Uppsala Software Factory - The APRIL Scam

APRIL is probably the best program I've never written. This page contains an account of its short history.


What was this all about ?

It all started when the following message was sent to the CCP4 and O-INFO bulletin boards, in the afternoon (Swedish time) of April 1, 1998.


Dear protein crystallographer !

The Uppsala Software Factory is proud to announce the
release of a new program, called APRIL.  APRIL stands
for "Ab-initio Phasing using Rotationally Induced
Likelihood".  The program can be used to solve the
phase problem in cases where you have two or more
non-isomorphous crystal forms of the same (or related,
e.g. mutants, complexes) compound.

The program exploits the inherent geometric redundancies
(Bricogne, 1974) to extract phase information, after
first solving the self-rotation (in case any of your
crystal forms contain NCS) and cross-rotation functions.
Trial phases are optimised using a maximum likelihood-based
objective function.

Initial tests (using different lysozymes) have
given excellent results, confirming previous
models for the structure of this protein.

Now, I would like to invite you to become a
beta-testing site in order to help optimise
and debug the software.

Executables of APRIL (release 1) are available for
SGI, OSF1, HP-UX, Solaris, Linux, and ZX-81. The
program is CCP4-compatible.  It requires at least two
MTZ files as input (one for each crystal form),
and some control information (e.g., number
of molecules per asymmetric unit for each crystal
form, resolution limits, etc.).

For more information about the program and
downloading instructions, please point your
browser to:

  http://xray.bmc.uu.se/usf/april.html

or to:

  http://xray.bmc.uu.se/usf/april.html

The beta version of APRIL will only be available
today so as to limit the number of bonafide
beta testers to a manageable number.

Happy phasing !

--Gerard Kleywegt
  CEO, Uppsala Software Factory
  ("21st century software with a 19th century interface,
    but, hey, it's free !")

Those who threw their web-browser at one of these URLs ended up here...


(Almost) true believers

Several people (almost) swallowed the story about APRIL. Some reactions:

One of the quickest to react was Eleanor:

----------------------------------

From:   SMTP%"o-info@kaktus.imsb.au.dk"
Subj:   Re: Phase problem solved !!!
From:   Eleanor Dodson 

That sounds pretty amazing.. Do you want more test data? Much more likely that
you will run it than me. But we have the PenV data; tetramer in P61; dimer in
C2 - some exptl phasing actaully but you neednt use that..
Congratulations Eleanor

-- 
------------------------------------------------------------------
Eleanor J.Dodson, Chemistry Department, University of York, U.K.
Tel: Home +44 (1904) 42 44 49, work:  +44 (1904) 43 25 65
------------------------------------------------------------------

Felix Frolow wrote what several other people probably thought:

----------------------------------

From:   SMTP%"cvfrolow@wicc.weizmann.ac.il"
Subj:   I am not an April Fool....
From:   Felix Frolow 

But it sounds so reasonable.......
-- 
_______________________________________
|                                     | 
| Dr.  Felix Frolow                   |
| Dept. of Chemical Services          |
| The Weizmann Institute of Science   |
| Rehovot, 76100   ISRAEL             |
| e-mail cvfrolow@wicc.weizmann.ac.il |
| FAX  (972)89-344136                 |
| Tel. (972)89-343580                 |
---------------------------------------

----------------------------------

From:   SMTP%"perozzo@harker.nrl.navy.mil"
Subj:   shortsheeting the internet
From:   Mary Ann Perozzo 

you really got me on that one!!!

----------------------------------

From:   SMTP%"matthewg@spitfire.biop.ox.ac.uk"
Subj:   (no subject)
From:   Matthew Groves 

To: The CEO, Uppsala Software Factory,

Hope you're not going to publish the list of people who accessed 
this page:)

---------------------------------------------------------------------

Matthew Groves                  Tel: 01865-275374
matthewg@biop.ox.ac.uk          http://www.bioch.ox.ac.uk/~mrg/ 

---------------------------------------------------------------------

----------------------------------

From:   SMTP%"kmi@calvin.niams.nih.gov"
Subj:   Another irate customer
From:   "Konstantin A. Miroshnikov" 

Yes, but I spent less time accessing your site then you spent putting it
together.  Great joke.   Adam Zlotnick

----------------------------------

From:   SMTP%"carter@pasteur.med.unc.edu"
Subj:   soopah
From:   "Charles W. Carter" 

CD,

I love it! I was totally taken in and it took the ensuing
junk email from the BB to clue me in. 

You're unequalled. Carry ON, Flying Dutchman!

Charles

----------------------------------

From:   SMTP%"bart@sherlock.mmid.ualberta.ca"
Subj:   Almost got me
From:   Bart Hazes 

Hi Gerard,

That was a good one. I had already forwarded your message to Randy and
felt excitement rushing in when I came across the ZX-81 executable. I
started "life" with Sinclairs machines and was amazed by their power, even
more so now than then, still 16 Kb of Ram is limitting for the kind of
work we do.

Have a good laugh today,  Bart

Of course, there was the odd cynic:

----------------------------------

From:   SMTP%"br@llnl.gov"
Subj:   APRIL
From:   Bernhard Rupp 

Dear Sir :

I am sincerely interested in a list of beta-testers for this 
program....

:) BR
-----------------------------------------------------------------
Carpe diem !
-----------------------------------------------------------------
Dr. Bernhard Rupp
Macromolecular Crystallography               Phone (925) 423-3273
LLNL-BBRP L452                              Phax  (925) 422-2282
POB 808                                      Emerg (800) 313-2310
Really urgent matters only                   Cell  (510) 410-5865
Livermore, CA 94551                          email    br@llnl.gov
URL                                 http://www-structure.llnl.gov
Private email/URL                       http://www.vienna-air.com
-----------------------------------------------------------------

----------------------------------

From:   SMTP%"subbu@xray.umdnj.edu"
Subj:   Re: Phase problem solved !!!
From:   Narayanan Ramasubbu 

OOPS!!
Got me!
subbu


Portability issues

Other people came up with further suggestions for ports to other machines than those mentioned in the original announcement:

----------------------------------

From:   SMTP%"rlc@crchul.ulaval.ca"
Subj:   Re: Phase problem solved !!!
From:   Robert Campbell 

Dear Gerard,

On Apr 1 you wrote:
> The Uppsala Software Factory is proud to announce the
> release of a new program, called APRIL.  APRIL stands

I enjoyed that!

