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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
