Dear Greg,
Try ARP/wARP 7.2, released a few days ago, which is better, more
stable and should have improved flash of error messages to the log
files.
ARP/wARP Loopy will not build a 33-residue loop at once, but Classic
model building may get the gap shortened.
Go to www.arp-warp.org for download. In parallel, from the same page
you can submit Classic protein model building for remote execution in
Hamburg, which also has ARP/wARP 7.2 installed.
Please get back if problems remain.
With best regards,
Victor
Quoting "Gregory Bowman" <[log in to unmask]>:
> Hi all,
>
> I have a large disordered loop (33aa) for a 2.0 Å dataset for which
> the rest of the structure is well-defined, and phases are decent
> (Rwork=19.6, Rfree=24.6). I can see some broken up density at one
> end, but have been unable to convincingly build into into this
> region manually. I would like to try arp/warp to improve density or
> possibly extend the loop termini but have been thwarted by some
> technical problems and would appreciate any advice. I've installed
> ccp4 6.2.0 on Mac OS X (10.6.8) with fink, both as 32-bit and 64-bit
> to allow me to run ARP/wARP (version 7.1) from the ccp4i GUI. I've
> been unable to get "loopy" to work, and also the standard ARP/wARP
> classic.
>
> When I run "ARP/wARP Loops" (a.k.a. loopy), I get the message in
> the log file: "Couldn't find any loop to build, loopy will simple
> copy the pdb file". The program is able to read the sequence .pir
> file and match it to the structure, and seems from the sequence
> alignment to identify the regions of the sequence for which there is
> no structure. I'm guessing that I'm not putting some obvious
> parameter into the GUI/starting script, but I don't know what that
> might be. The script generated from the GUI (21_loopy.def) is pasted
> below.
>
> When I try to run ARP/wARP classic for loop building, I get the
> following message in the logfile:
>
> QUITTING ... ARP/wARP module stopped with an error message:
> REFMAC
> *** Look for error message in the file:
> /Users/gbowman/Greg/20_warpNtrace_refine.last.log
>
> At the end of the warpNtrace_refine.last.log file, the program
> reports what seem to be close contacts. Since I don't see this in
> the structure, and don't have any problems or errors like this when
> I refine the structure with REMAC, is this from rebuilding, and is
> this the problem that halts REFMAC?
>
> Thanks!
> Greg
>
> ========= ========= ========= ========= ========= =========
> 20_warpNtrace_refine.last.log
> ========= ========= ========= ========= ========= =========
> <snip>
> Input file :restraints.pdb
> NUMBER OF MONOMERS IN THE LIBRARY : 11465
> with complete description : 11465
> NUMBER OF MODIFICATIONS : 53
> NUMBER OF LINKS : 66
> I am reading libraries. Please wait.
> - energy parameters
> - monomer"s description (links & mod )
> <B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
> <!--SUMMARY_END--></FONT></B>
> Number of atoms : 2463
> Number of residues : 859
> Number of chains : 3
> I am reading library. Please wait.
> mon_lib.cif
> INFO: link is found (not be used) dist= 1.907 ideal_dist= 1.432
> ch:AA res: 8 GLY at:CA .->ch:AA res: 50
> TYR at:OH .
> INFO: link is found (not be used) dist= 2.126 ideal_dist= 1.645
> ch:AA res: 13 ARG at:NH1 .->ch:AA res: 54
> MET at:SD .
> INFO: link is found (not be used) dist= 1.820 ideal_dist= 1.462
> ch:AA res: 13 ARG at:NH1 .->ch:AA res: 54
> MET at:CE .
> INFO: link is found (not be used) dist= 1.757 ideal_dist= 1.395
> ch:AA res: 13 ARG at:NE .->ch:AA res: 119
> PHE at:CD1 .
> INFO: link is found (not be used) dist= 1.572 ideal_dist= 1.462
> ch:AA res: 13 ARG at:NH2 .->ch:AA res: 125
> LEU at:CD2 .