> Initial tests (using different lysozymes) have
> given excellent results, confirming previous
> models for the structure of this protein.

Amazing how that could happen!

> Now, I would like to invite you to become a
> beta-testing site in order to help optimise
> and debug the software.

Oh.  No thanks.

> Executables of APRIL (release 1) are available for
> SGI, OSF1, HP-UX, Solaris, Linux, and ZX-81. The

Is there a parallel version to run on our array of 371 ZX-81's? It might
be solvable by the end of the next century then?  How about an Amiga
version or a version for the TRS-80?  That could really increase your use
base!

> program is CCP4-compatible.  It requires at least two
> MTZ files as input (one for each crystal form),
> and some control information (e.g., number
> of molecules per asymmetric unit for each crystal
> form, resolution limits, etc.).

Oh, and don't forget the complete coordinate information.
 
> For more information about the program and
> downloading instructions, please point your
> browser to:
> 
>   http://xray.bmc.uu.se/usf/april.html
> 
> or to:
> 
>   http://xray.bmc.uu.se/usf/april.html
> 
> The beta version of APRIL will only be available
> today so as to limit the number of bonafide
> beta testers to a manageable number.

I'm sure many of us are interested to know how many bonafide
beta testers volunteer!
 
Cheers,
Robert
-- 
Robert Campbell                 http://asterix.crchul.ulaval.ca/~rlc/
Lab. d'Endocrinologie Moleculaire,               rlc@crchul.ulaval.ca
Centre de recherche du CHUL,                     (418) 656-4141 x6348
Univ. Laval, Sainte-Foy, Quebec,   CANADA               FAX: 654-2761

Always eager to please my users:

----------------------------------

From:   XRAY::GERARD       "Gerard 'CD' Kleywegt"
Subj:   Re: Phase problem solved !!!

i have a version for the ZX-Spectrum, Atari 400, and Apple I
and am working on an assembler version for the PDP8
TRS-80 and BBC-1 are on my list of things to do ! honest !
i wasn't aware of the massively parallel ZX-81 monster
but i'll try to contact Sir Clive Sinclair to see if
i can get one on loan !

of course you don't have to input the coordinates;
but you do have to give your e-mail address
(APRIL needs this when it AutoDeps the final
model it builds and refines !)

----------------------------------

From:   SMTP%"rlc@crchul.ulaval.ca"
Subj:   Re: Phase problem solved !!!
From:   Robert Campbell 

On Apr 1 you wrote:
> i have a version for the ZX-Spectrum, Atari 400, and Apple I
> and am working on an assembler version for the PDP8
> TRS-80 and BBC-1 are on my list of things to do ! honest !

Hey great.  I can plug in my Apple I book end!

> i wasn't aware of the massively parallel ZX-81 monster
> but i'll try to contact Sir Clive Sinclair to see if
> i can get one on loan !

Oh no, this is our proprietary design.  I'll probably be
fired for revealing it to you!

> of course you don't have to input the coordinates;
> but you do have to give your e-mail address
> (APRIL needs this when it AutoDeps the final
> model it builds and refines !)

Wow, an updated version of APRIL already!  You hadn't
mentioned that in the original press release.

Cheers,
Robert
-- 
Robert Campbell                 http://asterix.crchul.ulaval.ca/~rlc/
Lab. d'Endocrinologie Moleculaire,               rlc@crchul.ulaval.ca
Centre de recherche du CHUL,                     (418) 656-4141 x6348
Univ. Laval, Sainte-Foy, Quebec,   CANADA               FAX: 654-2761

----------------------------------

From:   SMTP%"A.W.Ashton@dl.ac.uk"
Subj:   Re: Phase problem solved !!!
From:   Alun Ashton 

> 
> Executables of APRIL (release 1) are available for
> SGI, OSF1, HP-UX, Solaris, Linux, and ZX-81. The
> program is CCP4-compatible.  It requires at least two

Look Gerard, porting CCP4 to linux is difficult enough dont start giving
people ideas that its ZX81 compatible as well! Just for the record I went
to the web page just to see how you told people it was a joke and not
because I beleived you - honest.

Its good to see though that you recordnise the need to port to linux!

Alun
____________________________________________________  
Alun Ashton,  awa@dl.ac.uk      Tel: +44 1925 603528
CCP4,         ccp4@dl.ac.uk     Fax: +44 1925 603124
              http://www.dl.ac.uk/CCP/CCP4/main.html
Daresbury Laboratory, Daresbury, Warrington, WA4 4AD

----------------------------------

From:   SMTP%"o-info@kaktus.imsb.au.dk"
Subj:   Re: Phase problem solved !!!
From:   Scott Ware 

On Wed, 1 Apr 1998, Gerard 'CD' Kleywegt wrote:

> Executables of APRIL (release 1) are available for
> SGI, OSF1, HP-UX, Solaris, Linux, and ZX-81. 

I have been having some difficulties with the installation of the ZX81
version of APRIL.  Transferring the program files to cassette tape (using
the included "tapescreech" utiltity) seems to work properly;  however, any
attempts to run the program fail, returning only the "0/0" error message
and the "K" cursor.  Does anyone have any suggestions?  I've already
fastened the memory expansion module to the computer with a sufficient
quantity of duct tape, so RAM pack wobble shouldn't be an issue. 

Failing that, are there any plans for an RT-11 port any time in the near
future?  We've got quite a few users who are anxious to try APRIL, so it
seems like a waste to leave the PDP-11 idle while the ZX81 does all of the
work. 

Thanks in advance!

-- 
Scott Ware            NUMS-MPBC ZX81 BASIC Systems Administrator
    "With sufficient thrust, pigs fly just fine." - RFC 1925

----------------------------------

From:   XRAY::GERARD       "Gerard 'CD' Kleywegt"
Subj:   Re: Phase problem solved !!!

>however, any
>attempts to run the program fail, returning only the "0/0" error message
>and the "K" cursor.  Does anyone have any suggestions?

