October 2004 - modeller_usage

Merge twp alignment files
by HYUN CHUL KIM 04 Nov '04

04 Nov '04

Hi, all I made two alignment files with a threading program other than MODELLER. How can I merge these two alignment files? Each alignment file containts one query sequence and one template sequence. Query sequences from two alignment files are same to each other and have different gaps. Following sequences and gaps are made randomly. file1: 1aaab.ali >P1;source sequence: query : 1: : 700: : target sequence: unknown: : MASNMLDS--------KFLDKLDFJLSDKFLKDFLSJFDLJFLKDJFLDKFLS* >P1;1aaab structure: 1aaab: 100: B : 800: B: template: known structure: : M-ASDFSAFDSADFSAFSDFSADFSAFSAD--ASDFASFDSAD--------* file2: 1bbbc.ali >P1;source sequence: query : 1: : 700: : target sequence: unknown: : MASNMLDSKFLDKLDFJLSDKFLKD----------FLSJFDLJFLKDJFLDKFLS* >P1;1bbbc structure: 1bbbc : 40: C : 700: C : template: known structure: : M-ASDFSAFDSADFSAFSDFSADFSAFSAD--ASDFASFDSAD----------* ******MY TARGET ALIGNMENT FORM********************* >P1;source sequence: query : 1: : 700: : target sequence: unknown: : MASNMLDSKF---LDKLDFJLSDKFLKD--FLSJFDLJFLKDJFLDKFLS* >P1;1aaab structure: 1aaab: 100: B : 800: B: template: known structure: : M-ASDFSAFDSADFSAFSDFSADFSAFSAD--ASDFASFDSAD-----* >P1;1bbbc structure: 1bbbc : 40: C : 700: C : template: known structure: : M-ASDFSAFDSADFSAFSDFSADFSAFSAD--ASDFASFDS-----AD* ****************************************************** Sincerely, Kim

