<p><img src="../etc/copy_04.png" /></p>
 <p>
 This "select and paste" technique is very useful for building large molecules. Suppose we want to build an oligobenzamide.
 </p>
-<p><img src="../etc/tutorial_39.png" /></p>
+<p><img src="../etc/copy_05.png" /></p>
 <p>
 Create a "monomer", i.e. N-methyl-4-acetamidobenzamide. This is done by (1) create a benzene, (2) select H1, double-click, and enter "CONHCH3", (3) select H4, double-click, and enter "NHCOCH3". After entering each formula, you need to rotate the fragment to make the dihedral angle appropriate.
 </p>
-<p><img src="../etc/tutorial_29.png" /></p>
+<p><img src="../etc/copy_06.png" /></p>
 <p>
 Select the whole molecule except for the COCH3 group at the left. Do copy.
 </p>
-<p><img src="../etc/tutorial_30.png" /></p>
+<p><img src="../etc/copy_07.png" /></p>
 <p>
 Select the NHCH3 group at the right. Do paste.
 </p>
-<p><img src="../etc/tutorial_31.png" /></p>
+<p><img src="../etc/copy_08.png" /></p>
 <p>
-The newly created amide bond has a bad dihedral angle. Rotate the pasted fragment by the left rotation bar, so that the amide bond becomes properly trans.
+A new amide bond is created and the dimer is formed.
 </p>
-<p><img src="../etc/tutorial_32.png" /><img src="../etc/tutorial_33.png" /></p>
+<p><img src="../etc/copy_09.png" /></p>
 <p>
 Select "Fit to Screen" from the "Show" menu, to make the whole molecule visible.
 </p>
-<p><img src="../etc/tutorial_34.png" /></p>
-<p><img src="../etc/tutorial_35.png" /></p>
+<p><img src="../etc/copy_10.png" /></p>
 <p>
 Repeat these procedures to make the tetramer.
 </p>
-<p><img src="../etc/tutorial_36.png" /></p>
-<p><img src="../etc/tutorial_37.png" /></p>
-<p><img src="../etc/tutorial_38.png" /></p>
+<p><img src="../etc/copy_11.png" /></p>
+<p><img src="../etc/copy_12.png" /></p>
+<p><img src="../etc/copy_13.png" /></p>
+<p><img src="../etc/copy_14.png" /></p>
 <p>
 Make one more iteration to make the octamer.
 </p>
-<p><img src="../etc/tutorial_39.png" /></p>
+<p><img src="../etc/copy_15.png" /></p>
 </div>
 <div class="contents" lang="ja">
 <h1>第三段階：分子を編集する：カット・コピー・ペースト</h1>
@@ -687,57 +687,57 @@ Make one more iteration to make the octamer.
 <p>
 ふたたびトルエン分子から始めます。メチル基を選択して、コピーします。
 </p>
-<p><img src="../etc/tutorial_25.png" /></p>
+<p><img src="../etc/copy_01.png" /></p>
 <p>
 メチル基の選択を解除して、ペーストを実行します。他の原子と結合していないメチル基がもう一つ現れます。原子が選択されていない状態で「ペースト」すると、このような動作になります。
 </p>
-<p><img src="../etc/tutorial_26.png" /></p>
+<p><img src="../etc/copy_02.png" /></p>
 <p>
 今度は、ペーストする前に原子が選択されているときにどうなるかを見てみます。上と同じように、トルエンから始めて、メチル基を選択して、コピーします。メチル基の選択を解除して、今度はメチル基のオルト位の水素原子を選択します。
 </p>
-<p><img src="../etc/tutorial_27.png" /></p>
+<p><img src="../etc/copy_03.png" /></p>
 <p>
 ペーストを実行します。選択された水素原子がメチル基に置き換わります。オルト位の炭素とメチル基の間に新しい結合ができ、その長さと結合角が適切なものになっていることがわかります。
 </p>
-<p><img src="../etc/tutorial_28.png" /></p>
 <p class="note">
