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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
> [[log in to unmask]] on behalf of Randy Read [[log in to unmask]]
> Sent: 22 April 2015 09:04 To: [log in to unmask] 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 <[log in to unmask]>
>> 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:
> [log in to unmask] Cambridge CB2 0XY, U.K.
> www-structmed.cimr.cam.ac.uk
>
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