On-Line Help

The ARP/wARP input pre-processor gives warnings or error messages if something is wrong. These should be carefully checked. It is also advisable to check ARP/wARP input prior to submitting a long refinement job.

Here are a few examples of how the on-line commands can be used. To start just type 'arp_warp' and then the keyword you are interested in.

arp_warp
END
Input must start with the keyword MODE

arp_warp
MODE
Keyword MODE must be followed by 1 field(s)

Expected format:

MODE update waters/allatoms
MODE mirbuild
MODE shakemodel light/allatoms
MODE reflaver

arp_warp
MODE UPDATE WATERS
Optional keywords:
CELL cell parameters
REFINE waters/allatoms

Required keywords:
SYMM spacegroup
RESOLUTION resmin resmax
FIND ATOMS number CHAIN string CUTSIGMA number/AUTO
and/or REMOVE ATOMS number CUTSIGMA number [MERGE number] [KEEP ZEROOCC]
END (must be the last keyword)

arp_warp
MODE UPDATE WATERS
CELL
An error message:

This Data Card in not understood
Keyword CELL must be followed by 6 field(s)

Expected format:

CELL a b c alpha beta gamma

arp_warp
MODE UPDATE WATERS
CELL 30 45 37 90 90 90 A
This Data Card in not understood
CELL 30 45 37 90 90 90 A
Cannot accept field shown by arrows:
CELL 30 45 37 90 90 90 ==>A<==

arp_warp
MODE UPDATE WATERS
CELL 30 45 37 90 90 90
SYMM 4
RESOLUTION 20 1.5
FIND ATOMS 10 CHAIN W CUTSIGMA 3.0
REMOVE ATOMS 10 CUTSIGMA 1.0
END
Asymmetric unit limits 1/1   1/2   1/1

Comments: Space group 4 P21
Comments: Cell parameters 30.000 45.000 47.000 90.000 90.000 90.000
Comments: Remove 10 old atoms if below 1.0 sigma in MAPIN1
Comments: Analyse waters only for removal
- WARNING - This is not a standard use of ARP
- use of MERGE data card is advisable

Comments: Look for 10 new atoms in MAPIN2
Above threshold of 3.0 sigma
- WARNING - This is not a standard use of ARP
- use of CUTSIGMA AUTO option is recommended
- assuming that MAPIN2 is Fo-Fc map

Comments: New atoms will not be put closer than 2.30 to existing atoms
Comments: New atoms will be selected if there is N or O exists within 3.30
Comments: New atoms will not be put closer than 2.30 to each other
Comments: New atoms will have B-factors assigned on the basis of MAPIN2
- density hight as expected for resolution range 1.50 20.00
- MAPIN2 is assumed to be Fo-Fc map in absolute scale
Comments: New atoms will have chain name W

- No real space refinement will be made
- WARNING - This is not a standard use of ARP
- real space refinement of waters is advisable

So ARP/wARP actually accepts the command file input and the program only gives comments and warnings (if everything else is formally correct). It will also make additional checks during the run.