diff options
| author | Mark Sims <mark@nanorex.com> | 2007-09-26 01:52:55 +0000 |
|---|---|---|
| committer | Mark Sims <mark@nanorex.com> | 2007-09-26 01:52:55 +0000 |
| commit | 3b6b3eae3bc3038b22a87fe850d46777449c70c8 (patch) | |
| tree | 1d64069c04e48901803702dfd6e625075d076abd /cad/plugins/DNA/B-DNA/PAM3-bases | |
| parent | 94e9ec2840dabe9f498aaabd859071c0088477b9 (diff) | |
| download | nanoengineer-theirix-3b6b3eae3bc3038b22a87fe850d46777449c70c8.tar.gz nanoengineer-theirix-3b6b3eae3bc3038b22a87fe850d46777449c70c8.zip | |
PAM3 MMP base-pair files.
Diffstat (limited to 'cad/plugins/DNA/B-DNA/PAM3-bases')
| -rw-r--r-- | cad/plugins/DNA/B-DNA/PAM3-bases/EndBasePair.mmp | 35 | ||||
| -rw-r--r-- | cad/plugins/DNA/B-DNA/PAM3-bases/MiddleBasePair.mmp | 35 | ||||
| -rw-r--r-- | cad/plugins/DNA/B-DNA/PAM3-bases/README | 18 | ||||
| -rw-r--r-- | cad/plugins/DNA/B-DNA/PAM3-bases/SingleBasePair.mmp | 57 | ||||
| -rw-r--r-- | cad/plugins/DNA/B-DNA/PAM3-bases/StartBasePair.mmp | 35 |
5 files changed, 180 insertions, 0 deletions
diff --git a/cad/plugins/DNA/B-DNA/PAM3-bases/EndBasePair.mmp b/cad/plugins/DNA/B-DNA/PAM3-bases/EndBasePair.mmp new file mode 100644 index 000000000..55fefd1a4 --- /dev/null +++ b/cad/plugins/DNA/B-DNA/PAM3-bases/EndBasePair.mmp @@ -0,0 +1,35 @@ +mmpformat 050920 required; 070415 preferred
+kelvin 300
+group (View Data)
+info opengroup open = True
+csys (HomeView) (1.000000, 0.000000, 0.000000, 0.000000) (10.000000) (0.000000, 0.000000, 0.000000) (1.000000)
+csys (LastView) (0.707107, 0.000000, -0.707107, 0.000000) (10.000000) (0.000000, 0.000000, 0.000000) (1.000000)
+egroup (View Data)
+group (EndBasePair)
+info opengroup open = True
+mol (DNA-1) def
+atom 1 (300) (0, 0, 0) def
+atom 2 (301) (0, 8697, 0) def
+info atom dnaBaseName = a
+bond1 1
+atom 3 (301) (6361, -5931, 0) def
+info atom dnaBaseName = b
+bond1 1
+atom 4 (0) (7882, -3676, 1590) def
+bond1 3
+atom 5 (0) (-2688, 8271, 1590) def
+bond1 2
+atom 6 (0) (0, 0, 1590) def
+bond1 1
+atom 7 (306) (2210, 7978, -1374) def
+bond1 2
+atom 8 (304) (0, 0, -1590) inv
+bond1 1
+atom 9 (305) (3710, -7399, -1791) inv
+bond1 3
+egroup (EndBasePair)
+end1
+group (Clipboard)
+info opengroup open = True
+egroup (Clipboard)
+end molecular machine part EndBasePair
diff --git a/cad/plugins/DNA/B-DNA/PAM3-bases/MiddleBasePair.mmp b/cad/plugins/DNA/B-DNA/PAM3-bases/MiddleBasePair.mmp new file mode 100644 index 000000000..a6c543021 --- /dev/null +++ b/cad/plugins/DNA/B-DNA/PAM3-bases/MiddleBasePair.mmp @@ -0,0 +1,35 @@ +mmpformat 050920 required; 070415 preferred
+kelvin 300
+group (View Data)
+info opengroup open = True
+csys (HomeView) (1.000000, 0.000000, 0.000000, 0.000000) (10.000000) (0.000000, 0.000000, 0.000000) (1.000000)
+csys (LastView) (1.000000, 0.000000, 0.000000, 0.000000) (10.000000) (0.000000, 0.000000, 0.000000) (1.000000)
+egroup (View Data)
+group (MiddleBasePair)
+info opengroup open = True
+mol (DNA-1) def
+atom 1 (300) (0, 0, 0) tub
+atom 2 (301) (0, 8697, 0) def
+info atom dnaBaseName = a
+bond1 1
+atom 3 (301) (6361, -5931, 0) def
+info atom dnaBaseName = b
+bond1 1
+atom 4 (0) (0, 0, 1590) def
+bond1 1
+atom 5 (0) (-2688, 8271, 1590) def
+bond1 2
+atom 6 (0) (7882, -3676, 1590) def
+bond1 3
+atom 7 (0) (0, 0, -1590) def
+bond1 1
+atom 8 (0) (2688, 8271, -1590) def
+bond1 2
+atom 9 (0) (4216, -7607, -1590) def
+bond1 3
+egroup (MiddleBasePair)
+end1
+group (Clipboard)
+info opengroup open = False
+egroup (Clipboard)
+end molecular machine part MiddleBasePair
diff --git a/cad/plugins/DNA/B-DNA/PAM3-bases/README b/cad/plugins/DNA/B-DNA/PAM3-bases/README new file mode 100644 index 000000000..f91d6b6e4 --- /dev/null +++ b/cad/plugins/DNA/B-DNA/PAM3-bases/README @@ -0,0 +1,18 @@ +$Id: $
+
+Copyright 2006-2007 Nanorex, Inc. See LICENSE file for details.