-äº\8cé\9d¢è§\92ã\81¯é\81©å\88\87ã\81¨ã\81¯ã\81\84ã\81\88ã\81ªã\81\84ã\81\8bã\82\82ç\9f¥ã\82\8cã\81¾ã\81\9bã\82\93。その場合は、ペーストされたグループを左の回転バーを使って回転させて、適切な二面角にします。
+äº\8cé\9d¢è§\92ã\81¯é\81©å\88\87ã\81§ã\81ªã\81\84ã\81\93ã\81¨ã\82\82ã\81\82ã\82\8aã\81¾ã\81\99。その場合は、ペーストされたグループを左の回転バーを使って回転させて、適切な二面角にします。
 </p>
+<p><img src="../etc/copy_04.png" /></p>
 <p>
 この「選択してペースト」のテクニックは、大きな分子を作るときにたいへん役に立ちます。たとえば、オリゴベンズアミドを作りたいとします。
 </p>
-<p><img src="../etc/tutorial_39.png" /></p>
+<p><img src="../etc/copy_05.png" /></p>
 <p>
 まず、「モノマー」となる N-メチル-4-アセトアミドベンズアミドを作ります。次のようにします：(1) ベンゼンを作る、(2) H1 を選択してダブルクリックし、「CONHCH3」とタイプする、(3) H4 を選択してダブルクリックし、「NHCOCH3」とタイプする。化学式をタイプしたあとは、作成したフラグメントを回転させて二面角を調整しておきます。
 </p>
-<p><img src="../etc/tutorial_29.png" /></p>
+<p><img src="../etc/copy_06.png" /></p>
 <p>
 左端の COCH3 以外全部を選択し、コピーします。
 </p>
-<p><img src="../etc/tutorial_30.png" /></p>
+<p><img src="../etc/copy_07.png" /></p>
 <p>
 右端の NHCH3 を選択し、「ペースト」を実行します。
 </p>
-<p><img src="../etc/tutorial_31.png" /></p>
+<p><img src="../etc/copy_08.png" /></p>
 <p>
-新しく作られたアミド結合は二面角が不適切です。左の回転バーを使ってペーストしたフラグメントを回転し、アミド結合が正しく trans になるようにします。
+新しくアミド結合が作られ、二量体ができます。
 </p>
-<p><img src="../etc/tutorial_32.png" /><img src="../etc/tutorial_33.png" /></p>
+<p><img src="../etc/copy_09.png" /></p>
 <p>
 "Show" メニューから "Fit to Screen" を選び、分子全体が見えるようにします。
 </p>
-<p><img src="../etc/tutorial_34.png" /></p>
-<p><img src="../etc/tutorial_35.png" /></p>
+<p><img src="../etc/copy_10.png" /></p>
 <p>
 この操作を繰り返して、四量体を作ります。
 </p>
-<p><img src="../etc/tutorial_36.png" /></p>
-<p><img src="../etc/tutorial_37.png" /></p>
-<p><img src="../etc/tutorial_38.png" /></p>
+<p><img src="../etc/copy_11.png" /></p>
+<p><img src="../etc/copy_12.png" /></p>
+<p><img src="../etc/copy_13.png" /></p>
+<p><img src="../etc/copy_14.png" /></p>
 <p>
 もう一度繰り返して、八量体を作ります。
 </p>
-<p><img src="../etc/tutorial_39.png" /></p>
+<p><img src="../etc/copy_15.png" /></p>
 </div>
 <link id="#navigation" />
 </div>
@@ -748,36 +748,35 @@ Make one more iteration to make the octamer.
 <link id="#header" />
 <div class="contents" lang="en">
 <h1>Step Four: Ring Fusion</h1>
-<p>(Version 0.6.1 and later)</p>
 <h2>1. Ring fusion by double-click and type-in</h2>
 <p>
-Molby has a capability (from version 0.6.1 and upper) to create a fused ring structure. As an example, here is presented yet another method to make indane. This time, we start from a benzene.
+Molby has a capability to create a fused ring structure. As an example, here is presented yet another method to make indane. This time, we start from a benzene.
 </p>
-<p><img src="../etc/tutorial_4_01.png" /></p>
+<p><img src="../etc/ring_01.png" /></p>
 <p>
 Choose "select" mode, and select C1 and C2 by clicking on the C1-C2 bond.
 </p>
-<p><img src="../etc/tutorial_4_02.png" /></p>
+<p><img src="../etc/ring_02.png" /></p>
 <p>
 Double-click on the selection, and enter "cyclopentane" in the dialog box.