2 1

Frustrating simple problem!
by Joel Tyndall 31 Oct '04

31 Oct '04

Hi folks, I've got a frustrating problem when I try to run a modeller job. I know it works as I've used it previously. I have seen the error before on the bulletin board but can't find the cause of my problem. I get the error: read_al_375E> Unknown residue type,position,sequence: 1 1 I don't have any alt conformations. any help would be great. I have attached the top and ali files. Cheers J -- Joel Tyndall, PhD Lecturer National School of Pharmacy University of Otago PO Box 913 Dunedin New Zealand Ph +64 3 4797293 Fax +64 3 4797034 >P1;UP_ecoli structureX:1rxc:1 : :253 : :unknown:unknown:-1.00:-1.00 MSKSDVFHLGLTKN------DLQGATLAIVPGDPDRVEKIAALMDKPVKLAS-HREFTTW RAELD------GKPVIVCSTGIGGPSTSIAVEELAQLG------IRTFLRIGTTGAIQPH INVGDVLVTTASVR------LDGASLHFAPLEFPAVADFECTTALVEAAKSIGATTHVGV TASSDTFYPGQERYD-TYSGRVVRHFKGSMEEWQAMGVMNYEMESATLLTMCASQGLRAG MVAGVIVNRTQQEIPN--AETMKQTESHAVKIVVEAARRLL* >P1;1uph sequence:uph:1 : :282 : :unknown:unknown:-1.00:-1.00 MKEDILYHFNLTTSRHNFPALFGDVKFVCVGGSPSRMKAFIRCVGAELGLDCPGRDYPNI CAGTDRYAMYKVGPVLSVSHGMGIPSISIMLHELIKLLYYARCSNVTIIRIGTSGGIG-- LEPGTVVITEQAVDTCFKAEFEQIVLGKRVIRKTDLNKKLVQELLLCSAELSEFTTVVGN TMCTLDFYEGQGRLDGALCSYTEKDKQAYLEAAYAAGVRNIEMESSVFAAMCSACGLQAA VVCVTLLNRLEGDQISSPRNVLSEYQQRPQRLVSYFIKKKL* MODELLER 6v2, 17 Feb 2002 PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS Copyright(c) 1989-2002 Andrej Sali All Rights Reserved Written by A. Sali with help from A. Fiser, R. Sanchez, M.A. Marti-Renom, B. Jerkovic, A. Badretdinov, F. Melo, J.P. Overington & E. Feyfant Rockefeller University, New York, USA Harvard University, Cambridge, USA Imperial Cancer Research Fund, London, UK Birkbeck College, University of London, London, UK Kind, OS, HostName, Kernel, Processor: 4, Linux allroy.otago.ac.nz 2.6.5-1.358smp x86_64 Date and time of compilation : 07/16/2002 11:42:16 Job starting time (YY/MM/DD HH:MM:SS): 2004/10/29 16:08:43.499 TOP_________> 106 706 SET ALNFILE = 'UP_human_ecoli' TOP_________> 107 707 SET KNOWNS = '1rxc_mono' TOP_________> 108 708 SET MD_LEVEL = 'refine_3' TOP_________> 109 709 SET SEQUENCE = '1uph' TOP_________> 110 710 SET ATOM_FILES_DIRECTORY = './:../atom_files' TOP_________> 111 711 SET OUTPUT_DIRECTORY = './' TOP_________> 112 712 SET PDB_EXT = '.pdb' TOP_________> 113 713 SET ALIGNMENT_FORMAT = 'PIR' TOP_________> 114 714 SET STARTING_MODEL = 1 TOP_________> 115 715 SET ENDING_MODEL = 5 TOP_________> 116 716 SET DEVIATION = 4.000000 TOP_________> 117 717 SET FINAL_MALIGN3D = 1 TOP_________> 118 718 SET DO_LOOPS = 1 TOP_________> 119 719 SET RADII_FACTOR = 0.915 TOP_________> 120 720 SET LOOP_STARTING_MODEL = 1 TOP_________> 121 721 SET LOOP_ENDING_MODEL = 5 TOP_________> 122 722 SET LOOP_MD_LEVEL = 'refine_2' TOP_________> 123 723 CALL ROUTINE = 'model' TOP_________> 124 399 CALL ROUTINE = 'getnames' TOP_________> 125 509 STRING_IF STRING_ARGUMENTS = MODEL 'undefined', OPERATION; = 'EQ', THEN = 'STRING_OPERATE OPERATION = CONCATENA; TE, STRING_ARGUMENTS = SEQUENCE .ini, RESULT = MODEL' TOP_________> 126 510 STRING_IF STRING_ARGUMENTS = CSRFILE 'undefined', OPERATI; ON = 'EQ', THEN = 'STRING_OPERATE OPERATION = CONCATE; NATE, STRING_ARGUMENTS = SEQUENCE .rsr, RESULT = CSRFILE; ' TOP_________> 127 511 STRING_OPERATE OPERATION = 'CONCATENATE', ; STRING_ARGUMENTS = SEQUENCE '.sch', RESULT = SCHFILE TOP_________> 128 512 STRING_OPERATE OPERATION = 'CONCATENATE', ; STRING_ARGUMENTS = SEQUENCE '.mat', RESULT = MATRIX_FI; LE TOP_________> 129 513 SET ROOT_NAME = SEQUENCE TOP_________> 130 514 RETURN TOP_________> 131 400 CALL ROUTINE = 'homcsr' TOP_________> 132 106 READ_ALIGNMENT FILE = ALNFILE, ALIGN_CODES = KNOWNS SEQUE; NCE Dynamically allocated memory at amaxseq [B,kB,MB]: 2205269 2153.583 2.103 openf5__224_> Open 11 OLD SEQUENTIAL UP_human_ecoli.ali Dynamically allocated memory at amaxbnd [B,kB,MB]: 6262261 6115.489 5.972 openf5__224_> Open 11 OLD SEQUENTIAL UP_human_ecoli.ali read_al_375E> Unknown residue type,position,sequence: 1 1 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 Dynamically allocated memory at finish [B,kB,MB]: 6262261 6115.489 5.972 Starting time : 2004/10/29 16:08:43.499 Closing time : 2004/10/29 16:08:44.900 Total CPU time [seconds] : 1.38 INCLUDE # remove all the #'d bits. TOP FILE FOR EXTENSIVE REFINEMENT SET INITIAL_MALIGN3D = 1 # don't worry about this. SET OUTPUT_CONTROL = 1 1 1 1 1 # don't worry about this either SET ALNFILE = 'UP_human_ecoli' # alignment file, worry about this SET KNOWNS = '1rxc_mono' # refers to xtal name in algnmnt SET MD_LEVEL = 'refine_3' # sets simulated annealing level 1 high 3 low. 3 good to tansfer coords and fix major gliches. SET SEQUENCE = '1uph' # name of target seq in pir file SET ATOM_FILES_DIRECTORY = './:../atom_files' # for modeller use. It will tell you if it can't find its atoms. SET OUTPUT_DIRECTORY = './' # is exactly that; can alter this SET PDB_EXT = '.pdb' # leave all structures as this SET ALIGNMENT_FORMAT = 'PIR' # leave it this way; easier SET STARTING_MODEL = 1 # these two define the number of SET ENDING_MODEL = 5 # models to build. Unclear why it is this way SET DEVIATION = 4.000000 # defines how much variation is tolerated when building your model from the randomised coords. Leave as is. SET FINAL_MALIGN3D = 1 # don't worry about this SET DO_LOOPS = 1 # for explicit loop building SET RADII_FACTOR = 0.915 # the x factor for good structure. Always include this. SET LOOP_STARTING_MODEL = 1 #back to explicit loop modeling SET LOOP_ENDING_MODEL = 5 # i built 10 per model, 50 loops in total. Too much. 1 model 10 loops SET LOOP_MD_LEVEL = 'refine_2' # md level used; same as above CALL ROUTINE = 'model' # is the modeller key word for modelling building