+
+These files are used by Dna.py to create PAM3 DNA structures in the
+CAD program:
+
+- StartBasePair.mmp
+- MiddleBasePair.mmp
+- EndBasePair.mmp
+- SingleBasePair.mmp
+
+Each file contains two "Ss3" (Sugar) pseudo atoms named "a" and "b" (via the
+new Atom "dnaBaseName" info records) which get assigned their permanent
+base letters when the DNA structure is generated (see Dna.make()).
+The "a" atom belongs to "Strand1" and atom "b" (the complement of "a") belongs
+to "Strand2".
+
diff --git a/cad/plugins/DNA/B-DNA/PAM3-bases/SingleBasePair.mmp b/cad/plugins/DNA/B-DNA/PAM3-bases/SingleBasePair.mmp new file mode 100644 index 000000000..30ae27628 --- /dev/null +++ b/cad/plugins/DNA/B-DNA/PAM3-bases/SingleBasePair.mmp @@ -0,0 +1,57 @@ +mmpformat 050920 required; 070415 preferred
+kelvin 300
+group (View Data)
+info opengroup open = True
+csys (HomeView) (1.000000, 0.000000, 0.000000, 0.000000) (10.000000) (0.000000, 0.000000, 0.000000) (1.000000)
+csys (LastView) (1.000000, 0.000000, 0.000000, 0.000000) (10.000000) (0.000000, 0.000000, 0.000000) (1.000000)
+egroup (View Data)
+group (Untitled)
+info opengroup open = True
+mol (DNA-1) def
+atom 1 (300) (0, 0, 3180) def
+atom 2 (304) (0, 0, 4770) def
+bond1 1
+atom 3 (301) (-5112, 7036, 3180) def
+info atom dnaBaseName = A
+bond1 1
+atom 4 (305) (-7600, 5229, 3341) def
+info atom dnaStrandName = Strand1
+bond1 3
+bond_direction 4 3
+atom 5 (301) (8632, -1060, 3180) def
+info atom dnaBaseName = T
+bond1 1
+atom 6 (306) (7859, 586, 3179) def
+bond1 5
+bond_direction 5 6
+atom 7 (300) (0, 0, 0) def
+bond1 1
+atom 8 (301) (0, 8697, 0) def
+info atom dnaBaseName = B
+bond1 7 3
+atom 9 (301) (6361, -5931, 0) def
+info atom dnaBaseName = V
+bond1 7 5
+atom 10 (300) (0, 0, -3179) def
+bond1 7
+atom 11 (304) (0, 0, -4769) def
+bond1 10
+atom 12 (301) (5112, 7036, -3179) def
+info atom dnaBaseName = C
+bond1 10 8
+atom 13 (306) (5609, 5476, -3973) def
+bond1 12
+bond_direction 12 13
+atom 14 (301) (1659, -8537, -3179) def
+info atom dnaBaseName = G
+bond1 10 9
+atom 15 (305) (-1360, -9126, -3338) def
+info atom dnaStrandName = Strand2
+bond1 14
+bond_direction 15 14
+egroup (Untitled)
+end1
+group (Clipboard)
+info opengroup open = False
+egroup (Clipboard)
+end molecular machine part Untitled
diff --git a/cad/plugins/DNA/B-DNA/PAM3-bases/StartBasePair.mmp b/cad/plugins/DNA/B-DNA/PAM3-bases/StartBasePair.mmp new file mode 100644 index 000000000..e80f677e2 --- /dev/null +++ b/cad/plugins/DNA/B-DNA/PAM3-bases/StartBasePair.mmp @@ -0,0 +1,35 @@ +mmpformat 050920 required; 070415 preferred
+kelvin 300
+group (View Data)
+info opengroup open = True
+csys (HomeView) (1.000000, 0.000000, 0.000000, 0.000000) (10.000000) (0.000000, 0.000000, 0.000000) (1.000000)
+csys (LastView) (0.707107, 0.000000, -0.707107, 0.000000) (10.000000) (0.000000, 0.000000, 0.000000) (1.000000)
+egroup (View Data)
+group (StartBasePair)
+info opengroup open = True
+mol (DNA-1) def
+atom 1 (300) (0, 0, 0) def
+atom 2 (301) (0, 8697, 0) def
+info atom dnaBaseName = a
+bond1 1
+atom 3 (301) (6361, -5931, 0) def
+info atom dnaBaseName = b
+bond1 1
+atom 4 (0) (0, 0, -1590) def
+bond1 1
+atom 5 (0) (2688, 8271, -1590) def
+bond1 2
+atom 6 (0) (4216, -7607, -1590) def
+bond1 3
+atom 7 (305) (-2881, 7760, 1792) inv
+bond1 2
+atom 8 (304) (0, 0, 1590) inv
+bond1 1
+atom 9 (306) (7342, -3824, 1374) def
+bond1 3
+egroup (StartBasePair)
+end1
+group (Clipboard)
+info opengroup open = True
+egroup (Clipboard)
+end molecular machine part StartBasePair
|