Re: [ccp4bb] ample
Dear Patrick, Apologies for a partly non-CCP4 answer! You can use the HHPRED alignments in some of the software available in Phenix. One option is to provide the .hhr file to MRage, which will fetch the PDB entries, run Sculptor to modify the templates with one or more protocols, based on that alignment, and then test all the models that have been generated. That's fully automated and will often work. If it doesn't, an alternative is to run phenix.mr_model_preparation, which again will fetch the PDB entries and run the single best Sculptor protocol on all of them. I tend to prefer this option myself, because then you can look at whether it would be sensible to combine various alternative models as ensembles. One of the most powerful approaches is to run Ensembler (available in both CCP4 and Phenix, as is Sculptor) to make an ensemble, with the "trim=True" option turned on to trim any bits that don't agree among the structures in the ensemble. Cutting back to a conserved core has allowed a number of very recalcitrant structures to be solved with collections of models around the 20% sequence identity range. Best wishes, Randy > On 20 Jul 2017, at 23:13, Patrick Lollwrote: > > I’m intrigued by the prospect of using AMPLE to test multiple distant > homologs in a MR problem. I’ve used HHPRED to identify about 20 > high-probability homologs of known structure, each of which has about 20-25% > identity with the unknown protein. However, it’s not clear to me from the > documentation whether the program will use the alignments from HHPRED, and, > if so, how I should provide that information. > > Or does AMPLE perform its own alignment? I.e., do I simply point the program > to a directory containing 20 different PDB files and stand back? > > Thanks for any insights. > > Cheers, > > Pat > --- > Patrick J. Loll, Ph. D. > Professor of Biochemistry & Molecular Biology > Drexel University College of Medicine > Room 10-102 New College Building > 245 N. 15th St., Mailstop 497 > Philadelphia, PA 19102-1192 USA > > (215) 762-7706 > pjl...@gmail.com > pj...@drexel.edu -- Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: + 44 1223 336500 Wellcome Trust/MRC Building Fax: + 44 1223 336827 Hills RoadE-mail: rj...@cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk
Re: [ccp4bb] ample
Dear Pat Yes, AMPLE does it's own, purely structure-based, alignment of the homologs provided using GESAMT. You provide a directory of structures to work with and, crucially, give AMPLE the -homologs True flag so that it knows the inputs have different sequences (unlike in modelling mode), and need to be dealt with accordingly. There's more explanation and example files here http://ample.readthedocs.io/en/latest/examples/rst/homologs.html#example-dist-homologs In this mode AMPLE first finds the common core shared by all inputs and then produces graded further truncations of that with different side chain treatments. This sampling is often necessary in the hardest cases. What this means, however, is if the input set are ultra-diverse, then the GESAMT shared common core can be quite small. It can therefore also be worth trying a smaller set of not quite so diverse structures which share a somewhat larger core structure. Best wishes Daniel On 20/07/17 23:13, Patrick Loll wrote: I’m intrigued by the prospect of using AMPLE to test multiple distant homologs in a MR problem. I’ve used HHPRED to identify about 20 high-probability homologs of known structure, each of which has about 20-25% identity with the unknown protein. However, it’s not clear to me from the documentation whether the program will use the alignments from HHPRED, and, if so, how I should provide that information. Or does AMPLE perform its own alignment? I.e., do I simply point the program to a directory containing 20 different PDB files and stand back? Thanks for any insights. Cheers, Pat --- Patrick J. Loll, Ph. D. Professor of Biochemistry & Molecular Biology Drexel University College of Medicine Room 10-102 New College Building 245 N. 15th St., Mailstop 497 Philadelphia, PA 19102-1192 USA (215) 762-7706 pjl...@gmail.com pj...@drexel.edu -- Dr Daniel John Rigden Tel:(+44) 151 795 4467 Institute of Integrative Biology FAX:(+44) 151 795 4406 Room 101, Biosciences Building University of Liverpool http://pcwww.liverpool.ac.uk/~drigden/ Crown St., Liverpool L69 7ZB, U.K.
