Re: [ccp4bb] Phaser going into infinite loop in Ample
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Thanks for all the help! We will restart the job with the KILL option as Jens suggested. We will also send a copy of the Phaser log file to Randy. This is not a case of Phaser simply trying harder - it is doing the same search over and over again. After four days the log file is getting pretty long. I may have to use DropBox. We considered trying ARCIMBOLDO but the resolution of the data did not reach the 2.1 A limit usually suggested for that program. If we get AMPLE running, and it fails, we will give ARCIMBOLDO a try. Dale Tronrud Sarah Clark On 4/22/2015 2:06 AM, Thomas, Jens wrote: Dear Dale, This is a known issue with AMPLE and will be fixed with the next release. In the meantime you can tell AMPLE to pass the KILL option that Randy mentions to PHASER, by adding the following arguments to your script: -mr_keys PKEY KILL TIME 360 this will kill PHASER after 360 minutes (6 hours), which we've found if normally enough, although pick whatever time works for you, I should also point out that I think George is doing a disservice to SHELXE. In our last paper looking at coiled-coils, we saw successes at resolutions much lower than 2.1, in one case, AMPLE was able to solve a structure with a resolution of 2.9A: http://dx.doi.org/10.1107/S2052252515002080 If you have any issues getting the KILL command to work, please feel free to contact me off-list. Best wishes, Jens From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Randy Read [rj...@cam.ac.uk] Sent: 22 April 2015 09:04 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Phaser going into infinite loop in Ample Hi Dale, It must actually be AMPLE deciding how many copies to search for. Phaser will give you some information about how consistent the specified composition is with the Matthews volume, but it just searches for the number of copies that it's instructed to look for. We haven't put the intelligence into it to correlate the model(s) with the composition information and try out different possibilities. At the moment, we're leaving that level of analysis to pipelines like MRage. We're well aware of the tension between looking hard enough to find a solution in a difficult case and not throwing good CPU cycles after bad when it's hopeless. We're gradually introducing new features to make these decisions better, but we do tend to prefer wasting CPU time to missing solutions. However, we've introduced a couple of ways to limit the amount of time that Phaser spends pursuing very difficult or hopeless solutions, partly for the benefit of people such as the developers of Arcimboldo, AMPLE and the wide-search molecular replacement pipeline. One is the KILL command, which is a rather blunt instrument saying to give up if a solution isn't found in a certain length of time. In AMPLE, if you set quick mode, then the KILL time is set to 15 minutes. Another option (which I don't think AMPLE uses) is the PURGE command, where you can say (for instance) that Phaser should pursue a maximum of 25 partial solutions when adding the next component. If you're seeing an infinite loop, it would be handy if you could send me a copy of the logfile showing what is going on. There have been some bugs leading to such infinite loops under some circumstances, and if you're running into one of those there's a good chance that it has been fixed in a recent nightly build of Phaser available through Phenix. You can instruct CCP4 to use the Phaser executable from Phenix, and I think this should work fine in AMPLE, though I haven't tested it — I don't think any relevant syntax has changed. It's been a while since we've had a new stable release of Phaser in either CCP4 or Phenix, so we're aiming to get one out in the not too distant future. All the best, Randy On 22 Apr 2015, at 05:56, Dale Tronrud de...@daletronrud.com wrote: We are having a problem with AMPLE and hope someone can help. The protein is about 70 amino acids long and we suspect it forms a coiled-coil. Our previous attempts at molecular replacement have failed so we hoped that AMPLE, with its ability to generate a variety of potential models, would do the trick. Our problem is that all of our CPU cores are consumed by Phaser jobs that are not making progress. With this protein Phaser decides that it will look for 11 copies in the asymmetric unit. For a few of the possible ensembles it fails to find even one copy and gives up. That's fine with us. For other ensembles it finds a handful of possible first positions, goes on to look for a second and fails, then goes back to try to place a second copy again. We presume that the intent is to lower the acceptance criteria in the second pass, but in actuality Phaser simply repeats the same search that failed before and fails again
