-----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 > [[email protected]] on behalf of Randy Read [[email protected]] > Sent: 22 April 2015 09:04 To: [email protected] 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 <[email protected]> >> 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. 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 > > ------ 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 Road E-mail: > [email protected] Cambridge CB2 0XY, U.K. > www-structmed.cimr.cam.ac.uk > -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.22 (MingW32) iEYEARECAAYFAlU3xz4ACgkQU5C0gGfAG131lwCeK9o+d0NEufpw7Ui8OJroaGRY jvcAoLiw7h1+LIvQQTg6OYt93AYEV+7+ =Xij6 -----END PGP SIGNATURE-----
