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 ========= ========= ========= ========= =========