Re: [ccp4bb] Phaser going into infinite loop in Ample
Hi Dale, It must actually be AMPLE deciding how many copies to search for. Phaser will give you some information about how consistent the specified composition is with the Matthews volume, but it just searches for the number of copies that it's instructed to look for. We haven't put the intelligence into it to correlate the model(s) with the composition information and try out different possibilities. At the moment, we're leaving that level of analysis to pipelines like MRage. We're well aware of the tension between looking hard enough to find a solution in a difficult case and not throwing good CPU cycles after bad when it's hopeless. We're gradually introducing new features to make these decisions better, but we do tend to prefer wasting CPU time to missing solutions. However, we've introduced a couple of ways to limit the amount of time that Phaser spends pursuing very difficult or hopeless solutions, partly for the benefit of people such as the developers of Arcimboldo, AMPLE and the wide-search molecular replacement pipeline. One is the KILL command, which is a rather blunt instrument saying to give up if a solution isn't found in a certain length of time. In AMPLE, if you set quick mode, then the KILL time is set to 15 minutes. Another option (which I don't think AMPLE uses) is the PURGE command, where you can say (for instance) that Phaser should pursue a maximum of 25 partial solutions when adding the next component. If you're seeing an infinite loop, it would be handy if you could send me a copy of the logfile showing what is going on. There have been some bugs leading to such infinite loops under some circumstances, and if you're running into one of those there's a good chance that it has been fixed in a recent nightly build of Phaser available through Phenix. You can instruct CCP4 to use the Phaser executable from Phenix, and I think this should work fine in AMPLE, though I haven't tested it — I don't think any relevant syntax has changed. It's been a while since we've had a new stable release of Phaser in either CCP4 or Phenix, so we're aiming to get one out in the not too distant future. All the best, Randy On 22 Apr 2015, at 05:56, Dale Tronrud de...@daletronrud.com wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 We are having a problem with AMPLE and hope someone can help. The protein is about 70 amino acids long and we suspect it forms a coiled-coil. Our previous attempts at molecular replacement have failed so we hoped that AMPLE, with its ability to generate a variety of potential models, would do the trick. Our problem is that all of our CPU cores are consumed by Phaser jobs that are not making progress. With this protein Phaser decides that it will look for 11 copies in the asymmetric unit. For a few of the possible ensembles it fails to find even one copy and gives up. That's fine with us. For other ensembles it finds a handful of possible first positions, goes on to look for a second and fails, then goes back to try to place a second copy again. We presume that the intent is to lower the acceptance criteria in the second pass, but in actuality Phaser simply repeats the same search that failed before and fails again. The leads to an infinite loop. Once all the cores are occupied in this futile endeavor AMPLE makes no further progress. How can we get Phaser to either try harder to place a molecule or to give up? We are using CCP4 6.5.008 and the copy of Phaser that came with it. We used CCP4i to create a script which we modified slightly and ran using the at command. The command is: /usr/local/ccp4-6.5/bin/ccp4-python -u /usr/local/ccp4-6.5/bin/ample - -mtz /user/sarah/xray/1Apr_Athena/SD6004_2_001_mergedunique14.mtz - -fasta /user/sarah/xray/1Apr_Athena/swaseq.fa -mr_sequence /user/sarah/xray/1Apr_Athena/swaseq.fa -nmodels 500 -name MVD0 - -run_dir /home/sarah/AMPLE -nproc 6 -make_models True -rosetta_dir /usr/local/rosetta-3.5 -frags_3mers /user/sarah/xray/1Apr_Athena/aat000_03_05.200_v1_3 -frags_9mers /user/sarah/xray/1Apr_Athena/aat000_09_05.200_v1_3 -make_frags False - -F F -SIGF SIGF -FREE FreeR_flag -early_terminate True -use_shelxe True -shelx_cycles 15 -use_arpwarp False Any help is appreciated, Dale Tronrud Sarah Clark -BEGIN PGP SIGNATURE- Version: GnuPG v2.0.22 (MingW32) iEYEARECAAYFAlU3KhEACgkQU5C0gGfAG117JACfXahEX8z1k3ev043a7V2SzhNh p6UAnAmKkUZe46zbiXckdDTNgUQ0dgWq =A/Sj -END PGP SIGNATURE- -- 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] Phaser going into infinite loop in Ample
