trunk/debian/rings3d.1

.ad l
.nh
.TH RINGS3D 1 "" "Raster3D"
.SH NAME

rigns3d - produces a file of ring-filling triangles from a PDB file

.SH SYNOPSIS

rings3d [-bases] [-protein] [-sugars]  < infile.pdb > outfile.r3d

.PP
\fIrings3d\fP searches through a PDB file looking for residues containing
5- or 6-membered rings, then produces a Raster3D output file of ring-filling
triangles.

\fIrings3d\fP matches residue types from an internal list of residue and
atom names. It will fail to find residues not in its list, and fail to
recognize atoms with non-standard names.
.PP
.SH EXAMPLES
.PP
render a DNA molecule with the bases filled in:
.PP
     cat $R3D_LIB/dna.colours dna.pdb | rods -radius 0.05 > temp.1
     rings3d -bases < dna.pdb > temp.2
     cat temp.1 temp.2 | render -tiff dna.tiff
.SH OPTIONS

.B "-bases"
.PP
Fills in purine and pyrimidine rings from A C G T U residues.

.B "-protein"
.PP
Fills in sidechain rings of HIS PHE TRP and TYR residues.

.B "-sugars"
.PP
[This is the default] Fills in pyranose rings of GAL GLC NAG NGA MAN SIA
residues.

.SH BUGS
.B limited residue types
.PP
The database of residue types should be kept externally, so you don't
have to rebuild the program to add a new type.
There should be an option to search for ring systems in un-recognized
residue types.
.B crinkled planes
.PP
There should be an option to do a least-squares best plane through
supposedly flat rings. Then again, seeing a crease in a "flat" ring
may force people to consider whether their planarity restraints are
tight enough.

.SH SOURCE
.B anonymous ftp site:  
        ftp.bmsc.washington.edu
 
.B web URL:
        http://www.bmsc.washington.edu/raster3d/raster3d.html

.B contact:             
        Ethan A Merritt
        Dept of Biological Structure Box 357742
        University of Washington, Seattle WA 98195
        merritt@u.washington.edu

.SH SEE ALSO
Raster3D(l)
.PP
.SH AUTHORS

Ethan A Merritt.
.PP
This manual page was written by Nelson A. de Oliveira <naoliv@gmail.com>,
for the Debian project (but may be used by others).
1	.ad l
2	.nh
3	.TH RINGS3D 1 "" "Raster3D"
4	.SH NAME
5
6	rigns3d - produces a file of ring-filling triangles from a PDB file
7
8	.SH SYNOPSIS
9
10	rings3d [-bases] [-protein] [-sugars] < infile.pdb > outfile.r3d
11
12	.PP
13	\fIrings3d\fP searches through a PDB file looking for residues containing
14	5- or 6-membered rings, then produces a Raster3D output file of ring-filling
15	triangles.
16
17	\fIrings3d\fP matches residue types from an internal list of residue and
18	atom names. It will fail to find residues not in its list, and fail to
19	recognize atoms with non-standard names.
20	.PP
21	.SH EXAMPLES
22	.PP
23	render a DNA molecule with the bases filled in:
24	.PP
25	cat $R3D_LIB/dna.colours dna.pdb \| rods -radius 0.05 > temp.1
26	rings3d -bases < dna.pdb > temp.2
27	cat temp.1 temp.2 \| render -tiff dna.tiff
28	.SH OPTIONS
29
30	.B "-bases"
31	.PP
32	Fills in purine and pyrimidine rings from A C G T U residues.
33
34	.B "-protein"
35	.PP
36	Fills in sidechain rings of HIS PHE TRP and TYR residues.
37
38	.B "-sugars"
39	.PP
40	[This is the default] Fills in pyranose rings of GAL GLC NAG NGA MAN SIA
41	residues.
42
43	.SH BUGS
44	.B limited residue types
45	.PP
46	The database of residue types should be kept externally, so you don't
47	have to rebuild the program to add a new type.
48	There should be an option to search for ring systems in un-recognized
49	residue types.
50	.B crinkled planes
51	.PP
52	There should be an option to do a least-squares best plane through
53	supposedly flat rings. Then again, seeing a crease in a "flat" ring
54	may force people to consider whether their planarity restraints are
55	tight enough.
56
57	.SH SOURCE
58	.B anonymous ftp site:
59	ftp.bmsc.washington.edu
60
61	.B web URL:
62	http://www.bmsc.washington.edu/raster3d/raster3d.html
63
64	.B contact:
65	Ethan A Merritt
66	Dept of Biological Structure Box 357742
67	University of Washington, Seattle WA 98195
68	merritt@u.washington.edu
69
70	.SH SEE ALSO
71	Raster3D(l)
72	.PP
73	.SH AUTHORS
74
75	Ethan A Merritt.
76	.PP
77	This manual page was written by Nelson A. de Oliveira <naoliv@gmail.com>,
78	for the Debian project (but may be used by others).