[ccp4bb] ample
I’m intrigued by the prospect of using AMPLE to test multiple distant homologs in a MR problem. I’ve used HHPRED to identify about 20 high-probability homologs of known structure, each of which has about 20-25% identity with the unknown protein. However, it’s not clear to me from the documentation whether the program will use the alignments from HHPRED, and, if so, how I should provide that information. Or does AMPLE perform its own alignment? I.e., do I simply point the program to a directory containing 20 different PDB files and stand back? Thanks for any insights. Cheers, Pat --- Patrick J. Loll, Ph. D. Professor of Biochemistry & Molecular Biology Drexel University College of Medicine Room 10-102 New College Building 245 N. 15th St., Mailstop 497 Philadelphia, PA 19102-1192 USA (215) 762-7706 pjl...@gmail.com pj...@drexel.edu
Re: [ccp4bb] AMPLE failure
Hi Robert, Thanks for your interest in AMPLE and reporting this bug. There is a small bug that has come about as a result of the latest MRBUMP update last week that causes this problem. We're preparing a fix for it which should be in the next ccp4 update towards the end of this week or early next week. In the meantime I can send you (off list) the latest version of the code that you can manually install. Best wishes, Ronan On 12/07/14 18:58, Robert Kirchdoerfer wrote: Hi, I'm trying to run AMPLE from ccp4-6.4.0 on Linux Ubuntu. It looks like it found all the program dependencies that it needs and Rosetta looks like it ran okay and I think MRBUMP looks alright, but then the program stopped with the following error message: MR and shelx DONE ALL DONE (in 1.64101706141 hours) Saved results as file: /home/rob/Crystal/108_B7U_3/ccp4/ROSETTA_MR_1/resultsd.pkl *** * Information from CCP4Interface script *** The program run with command: /home/rob/Xstal_Programs/ccp4v640/destination/ccp4-6.4.0/bin/ccp4-python -u /home/rob/Xstal_Programs/ccp4v640/destination/ccp4-6.4.0/bin/ample -mtz /home/rob/Crystal/108_B7U_3/ccp4/XDS_ASCII_scaled2.mtz -fasta /home/rob/Crystal/108_B7U_3/phenix/RNK149.fasta -nmodels 1000 -name MVD0 -run_dir /home/rob/Crystal/108_B7U_3/ccp4 -nproc 8 -make_models True -rosetta_dir /home/rob/Xstal_Programs/Rosetta/rosetta-3.5 -frags_3mers /home/rob/Crystal/108_B7U_3/ccp4/aat000_03_05.200_v1_3 -frags_9mers /home/rob/Crystal/108_B7U_3/ccp4/aat000_09_05.200_v1_3 -make_frags False -F F_XDSdataset -SIGF SIGF_XDSdataset -FREE FreeR_flag -early_terminate True -use_shelxe True -use_arpwarp False has failed with error message Traceback (most recent call last): File /home/rob/Xstal_Programs/ccp4v640/destination/ccp4-6.4.0/bin/ample, line 838, in summary = amopt.final_summary() File /home/rob/Xstal_Programs/ccp4v640/destination/ccp4-6.4.0/share/ample/python/ample_options.py, line 197, in final_summary result_summary.append( getattr( result, title2attr[ h ] ) ) KeyError: 'SHELXE_ACL' Any thoughts on how I might troubleshoot this? Thanks and Best wishes, Rob -- Scanned by iCritical.