 </p>
-<p><img src="../etc/tutorial_4_03.png" /></p>
+<p><img src="../etc/ring_03.png" /></p>
 <p>
 After pressing "OK", you will see a five-membered ring fused to the benzene ring.
 </p>
-<p><img src="../etc/tutorial_4_04.png" /></p>
+<p><img src="../etc/ring_04.png" /></p>
 <p>
 Ring fusion also works when three or more atoms are selected in the original structure. For example, select the consecutive three carbons in indane as follows.
 </p>
-<p><img src="../etc/tutorial_4_05.png" /></p>
+<p><img src="../etc/ring_05.png" /></p>
 <p>
 Double-click on the selection, and enter "C6H6" (or "benzene").
 </p>
-<p><img src="../etc/tutorial_4_06.png" /></p>
+<p><img src="../etc/ring_06.png" /></p>
 <p>
 Now we have acenaphthene...almost.
 </p>
-<p><img src="../etc/tutorial_4_07.png" /></p>
+<p><img src="../etc/ring_07.png" /></p>
 <p>
 As shown in the above figure, there is an extra, leftover hydrogen atom on one bridgehead carbon. After all, Molby is not so smart --- it just removes one hydrogen from each terminal carbon atoms in the selection, and connect a portion of the fusing fragment ("benzene" in this case) so that the newly created ring has the same number of atoms. Consequently, the stereochemistry may become strange when sp3 carbons are present either in the original structure or in the fusing fragment. You may need to remove/append hydrogen atoms and clean up structures (see <a href="mm_minimize.html">"Energy Minimization"</a> for detail).
 </p>
@@ -785,60 +784,58 @@ As shown in the above figure, there is an extra, leftover hydrogen atom on one b
 <p>
 There is another way to make a ring fused structure, which includes copy and paste. Starting again from a benzene.
 </p>
-<p><img src="../etc/tutorial_4_01.png" /></p>
+<p><img src="../etc/ring_08.png" /></p>
 <p>
 Open the "File" menu, and select "Open Predefined" &rarr; "Alicyclic" &rarr; "cyclopentane".
 </p>
-<p class="note">(This is for Version 0.6.1 and later)</p>
-<p><img src="../etc/tutorial_4_08.png" /></p>
+<p><img src="../etc/ring_09.png" /></p>
 <p>
 A new window named "*cyclopentane*" opens with one cyclopentane molecule. Select a portion containing three CH2 groups, and copy it by command-C or ctrl-C.
 </p>
-<p><img src="../etc/tutorial_4_09.png" /></p>
+<p><img src="../etc/ring_10.png" /></p>
 <p>
 Return to the benzene molecule again, and this time select H1 and H2 (not C1 and C2).
 </p>
-<p><img src="../etc/tutorial_4_10.png" /></p>
+<p><img src="../etc/ring_11.png" /></p>
 <p>
 Do paste by command-V or ctrl-V. You now get a indane molecule.
 </p>
-<p><img src="../etc/tutorial_4_11.png" /></p>
+<p><img src="../etc/ring_12.png" /></p>
 <p>
 This "copy-and-paste" actually works in a similar way to previously described example (see <a href="cut-copy-paste.html">"Cut/Copy/Paste"</a>). When both the current selection and the fragment in the pasteboard have two terminals, they are connected and ring fusion takes place. This method of ring fusion is slightly more complicated than the "double-click and type-in" method, but it may be easier to understand.
