Hi Charlie,
This may not be what you want, but this perl script seemed to work just now on
1g9e.pdb
$base='1g9e';open(IN,$base.pdb);@indata = IN;$i=0;
foreach $line(@indata) {
if($line =~ /^MODEL/) {++$i;$file=${base}_$i.pdb;open(OUT,$file);next}
if($line =~ /^ENDMDL/) {next}
if($line =~
Does anyone know if it is possible to transform the continuous (compacted) pdf
format ino the older version where each atom occupies a single line (and vice
versa).
Rex Palmer
Birkbeck College
Dear Rex,
could you give us an example of a non-old version of the PDB format?
In all PDB files I have seen, each atom occupied its own line, and I am not
aware of any recent changes of the PDB.
Cheers, Tim
On Tue, Dec 14, 2010 at 11:34:11AM +, REX PALMER wrote:
Does anyone know if it is
Rex, as Tim says, the PDB format has always been 1 atom per line. But
which program are you using to display the PDB file? Some MS-Win
programs (Notepad is one that springs to mind) don't recognise
Unix-style line-breaks (i.e. newline char) and display the file as one
continuous string. If
Why, by the way, is the default text editor in windows, notepad, such
a lousy text editor? (Sounds like a riddle, I guess, but is really a
question...)
JPK
On Tue, Dec 14, 2010 at 6:02 AM, Ian Tickle ianj...@gmail.com wrote:
Rex, as Tim says, the PDB format has always been 1 atom per line.
It trains you to only use files created by MS Windows and complain if
you get files that use another standard. As usual, follow the money...
On Tue, Dec 14, 2010 at 14:45, Jacob Keller
j-kell...@fsm.northwestern.edu wrote:
Why, by the way, is the default text editor in windows, notepad, such
a
On Tue, 2010-12-14 at 08:02 +0100, Charles W. Carter, Jr wrote:
I've run aground trying to find a program to write out individual pdb files
from a long file with multiple (100) models. My file does not contain
separate chain IDs, so I cannot use moleman2 or splitpdb.p. I want to retain
I use NoteTabLight, which seems to work pretty well.
JPK
On Tue, Dec 14, 2010 at 11:05 AM, Kelly Daughtry kddau...@bu.edu wrote:
Notepad++ is a free windows text editor that recognizes the line breaks, and
does a multitude of other functions.
http://notepad-plus-plus.org/
Best,
Kelly
does cmakereference v0.2 in ccp4 6.1.13 require 'project', 'dataset'
or 'crystal' to be in the .mtz? because i thought by default, these
were eponymous
e.g my .mtz - that has labels F and sigF - :
* Dataset ID, project/crystal/dataset names, cell dimensions, wavelength:
1 project
Postdoctoral Position: Membrane Protein Structural Genomics
A postdoctoral position is available immediately (!) in the laboratory of
Michael Wiener, University of Virginia. His lab is one of three that comprise
the Membrane Protein Structural Biology Consortium (MPSBC, http://mpsbc.org,
one
Postdoctoral Position: Structural Biology of Bacterial Active Transport
A postdoctoral position is available immediately (!) in the laboratory of
Michael Wiener, University of Virginia. The laboratory has a long-running
program in structural and functional studies of TonB-dependent outer
On Tuesday, December 14, 2010 09:05:04 am Kelly Daughtry wrote:
Notepad++ is a free windows text editor that recognizes the line breaks, and
does a multitude of other functions.
http://notepad-plus-plus.org/
It's not relevant to editing PDB files, but be warned that
neither notepad nor
Hi all,
I can easily convert my composite omit map from cns to ccp4 format and
open it into coot.
However, how can I make coot use this map to fit density to my structure ?
I can only use this map for visual support and for example, coot doesn't
assign any density on the bar graph generated
Dear All
An opening is available in the laboratory of Dr. Stephen Fesik
(http://www.mc.vanderbilt.edu/root/vumc.php?site=fesiklab) for a research
associate. The position requires a B.S. or M.S. degree in biochemistry or a
related field with 1-2 years of experience in a research laboratory
You should have also gotten the .coeff file - try converting it to mtz
and using with coot.
On Tue, 2010-12-14 at 14:01 -0600, Julian Nomme wrote:
Hi all,
I can easily convert my composite omit map from cns to ccp4 format and
open it into coot.
However, how can I make coot use this map to
Well it's not as impressive as some solutions posted, but three lines of awk
will
do the job too. Search for END or ENDMDL as you wish.
BEGIN {file = 0; filename = charlie_ file .pdb}
/ENDMDL/ {getline; file ++; filename = charlie_ file .pdb}
{print $0 filename}
Call this script charlie.awk
On 08:02 Tue 14 Dec , Charles W. Carter, Jr wrote:
I've run aground trying to find a program to write out individual pdb
files from a long file with multiple (100) models. My file does not
contain separate chain IDs, so I cannot use moleman2 or splitpdb.p. I
want to retain information
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