I cannot to input several .ar files from different data collections into Scalepack. Is this possible?
One should be able to put many different .ar files. I tried up to 25. Be sure that they have different batch numbers! If not use the option
add 1000
file xxxx1.ar
add 2000
file xxxx2.ar
to give different batch numbers to different .ar files.
I am using an Scalepack on a VMS machine with multiwire .ar files. How or can I refine the mosaicity and the B factors using Scalepack?
You cannot refine mosaicity in *.ar files. It has not been implemented. However you can refine B factors, it is done by default, so you do not need to do anything special.
We run our data collection on a VMS machine, and when the data is transferred to a UNIX machine the file is corrupted (using ftp)
Some versions of ftp will create wrong file format on VMS. Change to UCX (native VMS implementation) in such a case. Also remember to use binary ftp not ASCII ftp (sometimes a default option in ftp!)
I sometime get a message like insufficient space in common/spots losing reflection. What does that mean?
Denzo is running out of memory and ignores some reflections. This may happen if the box is unreasonably large. Reduce the box size or use the DenzoBig version of the program.
Would you make a larger version of Scalepack as I have some 2.8A data on an I222 form of a virus crystal (a=328.2, b=341.8, c=363.75) and Scalepack can't quite cope with the number of reflections?
Use ScalepackBig or ScalepackVeryBig
We collect our data on an Raxis (VAX workstation) and transfer it using FTP to the SGI. We have no trouble getting the Denzo to run on the oscillations but the display program (the one we got is INST_CORNELL) gives a message that the data file may be corrupted. The sample data that was packed in the tar file runs just fine. Is this the right version of the display program?
Use INST_RX instead. INST_CORNELL is design to read in data scanned with KODAK scanner at Cornell (now decommissioned).
I believe that my copy of the Scalepack executable file is somehow corrupted, because every time I run it, it always return with strange error message:
crystal6% SCALEPACK SCALEPACK: syntax error at line 1: ^A_^H,>q^Ce^FMH^P^B^A^K^A ^
Yes, you are correct. This is not the right executable.
Scalepack runs, it reads the frames but then just sits there. I used the example as a guideline and I also tried with deleting the postrefinement stuff but it still just sits there.
Try Crtl D (UNIX) or Crtl Z (VMS), to terminate input into the program.
I tried to run Scalepack. I get an error message: 'Exec format error. Wrong Architecture. 'Any ideas?
You try to run program compiled for different operating system or OS version. Investigate.
I got back from SSRL collecting data on the MAR. I want to process data with Denzo as well on our Indigo and I was wondering if I need to swap bytes for INST?
INST and Denzo programs recognize swap bytes automatically.
How do I get the radial and angular offsets for SSRL scanner? Do you have those numbers?
Sorry, we do not know. Ask SSRL staff.
*** TERMINATING /usr/perutz1/wladek/DENZO /DENZO *** Received signal 10 (SIGBUS) Bus error
An error from old SUN version. Problem specific to SUN. If you get such an error contact authors of the program.
I have an older version of Scalepack, which I assume is fine to use. Or is it?
It should work but it is not as good as the new one.
Can you produce a version of Scalepack that will take up to 1,000,000 reflections
Yes, now it is a standard version.
Should we have y scale -1.0 for this MAR plate?
Yes, however it is a default value.
We are looking at some Daresbury MAR data. The rotation axis is horizontal and I thought that we always processed this with film rotation -90.0 (or 90.0) but now we are all using 0.0. Is this because the convention has changed ? I am worried that the polarization corrections may be all wrong....This is 0.9A data so the polarization correction will be quite important ...
I hope that you did not process Daresbury MAR with film rotation -90.0 (or 90.0). The data would be disastrously bad. Maybe you confused MAR with R-axis at Daresbury? R-axis with horizontal spindle (3 such machines exist) requires film rotation -90.0 or 90.0 Polarization number should be positive for horizontal spindle at Daresbury regardless of value of film rotation. If you specified polarization Daresbury you are safe both with MAR and R-axis.
When I tried to process one of virus images there was a message about sfprof too small
The program is running out of memory and ignores some reflections. This may happen if the profile fitting radius is unreasonably large. Reduce the profile fitting radius size or use the DenzoBig version of the program.