Scott: are you using one of those glue-on extended
keyboards ? Maybe there is a key with an attitude
problem ?  Try some superglue !

>so RAM pack wobble shouldn't be an issue

correct, but in fact you shouldn't need the 16K
expansion pack for APRIL.  The code is *very*
compactly written !

MORE APRIL NEWS:

- more requests for ports have come in, including
  the Palm Pilot, Psion, and Univac.  Since its
  userbase appears to be small, I have postponed
  a port to HAL until the year 2001

- someone insinuated that a full set of refined
  coordinates was part of APRIL's input.  This
  is NOT TRUE !  Fellow Americans, I told you
  once, and I'll say it again !  I am mystified
  and disappointed !  In fact, the only input
  item for which no sensible default value exists
  is the user's E-mail address (this is needed
  when the program AutoDeps the final model
  it has built and refined at Brookhaven; NOTE:
  this feature is only available in release
  1.4142136 !)

Keep those suggestions for improvements coming !

--Gerard

----------------------------------

From:   SMTP%"A.W.Ashton@dl.ac.uk"
Subj:   Re: Phase problem solved !!!
From:   Alun Ashton 

> 
> - more requests for ports have come in, including
>   the Palm Pilot, Psion, and Univac.  Since its
>   userbase appears to be small, I have postponed
>   a port to HAL until the year 2001

That reminds me is it year 2000 compliant?

Alun
____________________________________________________  
Alun Ashton,  awa@dl.ac.uk      Tel: +44 1925 603528
CCP4,         ccp4@dl.ac.uk     Fax: +44 1925 603124
              http://www.dl.ac.uk/CCP/CCP4/main.html
Daresbury Laboratory, Daresbury, Warrington, WA4 4AD

----------------------------------

From:   SMTP%"A.W.Ashton@dl.ac.uk"
Subj:   Re: Phase problem solved !!!
From:   Alun Ashton 

On Wed, 1 Apr 1998, Gerard 'CD' Kleywegt wrote:

> ha - i have had requests for ports for TRS-80 and Amigas !
> ;-)
> --gerard

is there a port for a psion? 

Alun
____________________________________________________  
Alun Ashton,  awa@dl.ac.uk      Tel: +44 1925 603528
CCP4,         ccp4@dl.ac.uk     Fax: +44 1925 603124
              http://www.dl.ac.uk/CCP/CCP4/main.html
Daresbury Laboratory, Daresbury, Warrington, WA4 4AD

----------------------------------

From:   SMTP%"j.murray-rust@mail.cryst.bbk.ac.uk"
Subj:   RE: Phase problem solved !!!
From:   Judith Murray-Rust 

On Wed, 1 Apr 1998, Gerard 'CD' Kleywegt wrote:

> >Thanks Gerard!
> you're welcome - it's all in a day's work
> 
> 
> people have started asking for other versions
> of APRIL as well; I am working on Atari 400,
> Apple I and PDP-8 (assembly code) versions,
> and requests have come in for Amiga and TRS-80.
> While I'm at it: anyone still using BBC-1s ?
> 

Nah, but how about one for the Palm-Pilot?

      * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
Judith Murray-Rust              http://www.cryst.bbk.ac.uk/~ubcg09j/home.html
Crystallography Department      FAX 0171 631 6803
Birkbeck College                ubcg09j@mail.cryst.bbk.ac.uk
LONDON WC1E 7HX.                

----------------------------------

From:   SMTP%"vogan@auriga.rose.brandeis.edu"
Subj:   RE: Phase problem solved !!!
From:   erik vogan 

how about a version for the US robotics palm pilot ?  solve a structure
over lunch ?

                                                        erik vogan

~ Of all the races in all of the Galaxy who could have come and said a big
hello to the planet Earth, he thought, didn't it just have to be the Vogons.
                                                        - HHGttG

homepage: http://www.rose.brandeis.edu/users/vogan

----------------------------------

From:   XRAY::GERARD       "Gerard 'CD' Kleywegt"
Subj:   RE: Phase problem solved !!!

or maybe i should hardcode it onto a chip
so you can plug it into your tv, microwave,
toaster, razor, or whatever ?
--gerard

----------------------------------

From:   SMTP%"schuller@uci.edu"
Subj:   Re: Phase problem solved !!!
From:   "David J. Schuller" 

> Executables of APRIL (release 1) are available for
> SGI, OSF1, HP-UX, Solaris, Linux, and ZX-81.

so many acronyms!  do you have a version compatible with the BMW Z3?  I
have been looking for a way to justify a sole-source acquisition off our
grant.

=======================================================================
"I never let myself get too cocky,
 there are too many dead nuns in my head."     -  Anne Meara
=======================================================================
                        Dave Schuller
                        modern man in a post-modern world
                        University of California-Irvine
                        schuller@uci.edu

----------------------------------

From:   SMTP%"jscarsda@hsc.vcu.edu"
Subj:   april port to massively parallel system
From:   "J.N. Scarsdale (Machine check while in kernal mode)" 

----------------------------------

From:   XRAY::GERARD       "Gerard 'CD' Kleywegt"
Subj:   RE: april port to massively parallel system

good idea - but why the abaci ?
you mean they can count further than 10
(or twenty if you include toes) ???
fascinating !
--gerard

----------------------------------

From:   SMTP%"o-info@kaktus.imsb.au.dk"
Subj:   RE: Phase problem solved !!!
From:   Mike Clark 

On Wed 01 Apr, Gerard 'CD' Kleywegt wrote:
[snip]
> While I'm at it: anyone still using BBC-1s ?
> 
> --gerard
> 
Unfortunately I no longer have my old BBC model B or BBC Master 512 having
given them away to local schools. However I have some Acorn A series
machines (A3000, A420, A5000) and some Acorn RiscPCs so it might be
possible to run the code under emmulation. 

Mike Clark,                        
-- 
  o/ \\    //        |\   ,_ o      Mike Clark
 <\__,\\  //   __o   | \ /  /\,   "A mountain climbing, cycling, skiing,
  ">    ||   _`\<,_  |__\  \> |  immunology lecturer, antibody engineer and
   `    ||  (_)/ (_) |   \corn computer user"

----------------------------------


The scam debunked !