[ccp4bb] AMPLE failure
Hi, I'm trying to run AMPLE from ccp4-6.4.0 on Linux Ubuntu. It looks like it found all the program dependencies that it needs and Rosetta looks like it ran okay and I think MRBUMP looks alright, but then the program stopped with the following error message: MR and shelx DONE ALL DONE (in 1.64101706141 hours) Saved results as file: /home/rob/Crystal/108_B7U_3/ccp4/ROSETTA_MR_1/resultsd.pkl *** * Information from CCP4Interface script *** The program run with command: /home/rob/Xstal_Programs/ccp4v640/destination/ccp4-6.4.0/bin/ccp4-python -u /home/rob/Xstal_Programs/ccp4v640/destination/ccp4-6.4.0/bin/ample -mtz /home/rob/Crystal/108_B7U_3/ccp4/XDS_ASCII_scaled2.mtz -fasta /home/rob/Crystal/108_B7U_3/phenix/RNK149.fasta -nmodels 1000 -name MVD0 -run_dir /home/rob/Crystal/108_B7U_3/ccp4 -nproc 8 -make_models True -rosetta_dir /home/rob/Xstal_Programs/Rosetta/rosetta-3.5 -frags_3mers /home/rob/Crystal/108_B7U_3/ccp4/aat000_03_05.200_v1_3 -frags_9mers /home/rob/Crystal/108_B7U_3/ccp4/aat000_09_05.200_v1_3 -make_frags False -F F_XDSdataset -SIGF SIGF_XDSdataset -FREE FreeR_flag -early_terminate True -use_shelxe True -use_arpwarp False has failed with error message Traceback (most recent call last): File /home/rob/Xstal_Programs/ccp4v640/destination/ccp4-6.4.0/bin/ample, line 838, in summary = amopt.final_summary() File /home/rob/Xstal_Programs/ccp4v640/destination/ccp4-6.4.0/share/ample/python/ample_options.py, line 197, in final_summary result_summary.append( getattr( result, title2attr[ h ] ) ) KeyError: 'SHELXE_ACL' Any thoughts on how I might troubleshoot this? Thanks and Best wishes, Rob
Re: [ccp4bb] AMPLE failure
Dear Rob, Sorry to hear that this issue has affected you - it's a known bug which will be fixed in the next ccp4 update. AMPLE has run to completion but crashed printing out the results. To see the results, you can run the following command at the terminal (command-line): /home/rob/Xstal_Programs/ccp4v640/destination/ccp4-6.4.0/bin/ccp4-python /home/rob/Xstal_Programs/ccp4v640/destination/ccp4-6.4.0/share/ample/python/mrbump_results.py /home/rob/Crystal/108_B7U_3/ccp4/ROSETTA_MR_1/MRBUMP/cluster_1 If that doesn't work or you need any additional help, please contact me off-list. Best wishes, Jens From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Robert Kirchdoerfer [rkirc...@scripps.edu] Sent: 12 July 2014 18:58 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] AMPLE failure Hi, I'm trying to run AMPLE from ccp4-6.4.0 on Linux Ubuntu. It looks like it found all the program dependencies that it needs and Rosetta looks like it ran okay and I think MRBUMP looks alright, but then the program stopped with the following error message: MR and shelx DONE ALL DONE (in 1.64101706141 hours) Saved results as file: /home/rob/Crystal/108_B7U_3/ccp4/ROSETTA_MR_1/resultsd.pkl *** * Information from CCP4Interface script *** The program run with command: /home/rob/Xstal_Programs/ccp4v640/destination/ccp4-6.4.0/bin/ccp4-python -u /home/rob/Xstal_Programs/ccp4v640/destination/ccp4-6.4.0/bin/ample -mtz /home/rob/Crystal/108_B7U_3/ccp4/XDS_ASCII_scaled2.mtz -fasta /home/rob/Crystal/108_B7U_3/phenix/RNK149.fasta -nmodels 1000 -name MVD0 -run_dir /home/rob/Crystal/108_B7U_3/ccp4 -nproc 8 -make_models True -rosetta_dir /home/rob/Xstal_Programs/Rosetta/rosetta-3.5 -frags_3mers /home/rob/Crystal/108_B7U_3/ccp4/aat000_03_05.200_v1_3 -frags_9mers /home/rob/Crystal/108_B7U_3/ccp4/aat000_09_05.200_v1_3 -make_frags False -F F_XDSdataset -SIGF SIGF_XDSdataset -FREE FreeR_flag -early_terminate True -use_shelxe True -use_arpwarp False has failed with error message Traceback (most recent call last): File /home/rob/Xstal_Programs/ccp4v640/destination/ccp4-6.4.0/bin/ample, line 838, in summary = amopt.final_summary() File /home/rob/Xstal_Programs/ccp4v640/destination/ccp4-6.4.0/share/ample/python/ample_options.py, line 197, in final_summary result_summary.append( getattr( result, title2attr[ h ] ) ) KeyError: 'SHELXE_ACL' Any thoughts on how I might troubleshoot this? Thanks and Best wishes, Rob
