*Copyright notices

*The wARP idea has been developed by Anastassis Perrakis*Titia

K*Sixma*Keith S*Wilsonand Victor Lamzin*and is described into

*wARP*Improvement and extension of initial crystallographic phases

by weighted averaging of multiple re*neddummy models** submitted

for publication*

*ARP and rename wat code is written by Victor Lamzin*

*wARP scripts are written by Anastassis Perrakis*

*When to use wARP

wARP is usable when an initial map is available from MIR*MAD*SIRAS or

whatever*This map should be of good enough quality to recognize at least

parts of the structure*** wARP will result in various degrees of improvement*

depending on the resolution of the data and the quality of the initial map*

In most cases it will give a map of excellent quality which will speed up

model building and will also enable some automatic interpretation programs

to work much better *

Remember*Your NATIVE data should extend to a resolution of at least ***

*

A *OR*to put it in a better way*You should have at least *** observations

for every expected atom in the protein - including waters *

*Installation

You also need CCP*programs and ARP running*ARP must be obtained

from Victor*embl*hamburg*de* You also need the *dmoleman program*

from the Rave suite by Gerard Kleywegt*available in the O WWW site*

Reading this*means most likley that you already unzipped and untared the

wARP*tar*gz *le* For the moment you need Irix *** to run wARP*The only

thing to do now is to add these two lines to your setup *le* *cshrc*

set path * * *path your*warp*directory *

setenv warpbin your*warp*directory

*

*Running wARP

First*create a directory where you plan to run wARP and follow the steps

below*

*** Getting the initial map

First*you need to have a map on a *negrid ****

*

A **covering a whole

assymetric unit as de*nedin ARP documentation*

To calculate this map you should use your best phase set*If your experimen

tal phases extend to worse than ***

*

A resolution*you should apply some

phase extension *withie DM*to that resolution ****

*

A **

Do NOT extend the phases too much*ie from ***

*

A to ***

*

A *ifyou have

native data to ***

*

A that is ***** However if you have good experimental

phases to say ***

*

A you might consider extending by *******

*

A *

The map should be in CCP*format *I recommend to always *extend* the

map to the correct assymetric unit after **t** sometimes the last section is

missing - this will cause ARP to complain and stop execution*

Name that *learp in*map

*** Getting the *seed* *le

Take a helix or so from any protein *around*** atoms* and place it approxi

mately in the core *centre of gravity* of your MIR map* in protein region* do

not bother to *t it exactly in density*** Save that *lein pdb format*without

any REMARKS*SCALE cards or whatsoever*Here is an example*

ATOM *OW*WAT A ******* ****** ****** **** **** *

ATOM *OW*WAT A ******* ***** ****** **** **** *ATOM *OW*WAT A ******* ****** ****** **** **** *ATOM *OW*WAT A ******* ****** ****** **** ***** *ATOM *OW*WAT A ****** ****** ****** **** **** *ATOM *OW*WAT A ******* ***** ****** **** **** *ATOM *OW*WAT A ******* ****** ****** **** ***** *ATOM *OW*WAT A ****** ****** ****** **** ***** *ATOM *OW*WAT A ****** ****** ****** **** ***** *ATOM ** OW*WAT A ** ****** ****** ****** **** ***** *ATOM ** OW*WAT A ** ***** ****** ****** **** ***** *ATOM ** OW*WAT A ** ****** ***** ****** **** ***** *ATOM ** OW*WAT A ** ****** ****** ****** **** ***** *Name that *leseed*brk

*

*** Setting wARP parameters

Copy the *le*warpbin*warp*par to the current directory*It is quite abvious

what to edit there *Take a quick look at the example*

*Systemparameters

*

*CCP*setup command*like*

*

set ccp*init**source*nfs*home*perrakis*psp*au to*ccp**setup*

*

*set machine**den

set machine**olijf

set machine* * berk

set machine* * spar

set machine* * den

set machine* * linde

*

************************** **** **** *** **** **** **** *** **** **** ****

*Additional required input*

*seed*brk* Initial atoms*NO header *

*arp*in*map *Input map on fine grid **Use extend to extend it in ARP assymetric unit

