check the data processing logs (or matrix file in mosflm), the final cell parameters should be there and should be the same as those in the CRYST card of your pdb file at least to the second decimal.

to delete the SCALE cards, just open the pdb file in a simple text editor (textedit in mac, emacs etc.), delete the lines starting with SCALE and save (under a new name to be safe)

[I keep forgetting that in this age of GUIs many people never open files with text editors anymore…it’s good practise to open all ASCII output files of any process you run and try to understand as much as possible of them...]


Mark J van Raaij
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
c/Darwin 3
E-28049 Madrid, Spain
tel. (+34) 91 585 4616
http://wwwuser.cnb.csic.es/~mjvanraaij






> On 22 Jan 2016, at 20:03, Alex Lee <[log in to unmask]> wrote:
> 
> Hi Robbie and Mark,
> 
> Thank you very much for the information. I wonder is there a verification tool which I can use to verify if my CRYST1 or SCALEx is right?  If my SCALEx is not right, how to delete it? is the SCALEx record in the pdb file generated by Phaser MR?
> 
> On Fri, Jan 22, 2016 at 12:54 AM, Robbie Joosten <[log in to unmask]> wrote:
> Hi Alex,
> 
>  
> 
> Refmac uses the SCALEx cards to convert the Cartesian coordinates in a PDB file to fractional coordinates. Unfortunately, sometimes the SCALEx cards are not correct and the model looks warped to Refmac in terms of geometry (I once had a PDB file in which the SCALEx cards gave the identity matrix, that didn’t end well). I guess that new versions of Refmac check for discrepancies between the CRYST1 card and the SCALEx cards and gives a warning. In such cases you should remove the SCALEx records and run Refmac again. Refmac will just use the CRYST1 card and, assuming it is correct,  refine you model properly.
> 
>  
> 
> Cheers,
> 
> Robbie
> 
>  
> 
> From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of Alex Lee
> Sent: Friday, January 22, 2016 01:26
> To: [log in to unmask]
> Subject: [ccp4bb] warning message after Refmac5
> 
>  
> 
> Dear All,
>  
> After I run Refmac5, I got a warning message of "WARNING: XYZOPEN2: Orthogonalisation code not determined. Possible disagreement between CRYST1 and SCALEx cards."
>  
> What does this mean?
>  
> When I integrate the data with HKL2000, the numbers of crystal rotation Y is on red color, for example :              X:  -16.859   -0.079     0.029
>                                                                                                                                                                    Y:   51.28     0.078      0.040
>                                                                                                                                                                    Z:  -74.721    0.012     0.008
> I do not know if this has a relation to do with the warning I see after refmac.
>  
> Thanks ahead.
>  
>  
>