Dear Dale, Isabel Uson's ARCIMBOLDO-LITE works well for coiled coils and has the same resolution requirements (2.1A or better) as AMPLE because both use SHELXE to expand the solution. It also employs PHASER to place a small fragment but it is often sufficient to let it search for just two or three copies in the asymmetric unit. Best wishes, George On 04/22/2015 06:56 AM, Dale Tronrud wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 We are having a problem with AMPLE and hope someone can help. The protein is about 70 amino acids long and we suspect it forms a coiled-coil. Our previous attempts at molecular replacement have failed so we hoped that AMPLE, with its ability to generate a variety of potential models, would do the trick. Our problem is that all of our CPU cores are consumed by Phaser jobs that are not making progress. With this protein Phaser decides that it will look for 11 copies in the asymmetric unit. For a few of the possible ensembles it fails to find even one copy and gives up. That's fine with us. For other ensembles it finds a handful of possible first positions, goes on to look for a second and fails, then goes back to try to place a second copy again. We presume that the intent is to lower the acceptance criteria in the second pass, but in actuality Phaser simply repeats the same search that failed before and fails again. The leads to an infinite loop. Once all the cores are occupied in this futile endeavor AMPLE makes no further progress. How can we get Phaser to either try harder to place a molecule or to give up? We are using CCP4 6.5.008 and the copy of Phaser that came with it. We used CCP4i to create a script which we modified slightly and ran using the at command. The command is: /usr/local/ccp4-6.5/bin/ccp4-python -u /usr/local/ccp4-6.5/bin/ample - -mtz /user/sarah/xray/1Apr_Athena/SD6004_2_001_mergedunique14.mtz - -fasta /user/sarah/xray/1Apr_Athena/swaseq.fa -mr_sequence /user/sarah/xray/1Apr_Athena/swaseq.fa -nmodels 500 -name MVD0 - -run_dir /home/sarah/AMPLE -nproc 6 -make_models True -rosetta_dir /usr/local/rosetta-3.5 -frags_3mers /user/sarah/xray/1Apr_Athena/aat000_03_05.200_v1_3 -frags_9mers /user/sarah/xray/1Apr_Athena/aat000_09_05.200_v1_3 -make_frags False - -F F -SIGF SIGF -FREE FreeR_flag -early_terminate True -use_shelxe True -shelx_cycles 15 -use_arpwarp False Any help is appreciated, Dale Tronrud Sarah Clark -BEGIN PGP SIGNATURE- Version: GnuPG v2.0.22 (MingW32) iEYEARECAAYFAlU3KhEACgkQU5C0gGfAG117JACfXahEX8z1k3ev043a7V2SzhNh p6UAnAmKkUZe46zbiXckdDTNgUQ0dgWq =A/Sj -END PGP SIGNATURE- -- Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-33021 or -33068 Fax. +49-551-39-22582
Re: [ccp4bb] Phaser going into infinite loop in Ample
Dear Dale, as George points out, you may be interested in trying ARCIMBOLDO, as it has been successfully applied to coiled coil proteins recently, as in the case of Franke et al (2014) Open Biology, 4. p. 130172 or Sammito et al (2013) Nature Methods 10: 1099-1101 . Different models can be searched for, starting from single helices with or without sidechains, going to precomputed libraries of helices in parallel or antiparallel configurations. If you need help or support to use it, please feel free to ask any question. Best wishes, Claudia Claudia Millán 2015-04-22 6:56 GMT+02:00 Dale Tronrud de...