Re: [ccp4bb] SCALA bugs in CCP4 6.3.0?

[Peter Goettig]

Dear David,

As suggested I have reinstalled Windows CCP4 6.2.0, but the problem of the 
missing information in the SCALA summary table was not abolished. In fact, it 
occurred in AIMLESS as well! I had done the original data processing in iMOSFLM 
1.0.7, followed by  a run of REINDEX to set the space group to P21212 with c as 
shortest axis including a reflection transformation.

Thus, I installed the Linux CCP4 6.3.0 and used the previous reindexed.mtz in 
SCALA. Everything worked perfectly and I obtained the desired tables with full 
information.

Regards,

Peter

Re: [ccp4bb] SCALA bugs in CCP4 6.3.0?

[David Waterman]

Hi Peter,

We're still working on the resolution of this bug. In the meantime you may
wish to replace 6.3.0's scala.exe with the one from 6.2.0, which is linked
to from the Windows Problems
pages.
Scala has not changed much between the two releases, only an increase in
the maximum number of allowed batches from 5000 to 1. If this limit is
a problem for you, then Phil's advice is to use Aimless instead.

Best regards

-- David


On 3 August 2012 19:02, Peter Goettig  wrote:

> In the Windows version of the new CCP4 release SCALA produces a summary
> table (same in the full text) that contains only some rudimentary data,
> such as
>
>   Overall  InnerShell
>  OuterShell
>   Low resolution limit   19.97 0.00  0.00
>   High resolution limit 3.00 0.00  0.00
>
>   Rmerge  0.000 0.000 0.000
>   Rmerge in top intensity bin0.115- -
>   Rmeas (within I+/I-)   0.000 0.000 0.000
>
>   aso
>
> while the final statement of SCALA is ** Normal termination **
>
> Has anyone else experienced similar problems and found a way to solve
> them? Otherwise, I would ask the developpers to take care of the bugs.
> However, the corresponding tables generated by AIMLESS contain the full
> information.
>
> Regards,
>
> Peter
>
>
> Peter Goettig
> Structural Biology
> University of Salzburg
> Billrothstrasse 11
> Salzburg, Austria
>

Re: [ccp4bb] SCALA bugs in CCP4 6.3.0?

[David Waterman]

Yep, it's definitely our problem not yours, Phil ;-). I believe the only
change to scala source since 6.2.0 was to up the maximum number of batches
again. This new bug is probably related to the change of compiler for 6.3.0.

We'll be trying to make sense out of this next week.

Cheers
D
On Aug 4, 2012 2:34 PM, "Phil Evans"  wrote:

> This must be a problem on Windows as it doesn't show up on OSX or Linux,
> and this code hasn't changed for a long time, I think
>
> David I guess you will feed this back to me: I don't have any way of
> testing on Windows
>
> Anyway, Aimless should be better :-)
>
> Phil
>
> On 4 Aug 2012, at 14:26, David Waterman wrote:
>
> > Dear Peter,
> >
> > You are not alone with this. We have just found out about this bug. It
> appears to just be a problem with output formatting (the MTZ should be
> fine). We'll get a fix as soon as we can and will provide a link to 6.2.0's
> version of scala from the problems page as a workaround early next week.
> >
> > Sorry about this.
> > David
> > (CCP4)
> >
> > On Aug 3, 2012 7:13 PM, "Peter Goettig"  wrote:
> > In the Windows version of the new CCP4 release SCALA produces a summary
> table (same in the full text) that contains only some rudimentary data,
> such as
> >
> >   Overall
>  InnerShell  OuterShell
> >   Low resolution limit   19.97 0.00  0.00
> >   High resolution limit 3.00 0.00  0.00
> >
> >   Rmerge  0.000 0.000
> 0.000
> >   Rmerge in top intensity bin0.115- -
> >   Rmeas (within I+/I-)   0.000 0.000 0.000
> >
> >   aso
> >
> > while the final statement of SCALA is ** Normal termination **
> >
> > Has anyone else experienced similar problems and found a way to solve
> them? Otherwise, I would ask the developpers to take care of the bugs.
> However, the corresponding tables generated by AIMLESS contain the full
> information.
> >
> > Regards,
> >
> > Peter
> >
> >
> > Peter Goettig
> > Structural Biology
> > University of Salzburg
> > Billrothstrasse 11
> > Salzburg, Austria
>

Re: [ccp4bb] SCALA bugs in CCP4 6.3.0?