[ccp4bb] Ample fails
Dear all, I'm trying to use Ample from CCP4 (6.4) to solve a structure of 2x197 residues from 2.0 A data. After the generation of initial (120) models by Rosetta (3.3) Ample stops with the error-message below. Could anyone provide me information about the origin of this error and possibly how to solve the problem? Thanks in advance for your replies! Best wishes, Florian *** * Information from CCP4Interface script *** The program run with command: /home/flo/crystallography/ccp4-6.4.0/bin/ccp4-python -u /home/flo/crystallography/ccp4-6.4.0/bin/ample -mtz /home/flo/crystallography/Virchow/ESRF_20140707/CM133A/ccp4/pos5wedge3scaled.mtz -fasta /home/flo/Desktop/arch.seq -name MVD0 -run_dir /home/flo/crystallography/Virchow/ESRF_20140707/pos7au/ccp4 -nproc 3 -F F_XDSdataset -SIGF SIGF_XDSdataset -FREE FreeR_flag -models_dir /home/flo/crystallography/Virchow/ESRF_20140707/pos7au/ccp4/ROSETTA_MR_0/models/models_1 -early_terminate True -use_shelxe True -use_arpwarp False has failed with error message Traceback (most recent call last): File /home/flo/crystallography/ccp4-6.4.0/bin/ample, line 757, in ensemble.create_ensembles( amopt.d ) File /home/flo/crystallography/ccp4-6.4.0/share/ample/python/ensemble.py, line 85, in create_ensembles ensembles = ensemble_models( amoptd['spicker_results'][ cluster-1 ].pdb_list, amoptd, ensemble_id=cluster ) File /home/flo/crystallography/ccp4-6.4.0/share/ample/python/ensemble.py, line 58, in ensemble_models percent=amoptd['percent'] ) File /home/flo/crystallography/ccp4-6.4.0/share/ample/python/ample_ensemble.py, line 168, in generate_ensembles self.make_truncated_ensembles() File /home/flo/crystallography/ccp4-6.4.0/share/ample/python/ample_ensemble.py, line 312, in make_truncated_ensembles clusterer.generate_distance_matrix( self.truncated_models[tcount] ) File /home/flo/crystallography/ccp4-6.4.0/share/ample/python/cluster_with_MAX.py, line 55, in generate_distance_matrix retcode = ample_util.run_command( cmd, logfile=log_name ) File /home/flo/crystallography/ccp4-6.4.0/share/ample/python/ample_util.py, line 274, in run_command p = subprocess.Popen( cmd, stdin=stdin, stdout=logf, stderr=subprocess.STDOUT, cwd=directory, **kwargs ) File /home/flo/crystallography/ccp4-6.4.0/lib/python2.7/subprocess.py, line 711, in __init__ errread, errwrite) File /home/flo/crystallography/ccp4-6.4.0/lib/python2.7/subprocess.py, line 1308, in _execute_child raise child_exception OSError: [Errno 8] Exec format error *** -- Dr. Florian Sauer Rudolf Virchow Zentrum für Experimentelle Biomedizin Josef-Schneider-Str. 2, Haus D15 97080 Würzburg
Re: [ccp4bb] Ample fails