In the end, it was Eric Fauman who blew the whistle.

But first So Iwata reported a tremendous success of the program:

----------------------------------

From:   SMTP%"o-info@kaktus.imsb.au.dk"
Subj:   RE: Phase problem solved !!!
From:   IWATA@xray.bmc.uu.se

It's just amazing. Using the program APRIL, we have been already solved 
the structure of a protein complex (MW480kDa) using just two defferent 
crystal forms (three independent mols/assym). And we are going to submit 
the paper today! If you don't believe that, look, Janos and Rams are 
checking the manuscript now (only for Uppsala people).

Thanks Gerard!

So 

I had to explain the hardware situation in Uppsala to outsiders:

----------------------------------

From:   XRAY::GERARD       "Gerard 'CD' Kleywegt"
Subj:   RE: Phase problem solved !!!

>Thanks Gerard!
you're welcome - it's all in a day's work

for the non-Uppsala people: So solved his structure
on a single-processor ZX-81
I just learned that there is a 379-processor
massively parallel ZX-81 on the market
as well - this would reduce the turn-around
time for an APRIL job to about 5 seconds
(or was that decades ?)

people have started asking for other versions
of APRIL as well; I am working on Atari 400,
Apple I and PDP-8 (assembly code) versions,
and requests have come in for Amiga and TRS-80.
While I'm at it: anyone still using BBC-1s ?

--gerard

The first dark cloud on the horizon was the following mail:

----------------------------------

From:   SMTP%"paehler@atlas.rc.m-kagaku.co.jp"
Subj:   Re:  Phase problem solved !!!
From:   Arno PAHLER 

Too little, too late - Microsoft yesterday announced in a secret press
release that April-98, successor to the vastly successful April-97,
will not only come with a user-definable choice of phases (acentric
phases as an upgrade option), but also with a complimentary version of
Microsoft Speechless'00(*), the voice version of the well-known standard
product, that, in the parallelized version, can generate simultaneous
outputs for Cell, JMB, Nature, PNAS and Science plus a tape for Gordon
conferences - rumors that Linus Torvalds was hired as CEO, to push
this promising product to market, have however been vehemently denied.

(*) The Y2K bug-fix version will be released as soon as possible,
    no later than April 1, 2099.

Arno Paehler
Unauthorized Spokesperson for Megaschrott Enterprises

----------------------------------

From:   XRAY::GERARD       "Gerard 'CD' Kleywegt"
Subj:   Re:  Phase problem solved !!!

hahaha
i mean: damn ! does this mean they're not interested
in acquiring the Uppsala Software Factory for a
modest sum (plus 100,000,000 MS stock options) ?

there goes my plan for early retirement !

i guess i'll have write yet another brilliant
program then ... hmm, perhaps i can solve
the protein folding problem (would make April-98
obsolete instantly !) - give me 365 days, okay ?

--gerard

But with Fauman's first mail the excrement started to move in the direction of the rapidly rotating air transportation device:

----------------------------------

From:   SMTP%"fauman@biop.umich.edu"
Subj:   APRIL (release 1)
From:   Eric Fauman 

Gerard,
 
    I tried your beta-test version of APRIL (release 1)
on one of my structures.  It gave beautiful phasing statistics,
but when I looked at the maps, they were of lysozyme, not
my protein!  So while it looks like you have solved the
phase problem for lysozyme, I think the solution to the general 
phase problem remains elusive.
 
Good luck!
-Eric

I tried to control the damage by blaming the user:

----------------------------------

From:   XRAY::GERARD       "Gerard 'CD' Kleywegt"
Subj:   RE: APRIL (release 1)

that's probably due to a bug which makes that all
phase arrays are initialised with the lysozyme values
are you sure you crystallised the correct protein, by the way ???
if so, could you send me a copy of the output ?
--gerard

But to no avail ...

----------------------------------

From:   SMTP%"fauman@biop.umich.edu"
Subj:   RE: APRIL (release 1)
From:   Eric Fauman 

After getting your email, I double checked that I had the correct 
protein crystallized by running SDS-PAGE, CD, Mass Spec and activity
assays on the crystals, and all confirmed that I had my 401 amino
acid fragment of a gag-binding protein.

I'm not sure I gathered all the output from the program.  Here's
what I could find.  Hope it helps!
-Eric


 *** APRIL *** APRIL *** APRIL *** APRIL *** APRIL *** APRIL *** 

 Version  - 980401/1.0
 (C) 1998 Gerard J. Kleywegt

 Started  - Wed Apr 1 12:00:00 1998
 User     - fauman
 Mode     - batch
 Host     - zoe
 ProcID   - 26041
 Tty      - /dev/ttyq1

APRIL>

CELL 79.259 79.259 37.914 90.0 90.0 90.0
RESOLUTION OVERALL 200.0 1.50
SYMMETRY P43212

   symmetry=( x,     y,     z)
   symmetry=(-x,    -y,     z+1/2)
   symmetry=(-y+1/2, x+1/2, z+3/4)
   symmetry=( y+1/2,-x+1/2, z+1/4)
   symmetry=(-x+1/2, y+1/2,-z+3/4)
   symmetry=( x+1/2,-y+1/2,-z+1/4)
   symmetry=( y    , x    ,-z    )
   symmetry=(-y    ,-x    ,-z+1/2)


*******************************************************************
 list Harker Vectors for top 10 sites from cross scan
 less than ten sites are found the program will reset
  the upper limit to use all sites found
*******************************************************************

     >> mode = HARKER
     >>   0.4062  1.0000  0.1641       (solution   1)
     >>   0.1562  1.0000  0.1641       (solution  13)
     >>   0.2969  0.3839  0.1094       (solution  25)
     >>   0.2500  0.7500  0.0859       (solution  29)
     >>   0.1094  1.0000  0.0000       (solution  33)
     >>   0.3906  0.4911  0.0547       (solution  45)
     >>   0.8906  0.0000  0.0547       (solution  61)
     >>   0.7500  0.2500  0.0000       (solution  69)
     >>   0.8906  0.5000  0.1094       (solution  79)
     >>   0.6719  0.4911  0.0781       (solution  91)
     >> HARKER LIST >>

SOLUTION FOUND!!!

