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Also done a few more tests:
In my hands, changing from 'fit crystal cell' to 'fit crystal a*' and
'fit crystal c*' (for a hexagonal crystal) makes no difference: in both
cases the cell in the .sca file is the cell from the postrefinement, not
from the first .x file.
Changing the reference film from 1 to 5 to 10 makes no difference, the
cell is from postrefinement, not from the .x file.
BUT, with no reference film in (i.e. taking out the 'reference film'
keywords), the cell in the .sca file is the cell in the .x file for
image 1 and NOT the cell from postrefinement.
The cell from the postrefinement is still the same as the cell coming
out of the runs with a reference film keyword in (just as well!).
Not found another way of 'breaking' scalepack yet. By the way, this is
all with 'format denzo_ip'. Not tried 'format denzo_york1'.
Johan
Miller, Mitchell D. wrote:
I looked at a test this morning before I sent my original post and
observed the unit cell from the first .x file being placed in the
output .sca file header. With so many counter examples, I went back
and ran some more tests. It seems to depend on what keywords you use
whether or not the updated values are put in the .sca file. The way we
typically run scalepack from the C-shell scripts, the postrefined cell values
do NOT make it into thee .sca file. (This is with v1.98.3 on OSF1)
From postrefinement
CELL 61.3725 62.6230 70.3258 90.0000 90.0000 90.0000 270285.3
A 11001 61.3725 0.0032
B 11001 62.6230 0.0023
C 11001 70.3258 0.0036
From first .x file
unit cell 61.465 64.507 70.708 90.000 90.000 90.000
from .sca file
61.465 64.507 70.708 90.000 90.000 90.000 p222
After looking at the scale.in file produced by HKL2000 (which
does put the postrefined cell values in the .sca file). I found that
there are several small changes that will "break" the undocumented
feature Phil and Ed are relying on and one will end up with the cell
from the first .x file in the .sca file header.
For example, the hkl2000 generated scale.in file uses an undocumented
parameter for the fit command (fit cell). If I change this to 3 fit commands
(for a* b* and c* as outlined in the manual) for an orthorhombic crystal,
the postrefined cell values were not be placed in the .sca file header. Another
change that resulted in the postrefined cell not being added to the .sca file
header was to comment out the 'reference film' command. Without this command
the cell from the first .x file is placed in the .sca header.
Simply changing my script file to include a reference film and use fit cell
in place of fit a* fit b* and fit c* commands did not result in the post-refined
values being placed in the .sca file. So I suspect there are more combinations
of keywords that will prevent the postrefined values from being placed in
the .sca header.
Based on my tests and Alessio's original post, I would caution that one
check the header to confirm that they are getting the post-refined values
if they use their own scalepack scripts or edit the scalepack input files
from HKL2000.
Regards,
Mitch
-----Original Message-----
From: Phil Jeffrey [mailto:[EMAIL PROTECTED]
Sent: Tuesday, January 10, 2006 8:25 AM
To: Miller, Mitchell D.
Cc: Edward Berry; Alessio Accardi; [email protected]
Subject: Re: [ccp4bb]: Unit Cell Parameters
Miller, Mitchell D. wrote:
The behavior you attribute to early versions of scalepack is still
described in the current manual.
Which assumes that they updated the manual when they updated the
software. I've seen the same behavior that Ed Berry reported.
Here is an example with 1.97.2 on Linux, run again just now to check:
Cell from .sca file:
125.486 125.486 59.256 90.000 90.000 90.000
Cell from first .x (denzo output) file:
126.422 126.422 59.575 90.000 90.000 90.000
Cell from postrefinement in scalepack:
125.486 125.486 59.256 90.000 90.000 90.000
It would be very interesting to hear from anyone running 1.97 or later
that did NOT see this behavior, since like Ed I've come to rely
on/expect this new behavior.
Regards,
Phil Jeffrey
Princeton
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