 </p>
 </div>
 <div class="contents" lang="ja">
 <h1>第四段階：縮環構造の作成</h1>
-<p>(バージョン 0.6.1 以上）</p>
 <h2>1. ダブルクリック／キー入力による縮環</h2>
 <p>
-Molby は縮環構造を作るための機能を持っています（バージョン 0.6.1 以降）。例として、インダンを作るもう一つの方法を紹介します。今回は、ベンゼンから始めます。
+Molby は縮環構造を作るための機能を持っています。例として、インダンを作るもう一つの方法を紹介します。今回は、ベンゼンから始めます。
 </p>
-<p><img src="../etc/tutorial_4_01.png" /></p>
+<p><img src="../etc/ring_01.png" /></p>
 <p>
 "Select" モードにして、C1-C2 結合をクリックして C1 と C2 を選択します。
 </p>
-<p><img src="../etc/tutorial_4_02.png" /></p>
+<p><img src="../etc/ring_02.png" /></p>
 <p>
 選択部分をダブルクリックして、ダイアログボックスに "cyclopentane" と入力します。
 </p>
-<p><img src="../etc/tutorial_4_03.png" /></p>
+<p><img src="../etc/ring_03.png" /></p>
 <p>
 "OK" を押すと、５員環がベンゼン環に縮環します。
 </p>
-<p><img src="../etc/tutorial_4_04.png" /></p>
+<p><img src="../etc/ring_04.png" /></p>
 <p>
 選択部分が３個以上の原子を含んでいても、縮環は可能です。例えば、インダンで図のように３つの連続した炭素原子を選択してみます。
 </p>
-<p><img src="../etc/tutorial_4_05.png" /></p>
+<p><img src="../etc/ring_05.png" /></p>
 <p>
 選択部分をダブルクリックして、"C6H6"（または "benzene"）と入力します。
 </p>
-<p><img src="../etc/tutorial_4_06.png" /></p>
+<p><img src="../etc/ring_06.png" /></p>
 <p>
 そうすると、アセナフテンができます...だいたい。
 </p>
-<p><img src="../etc/tutorial_4_07.png" /></p>
+<p><img src="../etc/ring_07.png" /></p>
 <p>
 上の図に示したように、橋頭位の炭素に１つ余分な水素原子が残ってしまいます。実のところ、Molby はあんまり賢くありません。選択部分の両端の原子から水素原子を１つずつ取り除いて、縮環する分子（この場合はベンゼン）の一部をかわりに結合して、生成する環の原子数が一致するようにしているだけです。このため、元の選択部分または縮環する分子が sp3 炭素を含んでいると、立体化学が変になることがあります。水素原子を除いたり付け加えたりして、さらに構造を最適化する必要があるでしょう（詳しくは「<a href="mm_minimize.html">エネルギー最小化</a>」を見てください）。
 </p>
@@ -846,24 +843,23 @@ Molby は縮環構造を作るための機能を持っています（バージ
 <p>
 縮環構造を作るには、コピー／ペーストを使ったもう一つの方法があります。またベンゼンから始めましょう。
 </p>
-<p><img src="../etc/tutorial_4_01.png" /></p>
+<p><img src="../etc/ring_08.png" /></p>
 <p>
 "File" メニューを開き、"Open Predefined" &rarr; "Alicyclic" &rarr; "cyclopentane" を選んでください。
 </p>
-<p class="note">(これはバージョン 0.6.1 以降の機能です。よく使われる分子構造がこのメニューから選択できます。)</p>
-<p><img src="../etc/tutorial_4_08.png" /></p>
+<p><img src="../etc/ring_09.png" /></p>
 <p>
 "*cyclopentane*"という名前の新しいウィンドウが開き、シクロペンタン分子が入っています。３つのメチレン基を選択して、コマンド-C またはコントロール-C でコピーしてください。
 </p>
-<p><img src="../etc/tutorial_4_09.png" /></p>
+<p><img src="../etc/ring_10.png" /></p>
 <p>
 ベンゼン分子に戻って、今度は H1 と H2（C1 と C2 ではなく）を選択してください。
 </p>
-<p><img src="../etc/tutorial_4_10.png" /></p>
+<p><img src="../etc/ring_11.png" /></p>
 <p>
 コマンド-V またはコントロール-V でペーストしてください。インダンができます。
 </p>
-<p><img src="../etc/tutorial_4_11.png" /></p>
+<p><img src="../etc/ring_12.png" /></p>
 <p>
 この「コピー／ペースト」は、実は前に説明したのと (<a href="cut-copy-paste.html">カット／コピー／ペースト</a>) 同じように機能しています。現在の選択部分とクリップボードの内容がともに「２つの末端」を持っているとき、末端同士がつなぎあわされ、縮環したように見えるのです。この方法による縮環は「ダブルクリック／入力」の方法よりも少し複雑ですが、何が起きているかはこちらの方が理解しやすいかもしれません。
 </p>