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where to put the ligand?
by Youbin Tu 27 Oct '04

27 Oct '04

Hi all: Thanks for Alicia and Modeler taker's kind hlep last time. Here come some new questions. Basically I just want to build a homology model complexed with an additional ligand. This time, I created a small molecule(ethane) to test whether the method works. First,In InsightII, I built ethane and optimized using cvff ( the program did not allow me to use charmm22 at that time.) and output it as an RTF file in charmm22 force field.- Second, I did some modification to some of the library files: 1. append part of the content of RTF file to the end of top_allh.lib and top_heav.lib 2. add an entry to restyp.lib, use j as the one letter abbreviation. (142 | ETH | j | ETHL | ethyl ) Third, alignment was modified so that "j' was appended to the end of the target sequence and '-' was used in the relative position of the template sequence. The program worked well with the above changes, but I could not see any ligand shown in the created pdb file! I could see heme was shown as the 513th residue but no ethane was shown as the 514th residue! Here I attached the ali file,wish you can give me some suggestions. Again, I would like to ask whether it is correct for me to just put any ligand at the end of the target sequence in the alignment file? Is it necessary to create the restraint file when some ligands are introduced? If fact, in the above test, I just want to see the ligand are really in the final model, and I do not mind where is it? So, anyone can tell me how to make the ligand appear in the final model? youbin

1 0

Protein with uracil
by Michel Seigneuret 27 Oct '04

27 Oct '04

Dear Collègues, I am trying to model a protein with a bound uracil. I have a template also with bound uracil. I modified the testyp.lib file in order to name uracil "U" and I included /U* at the end of the alignment for both template and target. The modeling goes on smoothly but I get a strange uracil with protein backbone atoms: N, CA, C,... Therefore Modeller thinks U is an aminoacid. I tried various tricks: putting different chain names for the protein and the uracil in the template pdb file, or changing ATOM to HETATM for the uracil, adding HETATM_IO = on to the top file but the problem remains. Could you please help me ? Two more things: I still use Modeller 6v2. I am not currently a subscriber to the list, therefore please answer directly to me and/or send the message to the list if you think it is worth it. Thanks in advance; Michel Michel Seigneuret Institut Cochin, U567-UMR8104 Département de Biologie Cellulaire 22 rue Méchain, 75014 Paris, France Tel: 33 (0)1 40 51 64 50 Fax: 33 (0)1 40 51 64 54

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Error" Array too small. Increase MAXBND"
by Youbin Tu 27 Oct '04

27 Oct '04

Hi all: Anyone has met such an error " Array too small. Increase MAXBND"? I was trying to build a small ligand into the model, it seems that sth wrong with the process of creating topology. I tried both modeler6vs2 and modeler7v7, unfortunately they gave the same errors. Here is the final part of the log file: *********************************************************************** TOP_________> 135 91 CALL ROUTINE = 'create_topology' TOP_________> 136 106 GENERATE_TOPOLOGY ADD_SEQUENCE = OFF mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 1 513 4139 4201 0 0 1775 patch_______> segment topology patched using RTF: 1 ; MET ; NTER segments residues atoms bonds angles dihedrals impropers: 1 513 4139 4201 5696 6784 1775 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 1 513 4139 4201 5696 6784 1775 getf____223E> Array too small. Increase MAXBND current maximum, current need: 6948 6949 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 Dynamically allocated memory at finish [B,kB,MB]: 8307049 8112.353 7.922 Starting time : 2004/10/26 14:20:01.859 Closing time : 2004/10/26 14:20:05.468 Total CPU time [seconds] : 3.28 ********************************************************************* Anyone has some ideas about it? Thanks. youbin