[Phil Evans]

This must be a problem on Windows as it doesn't show up on OSX or Linux, and 
this code hasn't changed for a long time, I think

David I guess you will feed this back to me: I don't have any way of testing on 
Windows

Anyway, Aimless should be better :-)

Phil

On 4 Aug 2012, at 14:26, David Waterman wrote:

> Dear Peter,
> 
> You are not alone with this. We have just found out about this bug. It 
> appears to just be a problem with output formatting (the MTZ should be fine). 
> We'll get a fix as soon as we can and will provide a link to 6.2.0's version 
> of scala from the problems page as a workaround early next week.
> 
> Sorry about this.
> David
> (CCP4)
> 
> On Aug 3, 2012 7:13 PM, "Peter Goettig"  wrote:
> In the Windows version of the new CCP4 release SCALA produces a summary table 
> (same in the full text) that contains only some rudimentary data, such as
> 
>   Overall  InnerShell  
> OuterShell
>   Low resolution limit   19.97 0.00  0.00
>   High resolution limit 3.00 0.00  0.00
> 
>   Rmerge  0.000 0.000 0.000
>   Rmerge in top intensity bin0.115- -
>   Rmeas (within I+/I-)   0.000 0.000 0.000
> 
>   aso
> 
> while the final statement of SCALA is ** Normal termination **
> 
> Has anyone else experienced similar problems and found a way to solve them? 
> Otherwise, I would ask the developpers to take care of the bugs. However, the 
> corresponding tables generated by AIMLESS contain the full information.
> 
> Regards,
> 
> Peter
> 
> 
> Peter Goettig
> Structural Biology
> University of Salzburg
> Billrothstrasse 11
> Salzburg, Austria

Re: [ccp4bb] SCALA bugs in CCP4 6.3.0?

[David Waterman]

Dear Peter,

You are not alone with this. We have just found out about this bug. It
appears to just be a problem with output formatting (the MTZ should be
fine). We'll get a fix as soon as we can and will provide a link to 6.2.0's
version of scala from the problems page as a workaround early next week.

Sorry about this.
David
(CCP4)
On Aug 3, 2012 7:13 PM, "Peter Goettig"  wrote:

> In the Windows version of the new CCP4 release SCALA produces a summary
> table (same in the full text) that contains only some rudimentary data,
> such as
>
>   Overall  InnerShell
>  OuterShell
>   Low resolution limit   19.97 0.00  0.00
>   High resolution limit 3.00 0.00  0.00
>
>   Rmerge  0.000 0.000 0.000
>   Rmerge in top intensity bin0.115- -
>   Rmeas (within I+/I-)   0.000 0.000 0.000
>
>   aso
>
> while the final statement of SCALA is ** Normal termination **
>
> Has anyone else experienced similar problems and found a way to solve
> them? Otherwise, I would ask the developpers to take care of the bugs.
> However, the corresponding tables generated by AIMLESS contain the full
> information.
>
> Regards,
>
> Peter
>
>
> Peter Goettig
> Structural Biology
> University of Salzburg
> Billrothstrasse 11
> Salzburg, Austria
>

[ccp4bb] SCALA bugs in CCP4 6.3.0?

[Peter Goettig]

In the Windows version of the new CCP4 release SCALA produces a summary table 
(same in the full text) that contains only some rudimentary data, such as
   
  Overall  InnerShell  
OuterShell
  Low resolution limit   19.97 0.00  0.00
  High resolution limit 3.00 0.00  0.00

  Rmerge  0.000 0.000 0.000
  Rmerge in top intensity bin0.115- -
  Rmeas (within I+/I-)   0.000 0.000 0.000
 
  aso

while the final statement of SCALA is ** Normal termination **
  
Has anyone else experienced similar problems and found a way to solve them? 
Otherwise, I would ask the developpers to take care of the bugs. However, the 
corresponding tables generated by AIMLESS contain the full information.

Regards,

Peter


Peter Goettig
Structural Biology
University of Salzburg
Billrothstrasse 11
Salzburg, Austria