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----- >