 #####  #######    #    #######   ###    #####  #######   ###    #####   #####
#     #    #      # #      #       #    #     #    #       #    #     # #     #
#          #     #   #     #       #    #          #       #    #       #
 #####     #    #     #    #       #     #####     #       #    #        #####
      #    #    #######    #       #          #    #       #    #             #
#     #    #    #     #    #       #    #     #    #       #    #     # #     #
 #####     #    #     #    #      ###    #####     #      ###    #####   #####


 $$ <4SSQ/LL>
 Resolution(Angstroms)
 Number_acentric_reflections
 Isomorphous_difference_acentric
 Lack_of_closure_acentric
 Phasing_power_acentric
 Cullis_R_acentric(?<1.0)
 Number_centric_reflections
 Isomorphous_difference_centric
 Lack_of_closure_centric
 Phasing_power_centric
 Cullis_R_centric(?<1.0) $$
 <4SSQ/LL>  Resol   Nref_a DISO_a LOC_a PhP_a CullR_a Nref_c DISO_c LOC_cPhP_c CullR_c
 $$
   0.020     7.06     157   76.1   25.1 5.53   0.33      70   98.2   30.6 4.50 0.31
   0.047     4.62     551   76.4   35.4 3.46   0.46     153   88.1   40.2 2.84 0.46
   0.085     3.43    1145   74.6   46.7 2.17   0.63     241   91.3   50.1 1.81 0.55
   0.134     2.73    2033   63.8   40.8 1.97   0.64     339   73.9   45.8 1.68 0.62
   0.195     2.26    3070   48.0   31.6 1.95   0.66     389   59.8   36.6 1.60 0.61
   0.267     1.94    4075   39.6   28.7 1.58   0.73     416   49.6   32.4 1.25 0.65
   0.350     1.69    5481   28.0   19.0 1.73   0.68     444   32.4   22.9 1.27 0.71
   0.444     1.50    6149   16.7   12.4 1.81   0.74     461   19.4   14.5 1.33 0.75
  $$ 
   TOTAL            22661   36.8   24.5 1.91   0.67    2513   53.6   32.0 1.70 0.60

Overall FOM: CENTRIC 0.81481 NON-CENTRIC 0.90028 TOTAL 0.89025

DERIVED PHASES:

Reflection list:
 NREFlection=     19612
     12    0    0  45883.700  180.000
     14    0    0  12532.700  180.000
     16    0    0  68340.400  180.000
     18    0    0  71638.600  180.000
     20    0    0  50335.100    0.000
     22    0    0   3737.000  180.000
     24    0    0  34044.800  180.000
...Abbreviated...
     26    1   22   1132.000  249.543
     22   14   22   1258.700  303.518
     20    9   23    963.700  348.835
     19   11   23    864.000  131.353
     16   15   23   1425.200  163.532


Cycle   SFALL   RSTATS          FFT     
 Nr     RelInd  Rover   CCover  Sigma   
=====   ======  ======  ======  ======  
1       0.6699  0.594   0.508   3.07438

Cycle   SFALL   RSTATS          FFT    
 Nr     RelInd  Rover   CCover  Sigma  
=====   ======  ======  ======  ====== 
25      0.4037  0.366   0.852   2.71815


 *** APRIL *** APRIL *** APRIL *** APRIL *** APRIL *** APRIL *** 

 Version - 980113/5.4
 Started - Wed Apr 1 12:00:00 1998
 Stopped - Wed Apr 1 12:18:23 1998

 CPU-time taken :
 User    -    401.0 Sys    -    401.0 Total   -    401.0

 *** APRIL *** APRIL *** APRIL *** APRIL *** APRIL *** APRIL *** 

 >>>>>> This program: (C) 1998, GJ Kleywegt <<<<<<
 >>>>>>> E-mail: gerard@xray.bmc.uu.se  <<<<<<<<<<
 *** APRIL *** APRIL *** APRIL *** APRIL *** APRIL *** APRIL *** 

STOP ... Toodle pip ... statement executed

This is when I gave up.

----------------------------------

From:   XRAY::GERARD       "Gerard 'CD' Kleywegt"
Subj:   RE: APRIL (release 1)

hmm, very strange - it all looks okay to me
on the bright side: it took only 401 cpu seconds
to arrive at the wrong solution !
compare that to SHARP + SOLOMON + O + XPLOR + O + XPLOR + AUTODEP !!!!!
--gerard

----------------------------------

From:   SMTP%"fauman@biop.umich.edu"
Subj:   April v.1
From:   Eric Fauman 

That's true.  I suppose we could start trying to
solve structures by process of elimination -
first figure out everything the protein is not.
--Eric

----------------------------------

From:   XRAY::GERARD       "Gerard 'CD' Kleywegt"
Subj:   RE: April v.1

i could write a csh script to do that !
--gerard

On April 2, 1998, I decided that a retraction was the ethical thing to do under the circumstances, and the following message was sent to the CCP4 and O-INFO bulletin boards:

----------------------------------

From:   XRAY::GERARD       "Gerard 'CD' Kleywegt"
Subj:   OOPS ... (Was: "Phase problem Solved !!!")

The Uppsala Software factory wishes it to be known
that phase problem has not been solved quite yet.
Eric Fauman detected a bug in the APRIL program
(announced here yesterday), the effect of which
was that, no matter what the input, the result
was always lysozyme phases.  (We have therefore
donated the APRIL source code to Brian Matthews'
lab since they may be interested in further
development of the program.)

For a full account of this story, including dozens
of reactions from fellow crystallographers, AND
the output of APRIL that Fauman presented as proof
of the bug can be found on the web at URL:

http://xray.bmc.uu.se/usf/april_new.html

The Board of Directors of the Uppsala Software
Factory wishes to apologise for any inconvenience
their actions may have caused.  The company's
CEO has been fired and will not be allowed
anywhere near a keyboard in the future.
Over the next 364 days, all our efforts will
go into the development of our new program
that calculates the 3D structure of a protein,
given its amino-acid sequence !