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multiple alignment...
by limnoha 25 Oct '04

25 Oct '04

Hello all... I tried to run my code for multiple alignment. <top file> READ_MODEL FILE = '1ry2.pdb', MODEL_SEGMENT 'FIRST:A''LAST:A' SEQUENCE_TO_ALI ALIGN_CODES = '1ry2A' READ_MODEL FILE = '1pg4.pdb', MODEL_SEGMENT 'FIRST:B''LAST:B' SEQUENCE_TO_ALI ALIGN_CODES = ALIGN_CODES '1ry2A',ADD_SEQUENCE = on READ_MODEL FILE = '1t5d.pdb', MODEL_SEGMENT 'FIRST:X''LAST:X' SEQUENCE_TO_ALI ALIGN_CODES = ALIGN_CODES '1ry2A',ADD_SEQUENCE = on READ_MODEL FILE = '1t5h.pdb', MODEL_SEGMENT 'FIRST:X''LAST:X' SEQUENCE_TO_ALI ALIGN_CODES = ALIGN_CODES '1ry2A',ADD_SEQUENCE = on SET ATOM_FILES = '1ry2' '1pg4' '1t5d' '1t5h' MALIGN3D SET ADD_SEQUENCE = on, ALIGN_BLOCK = NUMB_OF_SEQUENCES READ_ALIGNMENT FILE = 'target.seq', ALIGN_CODES = ALIGN_CODES 'target' ALIGN2D WRITE_ALIGNMENT FILE = 'target.ali', ALIGNMENT_FORMAT = 'PIR' WRITE_ALIGNMENT FILE = 'target.pap', ALIGNMENT_FORMAT = 'PAP' But, my job wasn't termainate. And, it always made the same log file and stopped at the same point. <log file> Date and time of compilation : 09/14/2004 11:06:39 Job starting time (YY/MM/DD HH:MM:SS): 2004/10/23 00:03:24.704 # Sequence alignment of the structurally conserved regions # [average distance and standard deviation are with respect # to the framework (i.e., average structure)] # # N av ds st dv 1ry2A 1ry2A 1ry2A 1ry2A # ============================================= 1 0.585 0.177 A 95 G 43 K 89 K 89 2 0.520 0.238 T 96 K 44 S 90 S 90 # ============================================= 3 0.904 0.201 F 98 I 45 L 93 L 93 # ============================================= 4 0.927 0.182 S 102 I 49 V 109 V 109 # ============================================= 5 0.648 0.243 K 149 T 93 P 155 P 155 # ============================================= 6 1.286 0.094 A 150 A 94 F 157 F 157 # ============================================= 7 1.086 0.362 * I 151 I 95 I 173 I 173 8 1.203 0.241 I 152 I 96 P 174 P 174 # ============================================= 9 0.687 0.125 F 153 W 97 A 177 A 177 # ============================================= 10 1.147 0.112 M 198 M 141 R 181 R 181 11 1.499 0.072 * V 199 V 142 V 182 V 182 # ============================================= 12 1.603 0.195 A 221 G 164 M 185 M 185 # ============================================= 13 1.035 0.235 G 222 G 165 V 189 V 189 # ============================================= 14 0.604 0.191 T 255 L 198 R 192 R 192 15 1.418 0.057 K 256 K 199 H 193 H 193 # ============================================= 16 1.600 0.394 V 272 V 217 R 195 R 195 # ============================================= 17 0.982 0.421 V 274 V 219 D 222 D 222 # ============================================= 18 1.174 0.252 P 314 P 258 E 230 E 230 # ============================================= 19 0.735 0.103 L 318 L 262 A 250 A 250 # ============================================= 20 1.896 0.448 G 322 S 265 L 289 L 289 # ============================================= 21 1.220 0.197 G 325 G 269 Q 294 Q 294 22 1.196 0.192 A 326 K 270 H 295 H 295 23 1.671 0.053 P 327 P 271 L 296 L 296 # ============================================= 24 0.801 0.374 G 361 A 305 G 305 G 305 # ============================================= 25 1.195 0.112 V 372 L 316 T 307 T 307 # ============================================= 26 0.836 0.059 G 388 G 332 F 329 F 329 27 1.111 0.360 T 389 V 333 S 330 S 330 28 1.141 0.216 P 390 P 334 E 331 E 331 # ============================================= 29 0.968 0.251 Y 398 M 342 A 356 A 356 # ============================================= 30 1.430 0.434 I 401 V 345 A 357 A 357 # ============================================= 31 1.501 0.129 T 408 N 352 T 372 T 372 # ============================================= 32 0.657 0.212 R 437 R 381 E 374 E 374 # ============================================= 33 1.114 