Dear Florian, Sorry to hear that Ample isn't working for you. I haven't seen this error before, but my initial guess would be that you're trying to run Ample on Windows? If so then unfortunately the current release of Ample isn't supported on Windows. Most of the work to port Ample to Windows has been carried out, and it will be made available in a forthcoming release of CCP4, but until then the only solution is to run Ample on Linux or Mac OSX. If you're not running on Windows, please could you send me (off list) the file debug.log, which should have been created in the directory: /home/flo/crystallography/Virchow/ESRF_20140707/pos7au/ccp4/ROSETTA_MR_0 (the directory may be named ROSETTA_MR_0, ROSETTA_MR_1, ROSETTA_MR_2... etc. depending on how many runs you have attempted.) Just for information, at 197 residues your protein is on the large side (although well within the bounds of what Ample is capable of solving), but 120 models is far fewer then we would normally recommend. The usual recommendation is to make at least 1000 models. Best wishes, Jens From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Florian Sauer [florian.sau...@virchow.uni-wuerzburg.de] Sent: 11 July 2014 08:37 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Ample fails Dear all, I'm trying to use Ample from CCP4 (6.4) to solve a structure of 2x197 residues from 2.0 A data. After the generation of initial (120) models by Rosetta (3.3) Ample stops with the error-message below. Could anyone provide me information about the origin of this error and possibly how to solve the problem? Thanks in advance for your replies! Best wishes, Florian *** * Information from CCP4Interface script *** The program run with command: /home/flo/crystallography/ccp4-6.4.0/bin/ccp4-python -u /home/flo/crystallography/ccp4-6.4.0/bin/ample -mtz /home/flo/crystallography/Virchow/ESRF_20140707/CM133A/ccp4/pos5wedge3scaled.mtz -fasta /home/flo/Desktop/arch.seq -name MVD0 -run_dir /home/flo/crystallography/Virchow/ESRF_20140707/pos7au/ccp4 -nproc 3 -F F_XDSdataset -SIGF SIGF_XDSdataset -FREE FreeR_flag -models_dir /home/flo/crystallography/Virchow/ESRF_20140707/pos7au/ccp4/ROSETTA_MR_0/models/models_1 -early_terminate True -use_shelxe True -use_arpwarp False has failed with error message Traceback (most recent call last): File /home/flo/crystallography/ccp4-6.4.0/bin/ample, line 757, in ensemble.create_ensembles( amopt.d ) File /home/flo/crystallography/ccp4-6.4.0/share/ample/python/ensemble.py, line 85, in create_ensembles ensembles = ensemble_models( amoptd['spicker_results'][ cluster-1 ].pdb_list, amoptd, ensemble_id=cluster ) File /home/flo/crystallography/ccp4-6.4.0/share/ample/python/ensemble.py, line 58, in ensemble_models percent=amoptd['percent'] ) File /home/flo/crystallography/ccp4-6.4.0/share/ample/python/ample_ensemble.py, line 168, in generate_ensembles self.make_truncated_ensembles() File /home/flo/crystallography/ccp4-6.4.0/share/ample/python/ample_ensemble.py, line 312, in make_truncated_ensembles clusterer.generate_distance_matrix( self.truncated_models[tcount] ) File /home/flo/crystallography/ccp4-6.4.0/share/ample/python/cluster_with_MAX.py, line 55, in generate_distance_matrix retcode = ample_util.run_command( cmd, logfile=log_name ) File /home/flo/crystallography/ccp4-6.4.0/share/ample/python/ample_util.py, line 274, in run_command p = subprocess.Popen( cmd, stdin=stdin, stdout=logf, stderr=subprocess.STDOUT, cwd=directory, **kwargs ) File /home/flo/crystallography/ccp4-6.4.0/lib/python2.7/subprocess.py, line 711, in __init__ errread, errwrite) File /home/flo/crystallography/ccp4-6.4.0/lib/python2.7/subprocess.py, line 1308, in _execute_child raise child_exception OSError: [Errno 8] Exec format error *** -- Dr. Florian Sauer Rudolf Virchow Zentrum für Experimentelle Biomedizin Josef-Schneider-Str. 2, Haus D15 97080 Würzburg
[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