*

*Unit cell ***

set cell * ******** ****** ****** ***** ****** ******

*

*Symmetry

set sym ****

*Space group for sfall if LS is used*

*Data should be extended to that spacegroup

set sfsg **P**

*

*Mtzfile with native data

set data ***nfs*home*perrakis*psp*p sp*nat** *mtz*

*

*

*Resolution limits

set resol **** ****

*

* Grids for SF and FFT

set grid ***** *** ****

*

*Asym* unit limits compatible with arp

set xyzlim * ** *** * *** * ****

*

* B factor from Wilson plot

set wilsonb * ****

*

* Protein size in atoms * *NO waters*

set proteinsize * ****

*

* Refinement method

* Uncomment for Max Likelihood

set method * *ML*

* Uncomment for Least Squares

*set method * *LS*

*

* Cycles for initial * models and then for all *set firstref * **

set secondref * **

set thirdref * **

Some considerations are*

*Usually ccp*tries to de*neenvironment MANPATH as complementary

to existing MANPATH*During execution of remote shells MANPATH

does not exist*and crashes remote scripts *Copy the ccp**setup *le to

a local directory*and simply remove the line setenv MANPATH*and

then set *ccp*init* to that *le *

*

*Another annoying habbit in CCP*is checking if a *leexists and if yes

not overwrite it*Please change the line setenv CCP*OPEN NEW to

setenv CCP*OPEN UNKNOWN*I am doing normally some checking*

but it is quite likely if you had a crash to start getting errors*so play

it safe*

*Well*how many cycles to run *If you have time and *machines*run

***** * ** *If not*before decreasing cycles*edit warp all*shand

comment out the command runnign the script re*ne* and set thirdref

in warp*par to **Or *ndsome other logical way to compensate anyhow

*

*warp can be run in a parallel manner*by submitting di*erent jobs in

di*erent machines*You have to setup machine names of your cluster*

All of them must share common disk space*have you as a user and

be speci*edin *rhosts*le*** ie you must be able to use them without

logging in with password *ie*in priciple if you say *rshothermachine

*echo OK*you should get an OK in your screen*Ask the system man

ager for help*Machine names can be dublicate*triplicate or whatever*

It is obvious you should use more than once the most powerfull *ie

multiprocessor ** machine - if not *machines are available*Also it is

better to keep ***** as seperate as possible and if necessary to create

redundancy coupel *** *** and *** *

*Which re*nement method to use*Normal least squares *LS* or max

imum likelyhood *ML** My hint is*If you have good data to around

***

*

A **morethan ** observations per atom*use ml*If not use ls*If

in doubt try both and check R factors *

*Use your low resolution re*ections***

*

A or so** if you plan to use ML*

The default is to USE bulk solvent scaling* if low resolution is missing*

it will crash*If you want ML but have no good low resolution*edit the

*le*warpbin*mlarp*com and change *BULK* to *SIMPLE**

*If you use LS extend your data in a suitable space group*with cad*

During averaging wARP will anyhow extend them to P** a bit stupid

I admitt* but the only way to make it easily space group independent*

*

*** Running and Checking log *le

*** should be easy*

All you have to do is to run warp all*shBrie*ywhat it does*

**Puts lots and lots of atoms in the initial map density*according to

certain density and geometric criteria*

**From these creates three models*

**Re*nesthese models for *rstref cycles*

**Shakes these three models and resets B factors in order to create three

new models*

** Re*nesall six models for secondref cycles*

** Reject in one round lots of atoms in low density and then slightly

shakes*resets B*sand *nallyre*nesall six models for thirdref cycles*

** Does the averaging and calculates a map*

** Cleans up all intermidiate *lesand saves essential ones and then sum

marizes log *les* Everything is stores in directory log *les*

Please note*

*Most important is maybe that warp all*shmust be run in the fore

ground*csh does not allow to issue rsh commands in the background*

which you absolutely need*unless you are willing to spend *times

more time or you have a single machine*A bit unconvenient but you

*dbetter live with it *

*In case of crashed at some stage*you should keep in mind that warp all*sh

executes *other scripts*build*re*ne** re*ne** cleanup average*if you

wish to start from *themiddle*of the procedure you can call these

scripts directly*If*for example*one machine goes down at cycle ** or

so and everything crashes before the end* you can just run re*ne* and

then average*you do not have to build and re*ne* again *A good trick

to save more time is*If the crash was at cycle *** ie in ALL * dirs you

*

have junk *** edit warp*par set *rstref to ** *NO this is NOT a typo*

******** please do not ask why **** and secondref to as many cycles as

you wish*

*Examine the summaries of arp log *les*If you suspect that R

factors can go lower*you should run a few more cycles*You can do

that the same way as before OR shake *rstthe models a bit*I strongly

recommend the latter*All you have to do is set *rstref to an arbitary

number*say **** and endref to the number of cycles you wish to run*

Then run warp more*sh*This will copy from the directory log *les

your latest re*nedmodel *lesto new re*nement directories*run the

re*nement*do the averaging and cleanup *Note that in log *lesyour

**nal*brk *les are now the ones after the additional cycles*and the

arp **summarylog *lesare also referring to the last cycles *

*Rfactors should converge to ***** *for succesfull completion of the

job*If re*nement is not converge*try switching to LS *orML*and

rerun*If still not succesfull grow better crystals or get new derivatives*

More extended log *lesand intermidiate pdb *leswill be stored at subdirec

tory log *les* All other *lescreated during execution will be deleted *

The warp scripts should do everything for you*and it will result to a single

CCP*format map *le* warp FoFOM*map*Display it in the graphics and

have fun ***

*** Sample timings ***

I use our cluster here*with *machines for testing*One machine has to run

two jobs*Four are Indy*swith R**** *** MHz processors and ** MBytes of

memory*except one which has *** MBytes and which I use for running both

the *main* job and the *double* job*One is an Indigo with a slower *** MHz

processor*The protein is the same as in the example warp*par*le* around

**** atoms re*nedagainst more or less **** re*ections* re*ned for ** * **

cycles* Here are some characteristic *les* with their creation time next to

them*so you can see how long things take ***

*

NOT YET