@daletronrud.com: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 We are having a problem with AMPLE and hope someone can help. The protein is about 70 amino acids long and we suspect it forms a coiled-coil. Our previous attempts at molecular replacement have failed so we hoped that AMPLE, with its ability to generate a variety of potential models, would do the trick. Our problem is that all of our CPU cores are consumed by Phaser jobs that are not making progress. With this protein Phaser decides that it will look for 11 copies in the asymmetric unit. For a few of the possible ensembles it fails to find even one copy and gives up. That's fine with us. For other ensembles it finds a handful of possible first positions, goes on to look for a second and fails, then goes back to try to place a second copy again. We presume that the intent is to lower the acceptance criteria in the second pass, but in actuality Phaser simply repeats the same search that failed before and fails again. The leads to an infinite loop. Once all the cores are occupied in this futile endeavor AMPLE makes no further progress. How can we get Phaser to either try harder to place a molecule or to give up? We are using CCP4 6.5.008 and the copy of Phaser that came with it. We used CCP4i to create a script which we modified slightly and ran using the at command. The command is: /usr/local/ccp4-6.5/bin/ccp4-python -u /usr/local/ccp4-6.5/bin/ample - -mtz /user/sarah/xray/1Apr_Athena/SD6004_2_001_mergedunique14.mtz - -fasta /user/sarah/xray/1Apr_Athena/swaseq.fa -mr_sequence /user/sarah/xray/1Apr_Athena/swaseq.fa -nmodels 500 -name MVD0 - -run_dir /home/sarah/AMPLE -nproc 6 -make_models True -rosetta_dir /usr/local/rosetta-3.5 -frags_3mers /user/sarah/xray/1Apr_Athena/aat000_03_05.200_v1_3 -frags_9mers /user/sarah/xray/1Apr_Athena/aat000_09_05.200_v1_3 -make_frags False - -F F -SIGF SIGF -FREE FreeR_flag -early_terminate True -use_shelxe True -shelx_cycles 15 -use_arpwarp False Any help is appreciated, Dale Tronrud Sarah Clark -BEGIN PGP SIGNATURE- Version: GnuPG v2.0.22 (MingW32) iEYEARECAAYFAlU3KhEACgkQU5C0gGfAG117JACfXahEX8z1k3ev043a7V2SzhNh p6UAnAmKkUZe46zbiXckdDTNgUQ0dgWq =A/Sj -END PGP SIGNATURE-
Re: [ccp4bb] Phaser going into infinite loop in Ample
Dear Dale, This is a known issue with AMPLE and will be fixed with the next release. In the meantime you can tell AMPLE to pass the KILL option that Randy mentions to PHASER, by adding the following arguments to your script: -mr_keys PKEY KILL TIME 360 this will kill PHASER after 360 minutes (6 hours), which we've found if normally enough, although pick whatever time works for you, I should also point out that I think George is doing a disservice to SHELXE. In our last paper looking at coiled-coils, we saw successes at resolutions much lower than 2.1, in one case, AMPLE was able to solve a structure with a resolution of 2.9A: http://dx.doi.org/10.1107/S2052252515002080 If you have any issues getting the KILL command to work, please feel free to contact me off-list. Best wishes, Jens From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Randy Read [rj...@cam.ac.uk] Sent: 22 April 2015 09:04 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Phaser going into infinite loop in Ample Hi Dale, It must actually be AMPLE deciding how many copies to search for. Phaser will give you some information about how consistent the specified composition is with the Matthews volume, but it just searches for the number of copies that it's instructed to look for. We haven't put the intelligence into it to correlate the model(s) with the composition information and try out different possibilities. At the moment, we're leaving that level of analysis to pipelines like MRage. We're well aware of the tension between looking hard enough to find a solution in a difficult case and not throwing good CPU cycles after bad when it's hopeless. We're gradually introducing new features to make these decisions better, but we do tend to prefer wasting CPU time to missing solutions. However, we've introduced a couple of ways to limit the amount of time that Phaser spends pursuing very difficult or hopeless solutions, partly for the benefit of people such as the developers of Arcimboldo, AMPLE and the wide-search molecular replacement pipeline. One is the KILL command, which is a rather blunt instrument saying to give up if a solution isn't found in a certain length of time. In AMPLE, if you set quick mode, then the KILL time is set to 15 minutes. Another option (which I don't think AMPLE uses) is the PURGE command, where you can say (for instance) that Phaser should pursue a maximum of 25 partial solutions when adding the next component. If you're seeing an infinite loop, it would be handy if you could send me a copy of the logfile showing what is going on. There have been some bugs leading to such infinite loops under some circumstances, and if you're running into one of those there's a good chance that it has been fixed in a recent nightly build of Phaser available through Phenix. You can instruct CCP4 to use the Phaser executable from Phenix, and I think this should work fine in AMPLE, though I haven't tested it — I don't think any relevant syntax has changed. It's been a while since we've had a new stable release of Phaser in either CCP4 or Phenix, so we're aiming to get one out in the not too distant future. All the best, Randy On 22 Apr 2015, at 05:56, Dale Tronrud de...