Sincerely,

Sir Clive Sinclair
President and interim CEO
Uppsala Software Factory


Some other reactions

A selection of some of the other reactions:

Many people reminisced over their long-lost ZX-81s (see also above) ...

----------------------------------

From:   SMTP%"dyda@ulti.niddk.nih.gov"
Subj:   ZX-81
From:   Dyda 

Gerard,

you are funny.
Actually I was trying to get the ZX-81 version, this was the first
processor of my life, and I still think the best. Ab-initio phasing
would be just a thrill on it.

                                        Fred

----------------------------------

From:   SMTP%"tdoukov@unlgrad1.unl.edu"
Subj:   April
From:   Tzanko Doukov 

Good one Gerard! Congrats!

----------------------------------

From:   SMTP%"darren@biop.ox.ac.uk"
Subj:   You're slipping

*grin* not bad, but a bit slow . . . everyone in this area of the world has
already had about 30-40 of these thrown at them. I would have though that
00:00:01 GMT would have been the best time to post? ;-)

Anyway, I claim first access, unless your counter is bust. Thanks for the fun.

-Darren

----------------------------------

From:   SMTP%"A.Elwell@udcf.gla.ac.uk"
Subj:   Re: Phase problem solved !!!
From:   "Andrew Elwell" 

damn, Just as I thought i'd found something other than netscape to run on my 
ZX81... (check your weblogs for user_agent at 130.209.221.197.)

:-) 
--
Andrew Elwell    E-Mail: A.Elwell@udcf.gla.ac.uk Mobile: 0966 279286
Division of Biochemistry & Molecular Biology,    Maclay Hall, 18 Park Terrace
IBLS, University of Glasgow, Glasgow, G12 8QQ    Glasgow G3 6BX
Tel: 0141 330 6459, Fax: 0141 330 4620           T:0141 353 5679 F:0141 353 5671
HomePage: http://www.enzyme.gla.ac.uk/~andrew/
--
Thought for the day:
  I don't have a solution but I admire the problem.

----------------------------------

From:   SMTP%"j.murray-rust@mail.cryst.bbk.ac.uk"
Subj:   super-phasingx
From:   Judith Murray-Rust 

Liked it.....
But G, its too late!!! didn't get here till 13.50 ........and all our
structures for today are already solved.

Local UK rules, at least where I grew up, are that the "fool" is only
valid if perpetrated before noon! Other wise something *awful* happens
to the fool-er. You have been warned........
-- 
      * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
Judith Murray-Rust             
http://www.cryst.bbk.ac.uk/~ubcg09j/home.html
Crystallography Department      FAX 0171 631 6803
Birkbeck College                ubcg09j@mail.cryst.bbk.ac.uk
LONDON WC1E 7HX.

----------------------------------

----------------------------------

From:   SMTP%"mowbray@xray.bmc.uu.se"
Subj:   Re: Phase problem solved !!!
From: mowbray@xray.bmc.uu.se (Sherry Mowbray)

I was just telling Aaron that people around here were too busy for April
Fools. Does something awful happen if you go to that web page?

Sherry Mowbray
Swedish Agricultural University

----------------------------------

From:   SMTP%"mowbray@xray.bmc.uu.se"
Subj:
From: mowbray@xray.bmc.uu.se (Sherry Mowbray)

Hi, I decide you wouldn't actually do anything nasty, so I went and looked.
The number said 55. Did that mean my mailer is really slow, or that it took
you 54 loads to get it to blink :-) !
S/

Sherry Mowbray
Swedish Agricultural University

After the following mail hit the O-INFO bulletin board, a colleague (himself German !) remarked "yeah, trust a German to spoil a good joke" ...

----------------------------------

From:   SMTP%"o-info@kaktus.imsb.au.dk"
Subj:   Re: Phase problem solved !!!
From:   Jens Heese 

> Executables of APRIL (release 1) are available for
> SGI, OSF1, HP-UX, Solaris, Linux, and ZX-81. The
> program is CCP4-compatible.  It requires at least two

Since no other 'USF' tools are available as
linux exes one can safely assume this is an
April fools joke.

Cheers

----------------------------------

From:   SMTP%"segelke1@llnl.gov"
Subj:   Re: Phase problem solved !!!
From:   Brent Segelke 

You guys there at Uppsala have a hell of a sense of humor eh?  De Novo
Phasing on April 1st--this could be submitted to the ignoble prize committee.
-----------------------------------------------------------------
-----------------------------------------------------------------
If it crystallizes, it's important!
-----------------------------------------------------------------
-----------------------------------------------------------------
Brent Segelke, Ph.D.                         Phone (510) 424-4752
Lawrence Livermore National Laboratory       Phax  (510) 422-2282
Macromolecular Crystallography               
LLNL-BBRP L452                              
POB 808                                      
Livermore, CA 94551                       email segelke1@llnl.gov
URL             http://www-structure.llnl.gov/cvs/Brent/brent.htm
-----------------------------------------------------------------

----------------------------------

From:   SMTP%"lizp@yorvic.york.ac.uk"
Subj:   Re: Phase problem solved !!!
From:   Liz Potterton 

Gerard,

I was considering putting out alpha test version of CCP4 Interface (at least
gets us into eary 20th C I think) but delayed to more auspicious date.

Thanks for brightening the day.

Liz

----------------------------------

From:   SMTP%"CHARLES.LESBURG@spcorp.com"
Subj:   bravo!
From:   CHARLES.LESBURG@spcorp.com (CHARLES LESBURG)

Gerard,

I'm sure you realize that nobody would have believed it except for the reference
to Gerard Bricogne.  All of the sudden, anything is possible.

I hope everything is going well.

