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:
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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
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--
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