@daletronrud.com wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 We are having a problem with AMPLE and hope someone can help. The protein is about 70 amino acids long and we suspect it forms a coiled-coil. Our previous attempts at molecular replacement have failed so we hoped that AMPLE, with its ability to generate a variety of potential models, would do the trick. Our problem is that all of our CPU cores are consumed by Phaser jobs that are not making progress. With this protein Phaser decides that it will look for 11 copies in the asymmetric unit. For a few of the possible ensembles it fails to find even one copy and gives up. That's fine with us. For other ensembles it finds a handful of possible first positions, goes on to look for a second and fails, then goes back to try to place a second copy again. We presume that the intent is to lower the acceptance criteria in the second pass, but in actuality Phaser simply repeats the same search that failed before and fails again. The leads to an infinite loop. Once all the cores are occupied in this futile endeavor AMPLE makes no further progress. How can we get Phaser to either try harder to place a molecule or to give up? We are using CCP4 6.5.008 and the copy of Phaser that came with it. We used CCP4i to create a script which we modified slightly and ran using the at command. The command is: /usr/local/ccp4-6.5/bin/ccp4-python -u /usr/local/ccp4-6.5/bin/ample - -mtz /user/sarah/xray/1Apr_Athena/SD6004_2_001_mergedunique14.mtz - -fasta /user/sarah/xray/1Apr_Athena/swaseq.fa -mr_sequence /user/sarah/xray/1Apr_Athena/swaseq.fa -nmodels 500 -name MVD0
[ccp4bb] Phaser going into infinite loop in Ample
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 We are having a problem with AMPLE and hope someone can help. The protein is about 70 amino acids long and we suspect it forms a coiled-coil. Our previous attempts at molecular replacement have failed so we hoped that AMPLE, with its ability to generate a variety of potential models, would do the trick. Our problem is that all of our CPU cores are consumed by Phaser jobs that are not making progress. With this protein Phaser decides that it will look for 11 copies in the asymmetric unit. For a few of the possible ensembles it fails to find even one copy and gives up. That's fine with us. For other ensembles it finds a handful of possible first positions, goes on to look for a second and fails, then goes back to try to place a second copy again. We presume that the intent is to lower the acceptance criteria in the second pass, but in actuality Phaser simply repeats the same search that failed before and fails again. The leads to an infinite loop. Once all the cores are occupied in this futile endeavor AMPLE makes no further progress. How can we get Phaser to either try harder to place a molecule or to give up? We are using CCP4 6.5.008 and the copy of Phaser that came with it. We used CCP4i to create a script which we modified slightly and ran using the at command. The command is: /usr/local/ccp4-6.5/bin/ccp4-python -u /usr/local/ccp4-6.5/bin/ample - -mtz /user/sarah/xray/1Apr_Athena/SD6004_2_001_mergedunique14.mtz - -fasta /user/sarah/xray/1Apr_Athena/swaseq.fa -mr_sequence /user/sarah/xray/1Apr_Athena/swaseq.fa -nmodels 500 -name MVD0 - -run_dir /home/sarah/AMPLE -nproc 6 -make_models True -rosetta_dir /usr/local/rosetta-3.5 -frags_3mers /user/sarah/xray/1Apr_Athena/aat000_03_05.200_v1_3 -frags_9mers /user/sarah/xray/1Apr_Athena/aat000_09_05.200_v1_3 -make_frags False - -F F -SIGF SIGF -FREE FreeR_flag -early_terminate True -use_shelxe True -shelx_cycles 15 -use_arpwarp False Any help is appreciated, Dale Tronrud Sarah Clark -BEGIN PGP SIGNATURE- Version: GnuPG v2.0.22 (MingW32) iEYEARECAAYFAlU3KhEACgkQU5C0gGfAG117JACfXahEX8z1k3ev043a7V2SzhNh p6UAnAmKkUZe46zbiXckdDTNgUQ0dgWq =A/Sj -END PGP SIGNATURE-