-Chip

---------------------------------------------------

Charles A. Lesburg, Ph.D.
Schering-Plough Research Institute
K-15-B112C/1800                                            TEL: (908) 298-3515
2015 Galloping Hill Road                                   FAX: (908) 298-7545
Kenilworth, NJ  07033                       E-MAIL: Charles.Lesburg@spcorp.com


Gullible's travels

Some of the almost 300 domains from which the APRIL page was accessed:

  1. 128.253.219.20
  2. 129.64.32.147
  3. 129.64.32.202
  4. 130.238.37.251
  5. 130.239.193.185
  6. 130.69.122.64
  7. 130.87.173.49
  8. 131.152.112.39
  9. 133.1.169.231
  10. 133.50.21.56
  11. 134.68.57.17
  12. 140.109.32.202
  13. 146.203.4.30
  14. 150.146.1.8
  15. 160.103.107.8
  16. 160.103.2.152
  17. 200.136.164.44
  18. 202.54.37.18
  19. 203.255.24.128
  20. 207.135.78.97
  21. acara.csb.ki.se
  22. acs1.wustl.edu
  23. adrenaline.berkeley.edu
  24. afmb72.cnrs-mrs.fr
  25. alf1.mrc-lmb.cam.ac.uk
  26. alf2.mrc-lmb.cam.ac.uk
  27. alice.bmc.uu.se
  28. xray.bmc.uu.se
  29. alpha8.bioc.cam.ac.uk
  30. alphy.roca.csic.es
  31. amino.usask.ca
  32. angel.niams.nih.gov
  33. apty.sci.hokudai.ac.jp
  34. asio.molbio.su.se
  35. aztec.chemistry.mcmaster.ca
  36. badbart.wustl.edu
  37. banquo.imb-jena.de
  38. basfegw2.basf-ag.de
  39. batman.depauw.edu
  40. bcl4.biochem.uga.edu
  41. bcl9.biochem.uga.edu
  42. bdvpc1.rug.ac.be
  43. berigw.beri.co.jp
  44. bernal.biochem.ubc.ca
  45. bigfoot.chem.upenn.edu
  46. billmo.biosci.arizona.edu
  47. bio14.chemie.uni-freiburg.de
  48. biocisis.unizh.ch
  49. biomaster.uio.no
  50. blagny.u-strasbg.fr
  51. bluejay.bioc.aecom.yu.edu
  52. bmbsgi15.leeds.ac.uk
  53. bmbsgi17.leeds.ac.uk
  54. boadicea.phys.unsw.edu.au
  55. bolan.bioc.le.ac.uk
  56. bonzai.crchul.ulaval.ca
  57. bossa-nova.cnb.uam.es
  58. bragg.bioz.unibas.ch
  59. bragg.bmb.psu.edu
  60. bragg.chem.cornell.edu
  61. bragg.ifqsc.sc.usp.br
  62. bravais.bri.nrc.ca
  63. bsmir14.biochem.ucl.ac.uk
  64. butthead.embl-hamburg.de
  65. cache1.serveurs-nationaux.jussieu.fr
  66. california.bio.purdue.edu
  67. calliope.swmed.edu
  68. camier.ibs.fr
  69. capri.biop.ox.ac.uk
  70. ccp4e.dl.ac.uk
  71. centris.bmc.uu.se
  72. chaucer.life.uiuc.edu
  73. chem-tdoukov.unl.edu
  74. chem28.colorado.edu
  75. chemac168.ucdavis.edu
  76. chex8.ex.ac.uk
  77. chop.swmed.edu
  78. chpc-jhn-3.st-and.ac.uk
  79. coconut028045.nuts.nwu.edu
  80. cookie.biop.umich.edu
  81. cpc.mel.dbe.csiro.au
  82. crash.wwwcache.ja.net
  83. cressida.imb-jena.de
  84. crissy.ucsf.edu
  85. crusty.lsb.sbs.auckland.ac.nz
  86. crystal.icgeb.trieste.it
  87. csc-a1592.mgh.harvard.edu
  88. d124b-labtop.stanford.edu
  89. dc-air.med.umn.edu
  90. dc-elf.med.umn.edu
  91. dialin-107.dialin.unibas.ch
  92. djinn-open.gene.com
  93. dorothy.ifqsc.sc.usp.br
  94. dynapro.cshl.org
  95. eagle.glasnet.ru
  96. echo.med.harvard.edu
  97. eden.bioc.cam.ac.uk
  98. eel.biochem.mpg.de
  99. elqana.saclay.cea.fr
  100. elroy.qci.bioch.bcm.tmc.edu
  101. eurogate.pfizer.co.uk
  102. f1n3.u.arizona.edu
  103. fedmac2.dl.ac.uk
  104. fermat.mc.duke.edu
  105. ff380.hh.ri.ccf.org
  106. firewall.esrf.fr
  107. ganymede.nrtg.com
  108. gate.ggr.co.uk
  109. gatekeeper.astra.com
  110. genie-open.gene.com
  111. glu.sb.fsu.edu
  112. glutamate.bio.cornell.edu
  113. glycine.bio.cornell.edu
  114. godot.ibs.fr
  115. gold.isbdd.vcu.edu
  116. green.niaid.nih.gov
  117. greenock-bank.clyde.net.uk
  118. groucho.med.jhmi.edu
  119. gutemine.uni-muenster.de
  120. h9bsd5054.aist-nara.ac.jp
  121. haemo.scripps.edu
  122. hasson.bio.purdue.edu
  123. hecate.rai.kcl.ac.uk
  124. helix.bchs.uh.edu
  125. hemebase.bio.uci.edu
  126. hermes.biomol.uci.edu
  127. hewes.icl.ox.ac.uk
  128. hg.pharm.nwu.edu
  129. hirta.bioc.cam.ac.uk
  130. hmt5.hitachi.co.jp
  131. host-207-53-9-204.rdu.bellsouth.net
  132. huldra.uninett.no
  133. idefix.ebi.ac.uk
  134. igate.ascc.net
  135. igw-se.pnu.com
  136. igw3.merck.com
  137. inca.chemistry.mcmaster.ca
  138. indigo1.bio.uci.edu
  139. indigo12.mc.vanderbilt.edu
  140. indy2.cryst.bbk.ac.uk
  141. infosun-fd.rus.uni-stuttgart.de
  142. interlock.pprd.abbott.com
  143. iris6.biochem.mcw.edu
  144. its-www1.massey.ac.nz
  145. jackdaw.embl-heidelberg.de