> INFO: link is found (not be used) dist= 1.751 ideal_dist= 1.513
> ch:AA res: 33 ILE at:CG2 .->ch:AA res: 39
> PRO at:CG .
> INFO: link is found (not be used) dist= 1.451 ideal_dist= 1.513
> ch:AA res: 33 ILE at:CG2 .->ch:AA res: 39
> PRO at:CD .
> INFO: link is found (not be used) dist= 1.759 ideal_dist= 1.524
> ch:AA res: 58 LYS at:CD .->ch:AA res: 130
> LEU at:CB .
> INFO: link is found (not be used) dist= 1.725 ideal_dist= 1.513
> ch:AA res: 58 LYS at:CD .->ch:AA res: 130
> LEU at:CD1 .
> INFO: link is found (not be used) dist= 1.578 ideal_dist= 1.524
> ch:AA res: 83 ARG at:CD .->ch:AA res: 101
> PRO at:CG .
> INFO: link is found (not be used) dist= 1.843 ideal_dist= 1.457
> ch:AA res: 83 ARG at:NE .->ch:AA res: 101
> PRO at:CB .
> INFO: link is found (not be used) dist= 0.666 ideal_dist= 1.457
> ch:AA res: 83 ARG at:NE .->ch:AA res: 101
> PRO at:CG .
> INFO: link is found (not be used) dist= 1.275 ideal_dist= 1.510
> ch:AA res: 83 ARG at:CZ .->ch:AA res: 101
> PRO at:CB .
> INFO: link is found (not be used) dist= 1.102 ideal_dist= 1.510
> ch:AA res: 83 ARG at:CZ .->ch:AA res: 101
> PRO at:CG .
> INFO: link is found (not be used) dist= 1.191 ideal_dist= 1.457
> ch:AA res: 83 ARG at:NH1 .->ch:AA res: 101
> PRO at:CA .
> INFO: link is found (not be used) dist= 0.690 ideal_dist= 1.457
> ch:AA res: 83 ARG at:NH1 .->ch:AA res: 101
> PRO at:CB .
> INFO: link is found (not be used) dist= 1.891 ideal_dist= 1.457
> ch:AA res: 83 ARG at:NH1 .->ch:AA res: 101
> PRO at:CG .
> INFO: link is found (not be used) dist= 1.352 ideal_dist= 1.457
> ch:AA res: 165 VAL at:CG1 .->ch:AA res: 172
> TRP at:CZ3 .
> INFO: link is found (not be used) dist= 1.440 ideal_dist= 1.457
> ch:AA res: 165 VAL at:CG1 .->ch:AA res: 172
> TRP at:CE3 .
> INFO: link is found (not be used) dist= 1.367 ideal_dist= 1.320
> ch:AA res: 172 TRP at:CD1 .->ch:AA res: 176
> GLU at:OE1 .
> INFO: link is found (not be used) dist= 1.447 ideal_dist= 1.275
> ch:AA res: 172 TRP at:NE1 .->ch:AA res: 176
> GLU at:OE1 .
> INFO: link is found (not be used) dist= 1.760 ideal_dist= 1.360
> ch:AA res: 172 TRP at:CH2 .->ch:AA res: 253
> ARG at:CZ .
> INFO: link is found (not be used) dist= 1.690 ideal_dist= 1.309
> ch:AA res: 187 TYR at:OH .->ch:AA res: 198
> ASP at:OD2 .
