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I repeated a couple of tests. I had had a typo in one of the scripts. I can confirm Johan's findings that having a valid "reference film" appears to be the critical parameter as to whether or not the postrefined values get placed in the .sca header or not. Sorry for my incorrect conclusion about the fit cell vs fit a* b* c*, this does not appear to be important. Adding a valid reference film command to my standard script resulted in the postrefined values getting placed in the .sca header. Regards, Mitch -----Original Message----- From: Johan Turkenburg [mailto:[EMAIL PROTECTED] Sent: Wednesday, January 11, 2006 7:15 AM To: Miller, Mitchell D. Cc: Phil Jeffrey; Edward Berry; Alessio Accardi; Vaheh Oganesyan; [email protected] Subject: Re: [ccp4bb]: Unit Cell Parameters 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 > > > -- +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Dr. Johan P. Turkenburg X-ray facilities manager York Structural Biology Laboratory Chemistry Department Phone (+) 44 1904 328253 University of York Fax (+) 44 1904 328266 York YO10 5YW UK Email: [EMAIL PROTECTED] +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