  146. jade.cmc.uab.edu
  147. jade.dfci.harvard.edu
  148. jake.embl-hamburg.de
  149. jeckle.med.harvard.edu
  150. jess.bath.ac.uk
  151. jinky.bioch.dundee.ac.uk
  152. jkindigo5.rockefeller.edu
  153. jm2310.livjm.ac.uk
  154. juliet.med.jhmi.edu
  155. jurancon.mbb.ki.se
  156. kakerlak.biochem.mpg.de
  157. kirti.cshl.org
  158. laue.bioz.unibas.ch
  159. lbmo2.ibs.fr
  160. lccphp1.ibs.fr
  161. leda.nagaokaut.ac.jp
  162. lithium.biophys.mpg.de
  163. lmb.biop.ox.ac.uk
  164. loyal.bch.ed.ac.uk
  165. lynx.chem.ou.edu
  166. macbeth.imb-jena.de
  167. mackinn-pc3.rockefeller.edu
  168. mailgate.celltech.co.uk
  169. malone.ibs.fr
  170. manu100.manu.com
  171. map-pc.nrl.navy.mil
  172. marin7.bc.ic.ac.uk
  173. marqusee9.berkeley.edu
  174. mars.esrf.fr
  175. mcb44.mcb.ucdavis.edu
  176. mcbi-46.med.nyu.edu
  177. mccgwy.m-kagaku.co.jp
  178. med-biop10.bu.edu
  179. med-biophg.bu.edu
  180. med-bragg.bu.edu
  181. metra.ucc.su.oz.au
  182. metro.ucc.su.oz.au
  183. milli.oci.utoronto.ca
  184. miro.biochem.nwu.edu
  185. moon.bmc.uu.se
  186. morse.scripps.edu
  187. msg-atgw.ucsf.edu
  188. msk-201-118.mskcc.org
  189. mush.cc.huji.ac.il
  190. nagg.ibs.fr
  191. neent.bmc.uu.se
  192. net186-81.its.yale.edu
  193. nikonov.ipr.serpukhov.su
  194. nob.pdb.bnl.gov
  195. ns.ibo.ch
  196. obi-wab.biochem.ualberta.ca
  197. opus.wistar.upenn.edu
  198. oskgate0.mei.co.jp
  199. oskgate2.mei.co.jp
  200. paia.ucsf.edu
  201. pandora.wi.mit.edu
  202. pc-young-d.chemistry.mcmaster.ca
  203. pcbdv2.rug.ac.be
  204. pec2.sc.ch.man.ac.uk
  205. pec4.sc.ch.man.ac.uk
  206. peggy-mac.nrl.navy.mil
  207. penguin.biophys.mpg.de
  208. pfizergate.pfizer.com
  209. phe.mpimf-heidelberg.mpg.de
  210. pierre.hh.ri.ccf.org
  211. pmate09.oci.utoronto.ca
  212. pohaku.lvl.pri.bms.com
  213. poppy.wwwcache.ja.net
  214. potto.bioch.virginia.edu
  215. prawn.biochem.mpg.de
  216. proxy.rediris.es
  217. quater.cryst.bbk.ac.uk
  218. quest.rose.brandeis.edu
  219. rab.oci.utoronto.ca
  220. rbo2.csb.yale.edu
  221. rburnett.wistar.upenn.edu
  222. rhino.cabm.rutgers.edu
  223. rogue.bchem.washington.edu
  224. romac3.niams.nih.gov
  225. rzinet.gbf-braunschweig.de
  226. sahara.dupontmerck.com
  227. salam.mbfys.lu.se
  228. sarek.bmc.uu.se
  229. sbsf-114.als.lbl.gov
  230. scpc8.rdg.ac.uk
  231. seal.csb.ki.se
  232. sgraf1.sc.ch.man.ac.uk
  233. shamrock.ebi.ac.uk
  234. shelx2.uni-ac.gwdg.de
  235. sherman.med.harvard.edu
  236. sherry.bmc.uu.se
  237. silver.niaid.nih.gov
  238. sissels.chem.uit.no
  239. skua.embl-heidelberg.de
  240. smac.ethz.ch
  241. solon.bmsc.washington.edu
  242. sp.spcorp.com
  243. srisvr.sri.org
  244. staffa.chem.gla.ac.uk
  245. striper.bioc.aecom.yu.edu
  246. t2o8p52.telia.com
  247. tau.mbb.ki.se
  248. thira.colorado.edu
  249. threonine.ucdavis.edu
  250. thymine.rutgers.edu
  251. tiger.bioch.virginia.edu
  252. tiger.cabm.rutgers.edu
  253. tigger.chem.york.ac.uk
  254. tome.cbs.univ-montp1.fr
  255. tpr.biop.ox.ac.uk
  256. troilus.imb-jena.de
  257. ucxray1.berkeley.edu
  258. ulti.niddk.nih.gov
  259. utbc08.cm.utexas.edu
  260. valine.bio.cornell.edu
  261. vcgate0.mei.co.jp
  262. vicious.bioc.le.ac.uk
  263. vidya.cshl.org
  264. vp2.med.harvard.edu
  265. vraptor.als.orst.edu
  266. walterlab-mac6.ucsf.edu
  267. www.bio.titech.ac.jp
  268. wwwproxy1.ac.il
  269. xanadu.tch.harvard.edu
  270. xgi6.cshl.org
  271. xmac6.ethz.ch
  272. xmmt020.avisnet.or.jp
  273. xray.rockefeller.edu
  274. xray.umdnj.edu
  275. xray0.princeton.edu
  276. xray1.ucmp.umu.se
  277. xrd2.isbdd.vcu.edu
  278. xserv1.dl.ac.uk
  279. xtal1.joslin.harvard.edu
  280. xtal10.tch.harvard.edu
  281. xtal200.harvard.edu
  282. zappa.extern.kun.nl
  283. zeelt.chem.ruu.nl
  284. zen.sb.fsu.edu
  285. zeta.embl-heidelberg.de
  286. zeus.compulink.gr
  287. zip.scripps.edu


Conclusion

What can we learn from this ? If nothing else, at least that there are protein crystallographers with a sense of humour !

As to the question of how outlandish the purported method for solving the phase problem is - not all that much, I suppose. But it will take someone a lot cleverer than I to do it ;-)

Little known crystallographic fact: Eric Fauman's mother wears a moustache !


USF Latest update at 3 April, 1998.