> --------------------------------
> --- title of input coord file ---
>
> PDB_code:xxxx
> PDB_name:----
> PDB_date:XX-XXX-XX
> --------------------------------
> Number of chains : 3
> Total number of monomers : 859
> Number of atoms : 2463
> Number of missing atoms : 0
> Number of rebuilt atoms : 0
> Number of unknown atoms : 0
> Number of deleted atoms : 0
>
> Number of bonds restraints : 1863
> Number of angles restraints : 2492
> Number of torsions restraints : 1286
> Number of chiralities : 266
> Number of planar groups : 318
>
>
> loop_
> _atom_type_symbol
> _atom_type_scat_Cromer_Mann_a1
> _atom_type_scat_Cromer_Mann_b1
> _atom_type_scat_Cromer_Mann_a2
> _atom_type_scat_Cromer_Mann_b2
> _atom_type_scat_Cromer_Mann_a3
> _atom_type_scat_Cromer_Mann_b3
> _atom_type_scat_Cromer_Mann_a4
> _atom_type_scat_Cromer_Mann_b4
> _atom_type_scat_Cromer_Mann_c
>
>
> N 12.2126 0.0057 3.1322 9.8933 2.0125 28.9975
> 1.1663 0.5826 -11.5290
> C 2.3100 20.8439 1.0200 10.2075 1.5886 0.5687
> 0.8650 51.6512 0.2156
> S 6.9053 1.4679 5.2034 22.2151 1.4379 0.2536
> 1.5863 56.1720 1.0496
> O 3.0485 13.2771 2.2868 5.7011 1.5463 0.3239
> 0.8670 32.9089 0.2508
> ========= ========= ========= ========= ========= =========
>
>
> ========= ========= ========= ========= ========= =========
> 21_loopy.def
> ========= ========= ========= ========= ========= =========
> #CCP4I VERSION CCP4Interface 2.1.0
> #CCP4I SCRIPT DEF loopy
> #CCP4I DATE 25 Aug 2011 08:17:34
> #CCP4I USER gbowman
> #CCP4I JOB_ID 21
> #CCP4I PROJECT GDB210i
> #CCP4I TASKNAME loopy
> #CCP4I LOG_FILE 21_loopy.log
> #CCP4I EDIT_SCRIPT 0
> #CCP4I HTML_LOG 0
> #CCP4I REMOTE 0
> #CCP4I SERVER_HOST localhost
> #CCP4I SERVER_PORT 4441
> #CCP4I DATABASE_SERVER 0
> #CCP4I DATABASE_SERVER_HOST localhost
> #CCP4I DATABASE_SERVER_PORT 0
>
> ABORT_LEVEL 8
> ATOM_RADIUS 0.74
> B_FACTOR 20
> B_FACTOR_SIDE_CHAIN 26
> CA_DISTANCE 3.8
> CA_DISTANCE_ERROR 0.3
> CELL_1 38.670
> CELL_2 61.426
> CELL_3 76.771
> CELL_4 90.00
> CELL_5 104.17
> CELL_6 90.00
> CHECK_FIRST_ANGLE 1
> C_ANCHOR "A 1213"
> DIR_EXT_MAP_FILENAME TEMPORARY
> DIR_LOOPFIT_EXE_FILENAME "Full path.."
> DIR_LOOPFIT_LOG_FILENAME TEMPORARY
> DIR_MAP_FILENAME GDB210i
> DIR_MAP_FROM_MTZ TEMPORARY
> DIR_MESSAGE_FILENAME GDB210i
> DIR_MTZ_FILENAME GDB210i
> DIR_OUTPUT_PDB GDB210i
> DIR_PDB_INPUT_FILENAME GDB210i
> DIR_PRELOOPFIT_PDB TEMPORARY
> DIR_SAVE_LOOP_NAME GDB210i
> DIR_SAVE_PROP_PDB GDB210i
> DIR_SEQIN,0 ""
> DIR_SEQIN,1 GDB210i
> DIR_STRUCTURE_TO_C "Full path.."
> DIR_STRUCTURE_TO_N "Full path.."
