Dear friends,
I have a pipe delimited file having 5 columns.
However the column no-3 is having extra new line characters as the data owing to owing , I am having issues.
Ideally my file should have only newline termination at the end of each record and not within column data of any of... (1 Reply)
How to manipulate first column and reverse the line order in third and fourth column as follws?
For example i have a original file like this:
file1
0.00000000E+000 -1.17555359E-001 0.00000000E+000
2.00000000E-002 -1.17555359E-001 0.00000000E+000
... (1 Reply)
Hi Gurus,
We have a ftpserver from which we do a dir command and output it to a local file.
The content of the ftpfile is:
07-15-09 06:06AM 5466 ABC_123_ER19057320090714082723.ZIP
07-15-09 06:07AM 3801 ABC_123_ER19155920090714082842.ZIP
07-15-09 06:07AM ... (14 Replies)
Given a file such as this I need to remove the duplicates.
00060011 PAUL BOWSTEIN ad_waq3_921_20100826_010517.txt
00060011 PAUL BOWSTEIN ad_waq3_921_20100827_010528.txt
0624-01 RUT CORPORATION ad_sade3_10_20100827_010528.txt
0624-01 RUT CORPORATION ... (13 Replies)
Hello ,
i have a text file like this :
A123 c12AB c32DD aaaa
B123 23DS 12QW bbbb
C123 2GR 3RG cccccc
i want to remove the numbers from second and third column only.
i tried this :
perl -pe 's///g' file.txt > newfile.txt
but it will remove the number from... (7 Replies)
Hi friends,
My input file is this way
chr1 100 200 "abc"
chr1 350 400 "abc"
chr2 450 600 "def"
chr2 612 780 "def"
How do I make this file into
chr1 100 400 "abc"
chr2 450 780 "def"
This is basically matching on the fourth column and taking the minimum of second column and the... (4 Replies)
Hi Experts,
I am new to UNIX. One of my file records are like below
220 IN C/A 515013 NULL NULL
220 IN C/A 515017 NULL NULL
225 IN C/A 333701 NULL NULL
225 IN C/A 515034 NULL NULL
225 IN C/A 499201 NULL NULL
225 IN C/A 499202 NULL NULL
The above mentioned records delimiter is... (4 Replies)
Hi,
I am a newbie to shell scripting (.sh). Please guide me on how to do the below issue.
My input file has below data.
I want to remove $ sysmbol from the fourth column of each line. (ie, between 4th and 5th pipe symbol)
ABC25160|51497|06/02/2010|$32,192.07|MARK|$100|A... (3 Replies)
Hi,
I came across one issue recently where output from one of the columns of the table from where i am creating input file has newline characters hence, record in the file is spread over multiple lines. Fields in the file are separated by pipe (|) delimiter. As header will never have newline... (4 Replies)
Discussion started by: Prathmesh
4 Replies
LEARN ABOUT DEBIAN
rods
RODS(1) General Commands Manual RODS(1)NAME
rods - Raster3D preprocessor for ball-and-stick models
SYNOPSIS
rods [-h] [-b] [-radius R] [-Bcolor Bmin Bmax]
Rods reads a file describing atom colours and/or a PDB coordinate file and produces a file containing Raster3D descriptor records. The
file produced by rods may be fed directly to render or it may be combined with descriptor files produced by other Raster3D utilities.
EXAMPLES
To describe a simple bonds-only model coloured by residue type:
cat mycolours.pdb protein.pdb | rods | render > mypicture.png
To render the same molecule as ball-and-stick:
cat mycolours.pdb protein.pdb | rods -b | render > mypicture.png
OPTIONS -h
Suppress header records in output. By default rods will produce an output file which starts with header records containing a default set
of scaling and processing options. The -h flag will suppress these header records so that the output file contains only object descrip-
tors. This option is useful for producing files which describe only part of a scene, and which are to be later combined with descriptor
files produced by other programs.
-b
By default rods will describe bonds only; the -b flag will cause it to include spheres at the atom positions also, yielding a ball-and-
stick representation.
-radius R
By default rods will draw bonds as cylinders with a 0.2A radius. The radius option allows you to change this cylindrical radius.
-Bcolor Bmin Bmax
Assign colors based on B values rather than from atom or residue types. Atoms with B <= Bmin will be colored dark blue; atoms with B >=
Bmax will be colored light red; atoms with Bmin < B < Bmax will be assigned colors shading smoothly through the spectrum from blue to red.
DESCRIPTION
The input to rods consists of a single text file containing colour information and atomic coordinates in PDB data bank format. Coordinates
are output as Raster3D descriptor records with colours and sphere radii assigned according to the COLO records described below. Ball-and-
stick figures have atoms drawn at 0.2 * VanderWaals radius, connected by rods with a default 0.2A cylindrical radius. Bonds are drawn for
atoms which lie closer to each other than 0.6 * (sum of VanderWaals radii). By default the output file contains a set of header records as
required by the render program. The header is constructed to include a TMAT matrix corresponding to the transformation matrix contained in
file setup.matrix (if it exists), or to the Eulerian angles contained in file setup.angles (if it exists).
Colours are assigned to atoms using a matching process, using COLOUR records prepended to the input PDB file. If no COLOUR records are
present in the input file, atoms will receive default CPK colors (C=grey, O=red, N=blue, S=yellow, P=green, other=magenta). Raster3D uses
a pseudo-PDB record type with the same basic layout as the above but with COLO in the first 4 columns:
Columns
1 - 4 COLO
7 - 30 Mask (described below)
31 - 38 Red component
39 - 46 Green component
47 - 54 Blue component
55 - 60 van der Waals radius in Angstroms
61 - 80 Comments
Note that the Red, Green, and Blue components are in the same positions as the X, Y, and Z components of an ATOM or HETA record, and the
van der Waals radius goes in place of the Occupancy. The Red, Green, and Blue components must all be in the range 0 to 1.
The Mask field is used in the matching process as follows. First the program reads in and stores all the ATOM, HETA, and COLO records in
input order. Then it goes through each stored ATOM/HETA record in turn, and searches for a COLO record that matches the ATOM/HETA record
in all of columns 7 through 30. The first such COLO record to be found determines the colour and radius of the atom.
In order that one COLO record can provide colour and radius specifications for more than one atom (e.g., based on residue or atom type, or
any other criterion for which labels can be given somewhere in columns 7 through 30), the "#" symbol is used as a wildcard. I.e. a # in a
COLO record matches any character in the corresponding column in an ATOM or HETA record. All other characters must match literally to
count as a match. Note that the very last COLO record in the input should have # symbols in all of columns 7 through 30 in order to pro-
vide a colour for any atom whose ATOM/HETA record fails to match any previous COLO record. This idea of matching masks for colour specifi-
cations is due to Colin Broughton.
ENVIRONMENT
The files setup.matrix and setup.angles, if they exist, affect the header records produced by rods.
SOURCE
web URL:
http://www.bmsc.washington.edu/raster3d/raster3d.html
contact:
Ethan A Merritt
University of Washington, Seattle WA 98195
merritt@u.washington.edu
SEE ALSO
render(l), ribbon(l), balls(l)
AUTHORS
Ethan A Merritt
Raster3D 8 May 1999 RODS(1)