0.104 G 440 G 384 S 384 S 384 34 1.061 0.137 S 441 S 385 D 385 D 385 # ============================================= 35 1.024 0.321 P 445 P 389 L 398 L 398 # ============================================= 36 0.638 0.207 D 467 D 411 R 400 R 400 # ============================================= 37 1.117 0.411 S 493 S 436 M 404 M 404 # ============================================= 38 1.524 0.844 P 508 D 450 A 424 A 424 39 1.217 0.673 N 509 N 451 P 425 P 425 # ============================================= 40 0.940 0.301 A 524 V 465 E 429 E 429 # ============================================= 41 1.773 0.332 K 563 R 504 V 432 V 432 # ============================================= 42 1.163 0.303 D 564 D 505 V 444 V 444 # ============================================= # Sequence alignment of the structurally conserved regions # [average distance and standard deviation are with respect # to the framework (i.e., average structure)] # # N av ds st dv 1ry2A 1ry2A 1ry2A 1ry2A # ============================================= 1 0.706 0.084 A 95 G 43 K 89 K 89 2 0.693 0.277 T 96 K 44 S 90 S 90 # ============================================= 3 0.982 0.231 F 98 I 45 L 93 L 93 # ============================================= 4 0.595 0.283 S 102 I 49 V 109 V 109 # ============================================= 5 0.896 0.032 K 149 T 93 P 155 P 155 # ============================================= 6 1.152 0.046 A 150 A 94 F 157 F 157 # ============================================= 7 1.021 0.088 * I 151 I 95 I 173 I 173 8 0.926 0.038 I 152 I 96 P 174 P 174 # ============================================= 9 0.619 0.086 F 153 W 97 A 177 A 177 # ============================================= 10 0.929 0.116 M 198 M 141 R 181 R 181 11 1.627 0.065 * V 199 V 142 V 182 V 182 # ============================================= 12 1.365 0.199 A 221 G 164 M 185 M 185 # ============================================= 13 0.840 0.173 G 222 G 165 V 189 V 189 # ============================================= 14 0.537 0.054 T 255 L 198 R 192 R 192 15 1.201 0.041 K 256 K 199 H 193 H 193 # ============================================= 16 1.548 0.190 V 272 V 217 R 195 R 195 # ============================================= 17 0.956 0.153 L 273 I 218 D 222 D 222 # ============================================= 18 1.004 0.175 P 314 P 258 E 230 E 230 # ============================================= 19 0.617 0.067 L 318 L 262 A 250 A 250 # ============================================= 20 0.818 0.094 G 325 G 269 Q 294 Q 294 # ============================================= 21 1.170 0.262 A 326 K 270 L 296 L 296 # ============================================= 22 0.692 0.159 G 361 A 305 G 305 G 305 # ============================================= 23 1.107 0.040 V 372 L 316 T 307 T 307 # ============================================= 24 0.727 0.091 G 388 G 332 F 329 F 329 25 0.677 0.232 T 389 V 333 S 330 S 330 26 0.911 0.197 P 390 P 334 E 331 E 331 # ============================================= 27 0.373 0.111 Y 398 M 342 A 356 A 356 # ============================================= 28 1.333 0.184 I 401 V 345 A 357 A 357 # ============================================= 29 1.131 0.064 T 408 N 352 T 372 T 372 # ============================================= 30 1.428 0.154 S 435 S 379 A 373 A 373 # ============================================= 31 0.724 0.277 R 437 R 381 E 374 E 374 # ============================================= 32 1.053 0.062 G 440 G 384 S 384 S 384 33 0.969 0.111 S 441 S 385 D 385 D 385 # ============================================= 34 1.728 0.101 E 444 E 388 I 397 I 397 35 0.827 0.113 P 445 P 389 L 398 L 398 # ============================================= 36 0.442 0.180 D 467 D 411 R 400 R 400 # ============================================= 37 1.048 0.082 S 493 S 436 M 404 M 404 # ============================================= 38 1.158 0.402 P 