> DIR_XML_MESSAGE_FILENAME GDB210i
> DUMMY_REMOVAL_THRESHOLD 0.1
> EXTEND_GAP_SMALLER_THAN 5
> EXTEND_REFINEMENT 0
> EXT_MAP_FILENAME ""
> F1 FWT
> FITTARGET 1
> FORCE_MIN_CAS_KEPT 1
> GRID_NUMBER 378
> GRID_TYPE 0
> INCLUDE_ALL 1
> INCLUDE_CHAINS ""
> KEEP_NEG_DENS_HALFWAY 0
> LIKELIHOOD_THRESHOLD -5
> LOOPFIT_EXE_FILENAME
> /Users/gbowman/Greg/arp_warp_7.1/bin/bin-i386-Darwin/loopfit
> LOOPFIT_LOG_FILENAME loopfit.log
> LOOPS_TO_BUILD A1213(33)A1245
> LOOP_BOTH_WAYS 1
> LOOP_DENSITY_CUTOFF_NO 100
> LOOP_LENGTH 33
> LOOP_MAIN_CHAIN_DENS_NO 12
> LOOP_OVERLAP 0
> LOOP_RMS 0.5
> LOOP_SEQUENCE ""
> LOOP_STRUCTURE_CUTOFF_NO -1
> LOOP_STRUCTURE_MIN_NO 0
> LOOP_STRUCTURE_THRESHOLD -7
> LOOP_TO_C 1
> MAP_FILENAME ""
> MAP_FROM_MTZ 160BDNAmerged2011aug09_loopy2.map
> MAP_INPUT_MODE MTZ
> MAX_DISTANCE_BETWEEN_ANCHORS -1.
> MAX_LOOPS_AFTER_MC_PLANE 50
> MAX_LOOP_LENGTH 15
> MAX_NO_CAS_KEPT 5
> MESSAGE_FILENAME loopy.msg
> MESSAGE_LEVEL 5
> MET_IS_SEL,0 0
> MET_IS_SEL,1 0
> MINIMAL_DISTANCE 0.45
> MODE_LOOPY 0
> MTZ_FILENAME 160BDNAmerged2011aug09_refmacGDB210i-215.mtz
> NMOL,0 1
> NMOL,1 1
> NRES,0 ""
> NRES,1 272
> NRESMOL,0 ""
> NRESMOL,1 272
> NSEQFILES 1
> N_ANCHOR "A 1245"
> OUTPUT_PDB 2011aug24-GDB210i-renameDNA-3_loopy1.pdb
> OVERLAP_REMOVAL_THRESHOLD 0.1
> PDB_INPUT_FILENAME 2011aug24-GDB210i-renameDNA-3_refmac1b.pdb
> PHI PHWT
> PRELOOPFIT_PDB pre_loopfit.pdb
> REFINEMENT 1
> REMOVAL_FACTOR 1.
> SAVE_BEST_NUMBER 2
> SAVE_LOOPS 1
> SAVE_LOOP_BASENAME 2011aug24-GDB210i-renameDNA-3_loop
> SAVE_LOOP_DIR /Users/gbowman/Greg
> SAVE_LOOP_NAME 2011aug24-GDB210i-renameDNA-3_loop1.pdb
> SAVE_LOOP_PROP_BASE 2011aug24-GDB210i-renameDNA-3_proposed
> SAVE_LOOP_PROP_DIR /Users/gbowman/Greg
> SAVE_PROP_PDB 2011aug24-GDB210i-renameDNA-3_proposed1.pdb
> SEQIN,0 ""
> SEQIN,1 160B.pir
> SHELL_THICKNESS 1
> SHOW_DETAILS_DENSITY 0
> SHOW_DETAILS_LIKELIHOOD 0
> SHOW_PRUNING_DETAILS 0
> SPACEGROUP P21
> SPACEGROUP_NUMBER 4
> STRUCTURE_TO_C
> /Users/gbowman/Greg/arp_warp_7.1/bin/bin-i386-Darwin/set_1200_2C_my_0.3b_cos_log.llh
> STRUCTURE_TO_N
> /Users/gbowman/Greg/arp_warp_7.1/bin/bin-i386-Darwin/set_1200_2N_my_0.3b_cos_log.llh
> TITLE "build 1213 loop with loopy"
> USER_SETTING_MAX_NO_CAS 0
> USE_PIR_FILE 1
> WEIGHT_DENSITY 1.
> WEIGHT_DISTANCE 1.
> WEIGHT_STRUCTURE 1.
> XML_MESSAGE_FILENAME loopy.xml
>
> ========= ========= ========= ========= =========
>
>
>
>
>
>
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