[PyMOL] FW: [ccp4bb]: Announcing PerlMol

[Warren D. <wa...@de...>]

; )
-----Original Message-----
From: own...@dl... [mailto:own...@dl...] On Behalf Of Perl
Mol
Sent: Wednesday, March 31, 2004 10:16 PM
To: cc...@dl...
Subject: [ccp4bb]: Announcing PerlMol

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Announcing PerlMol!

PerlMol, written in 100% pure Perl, is a drop-in replacement for all of your
structure solution/modeling/dynamics/presentation needs. Based on an
open-source core, PerlMol is completely scriptable in the official "Greatest
Programming Language in the World": Perl.

Take a look at these features:

FLEXIBLE! Because PerlMol is written entirely in Perl, it is easy to use and
automate. Just look at this simple script written exclusively in the Perl
language:

@P=split//,".URRUU\c8R";@d=split//,"\nrekcah xinU / lreP rehtona tsuJ";sub
p{
@p{"r$p","u$p"}=(P,P);pipe"r$p","u$p";++$p;($q*=2)+=$f=!fork;map{$P=$P[$f^or
d
($p{$_})&6];$p{$_}=/
^$P/ix?$P:close$_}keys%p}p;p;p;p;p;map{$p{$_}=~/^[P.]/&&
close$_}%p;wait until$?;map{/^r/&&<$_>}%p;$_=$d[$q];sleep
rand(2)if/\S/;print

Imagine harnessing the flexibility of this awesome language for your
structure solving needs, generating reusable and extensible code that you
can share with your colleagues.

Because of its Perl guts, the PerlMol motto is "There's More Than One Way To
Solve Your Structure."

TEXTUAL! Because Perl is the language of PerlMol, PerlMol output is purely
text based. For example, check out this representation of the amino acid
alanine (generated straight from a PDB file):

                       O(-)
                (+)H   |
                  HN-C-C=O
                   H \
                     HCH
                      H

It even got the charges right and correctly calculated the positions of the
hydrogens! No longer do you have to wait for memory wasting bitmaps to load
onto your computer screen or worry about your attachments getting bounced
because they overfill your colleagues' mail boxes. These platform
independent textual representations can load onto any computer with just
about any email client you can find and they don't take much space at all!

FAST! PerlMol is fast because it uses the patented "Mobius Looping
Architecture" developed through a major collaborative effort during the
early 1960's at Xerox PARC and Los Alamos National Laboratories. Check out
these comparisons:


         25K K Simulated    150 Cycles CGE    Rotational    Translational
            Anneeling        Minimization     MR Search        Search
PerlMol      < 1 s               < 1 s          < 1 s          < 1 s
CNS          240 min             384 s          431 min         35 min
CCP4         281 min             460 s          396 min         41 min


POWERFUL! Tired of poor diffraction slowing your important scientific
research? PerlMol's automated solution process uses new "Bayesian Spaghetti
Threading" (BST) to solve structures faster than ever before possible with a
minimum of diffraction quality. In a recent demonstration, PerlMol solved
the structure of human telomerase to 1.8 Angstroms using just three
reflections! Moreover, it did this over only 122 CPU cycles, taking a
fraction of a microsecond (1.4 GHz dual Opteron running Windows 98).

VERSATILE! Its no secret that Perl has the most powerful regular expression
engine in existence. Look how easy it is to make a poly-ala search model for
molecular replacement: "s/./A/g". Plug that baby into the PerlMol molecular
replacement engine! Tired of living in the RNA world? Working with DNA was
never so easy. Just replace those silly U's: "s/U/T/g". No problem. But
PerlMol doesn't stop at mere mutagenesis. Regular expressions were created
to search for complex sequences of characters in mass amounts of data. 
Harnessing the power of regular expressions, PerlMol will eventually replace
BLAST as the de facto standard in sequence mining.

FREE! Because its open source, PerlMol is absolutely free except for a
nominal yearly licensing "contribution". You can download PerlMol at
www.perlmol.com/downloads/ after you complete the appropriate forms at
www.perlmol.com/license/ and send three copies of your passport to the
address at www.perlmol.com/contact-info/ (please include a valid credit card
number, present address, personal photo, and mother's maiden name to avoid
unnecessary delays in processing your license request).

DEMO! Want to get an idea of PerlMol's powerful scripting features? Great,
because Perl is distributed with nearly every modern operating system. Just
open a terminal and start typing your commands into a new perl script file. 
No need to download anything. Use "man perl" for more info.

TESTIMONIALS! Geraldo "8-trac" Keldwet at the famous Ugala Software Foundry
(USF) in Ugala, Switzerland says this: "im compelled to admit that perlmol
has opened my eyes to the power of perl. from now on, your going to see [usf
software] written entirely in this amazing language." Even vocal Python
advocate Wally Delgado agrees: "PerlMol will revolutionize structural
biology as we know it."

Get PerlMol Now!

-TMTOWTSYS

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