[ccp4bb] Ample, shelxe-beta and F to I conversion confusion
Hi, I've been running Ample and I'm a bit confused about the input for the shelxe-beta auto-tracing. The input mtz for Ample has F, SIGF and FreeR and it appears that Ample converts the structure factor amplitudes to intensities using mtz2various with the FSQUARED keyword as the log file contains the following: Data line--- LABIN FP=F SIGFP=SIGF FREE=FreeR_flag Data line--- OUTPUT SHELX Data line--- FSQUARED Fs are squared on output - better to use original Is from TRUNCATE output Data line--- END However then shelxe is run with the command: shelxe shelxe-input.pda -a15 -q -s0.4779 -o -f -n -t3 I thought that the -f flag tells shelxe that the input hkl file contains Fs not Is so this should not be present? When I run shelxe with the phaser/molrep solutions and a hkl file generated either from the merged intensities with mtz2hkl or unmerged intensities with xdsconv I get much lower CCs for the autotracing which makes sense as all of the solutions so far are rubbish! The Ample logs contain CCs 30 for all solutions which doesn't seem correct. Any information would be greatly appreciated! Thanks, Huw
Re: [ccp4bb] Ample, shelxe-beta and F to I conversion confusion
Dear Huw, It looks as though you have correctly diagnosed a problem with AMPLE. For expansion from borderline partial structures, I recommend the latest SHELXE (on my beta-test server since Jan. 20th) and experimenting with the -O and -F switches, e.g. -F0.9 -O100 -a30 However SHELXE is still a work in progress, so this may change in future versions. Best wishes, George Hi, I've been running Ample and I'm a bit confused about the input for the shelxe-beta auto-tracing. The input mtz for Ample has F, SIGF and FreeR and it appears that Ample converts the structure factor amplitudes to intensities using mtz2various with the FSQUARED keyword as the log file contains the following: Data line--- LABIN FP=F SIGFP=SIGF FREE=FreeR_flag Data line--- OUTPUT SHELX Data line--- FSQUARED Fs are squared on output - better to use original Is from TRUNCATE output Data line--- END However then shelxe is run with the command: shelxe shelxe-input.pda -a15 -q -s0.4779 -o -f -n -t3 I thought that the -f flag tells shelxe that the input hkl file contains Fs not Is so this should not be present? When I run shelxe with the phaser/molrep solutions and a hkl file generated either from the merged intensities with mtz2hkl or unmerged intensities with xdsconv I get much lower CCs for the autotracing which makes sense as all of the solutions so far are rubbish! The Ample logs contain CCs30 for all solutions which doesn't seem correct. Any information would be greatly appreciated! Thanks, Huw -- Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-22582
Re: [ccp4bb] Ample, shelxe-beta and F to I conversion confusion
Hi Huw, Well spotted! We originally gave structure factors to SHELXE in our testing as for most of our test cases we only had F/SIGF available. We were advised to change to intensities but somehow in the released version the -f flag remained. I'll make the change and put it in a CCP4 update. Ideally we should be using the original intensities rather than converting the structure factors so we'll look to adding that as an input option. Thanks again for spotting this. Best wishes, Ronan -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Huw Jenkins Sent: 28 January 2013 10:14 To: ccp4bb Subject: [ccp4bb] Ample, shelxe-beta and F to I conversion confusion Hi, I've been running Ample and I'm a bit confused about the input for the shelxe-beta auto-tracing. The input mtz for Ample has F, SIGF and FreeR and it appears that Ample converts the structure factor amplitudes to intensities using mtz2various with the FSQUARED keyword as the log file contains the following: Data line--- LABIN FP=F SIGFP=SIGF FREE=FreeR_flag Data line--- OUTPUT SHELX Data line--- FSQUARED Fs are squared on output - better to use original Is from TRUNCATE output Data line--- END However then shelxe is run with the command: shelxe shelxe-input.pda -a15 -q -s0.4779 -o -f -n -t3 I thought that the -f flag tells shelxe that the input hkl file contains Fs not Is so this should not be present? When I run shelxe with the phaser/molrep solutions and a hkl file generated either from the merged intensities with mtz2hkl or unmerged intensities with xdsconv I get much lower CCs for the autotracing which makes sense as all of the solutions so far are rubbish! The Ample logs contain CCs 30 for all solutions which doesn't seem correct. Any information would be greatly appreciated! Thanks, Huw -- Scanned by iCritical.
Re: [ccp4bb] Ample, shelxe-beta and F to I conversion confusion
Correct, shelxe does not use the free -R flags, and works just as well with the original unmerged unctruncated intensities. George Hi Ronan, On 28 Jan 2013, at 12:18, ronan.kee...@stfc.ac.uk wrote: Well spotted! We originally gave structure factors to SHELXE in our testing as for most of our test cases we only had F/SIGF available. We were advised to change to intensities but somehow in the released version the -f flag remained. I'll make the change and put it in a CCP4 update. Ideally we should be using the original intensities rather than converting the structure factors so we'll look to adding that as an input option. Thanks for confirming that! Perhaps the option to add a hkl file for shelxe would be a useful? Since I use XDS to integrate and scale data it's as easy to generate the shelx format hkl file from the unmerged XDS_ASCII.HKL as it is to use the merged intensities in the mtz from the aimless/truncate/unique/freerflag pipeline. The only issue with this I can see is that there will be no freeR flags but I don't think that shelxe uses these anyway? Thanks, Huw -- Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-22582