508 N 451 A 424 A 424 # ============================================= 39 1.107 0.657 E 512 G 453 G 426 G 426 # ============================================= 40 0.713 0.102 A 524 V 465 E 429 E 429 # ============================================= 41 1.767 0.252 K 563 R 504 V 432 V 432 # ============================================= 42 0.397 0.229 D 566 D 507 L 435 L 435 # ============================================= # Sequence alignment of the structurally conserved regions # [average distance and standard deviation are with respect # to the framework (i.e., average structure)] # # N av ds st dv 1ry2A 1ry2A 1ry2A 1ry2A # ============================================= 1 0.764 0.077 A 95 G 43 K 89 K 89 2 0.723 0.284 T 96 K 44 S 90 S 90 # ============================================= 3 0.989 0.125 F 98 I 45 L 93 L 93 # ============================================= 4 0.586 0.237 S 102 I 49 V 109 V 109 # ============================================= 5 0.968 0.053 K 149 T 93 P 155 P 155 # ============================================= 6 1.242 0.038 A 150 A 94 F 157 F 157 # ============================================= 7 0.976 0.067 * I 151 I 95 I 173 I 173 8 0.852 0.041 I 152 I 96 P 174 P 174 # ============================================= 9 0.808 0.096 F 153 W 97 A 177 A 177 # ============================================= 10 0.820 0.129 M 198 M 141 R 181 R 181 # ============================================= 11 1.204 0.208 A 221 G 164 M 185 M 185 # ============================================= 12 0.918 0.216 G 222 G 165 V 189 V 189 # ============================================= 13 0.746 0.066 T 255 L 198 R 192 R 192 14 1.117 0.062 K 256 K 199 H 193 H 193 # ============================================= 15 1.447 0.158 V 272 V 217 R 195 R 195 # ============================================= 16 0.764 0.146 L 273 I 218 D 222 D 222 # ============================================= 17 1.130 0.160 P 314 P 258 E 230 E 230 # ============================================= 18 0.592 0.048 L 318 L 262 A 250 A 250 # ============================================= 19 0.713 0.133 G 325 G 269 Q 294 Q 294 # ============================================= 20 1.162 0.358 A 326 K 270 L 296 L 296 # ============================================= 21 0.755 0.173 G 361 A 305 G 305 G 305 # ============================================= 22 1.029 0.038 V 372 L 316 T 307 T 307 # ============================================= 23 0.697 0.088 G 388 G 332 F 329 F 329 24 0.516 0.222 T 389 V 333 S 330 S 330 25 0.803 0.290 P 390 P 334 E 331 E 331 # ============================================= 26 0.399 0.067 Y 398 M 342 A 356 A 356 # ============================================= 27 1.485 0.185 I 401 V 345 A 357 A 357 # ============================================= 28 0.983 0.083 T 408 N 352 T 372 T 372 # ============================================= 29 1.326 0.211 S 435 S 379 A 373 A 373 # ============================================= 30 0.837 0.266 R 437 R 381 E 374 E 374 # ============================================= 31 1.013 0.090 G 440 G 384 S 384 S 384 32 0.911 0.144 S 441 S 385 D 385 D 385 # ============================================= 33 1.568 0.072 E 444 E 388 I 397 I 397 34 0.663 0.120 P 445 P 389 L 398 L 398 # ============================================= 35 0.501 0.235 D 467 D 411 R 400 R 400 # ============================================= 36 0.950 0.117 S 493 S 436 Please solve my problem...

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error on 'special_patches' routine for PATCH S-S bonds
by Dr. Daniel James White PhD 25 Oct '04

25 Oct '04

Hi Modellers, I get a "command not recognized" error, see log below when trying to use the 'special_patches' routine, to tell modeller to make 2 S-S bonds in a loop I am modelling, I can't see any error in my top file or alignment, I used the code directly from the manual FAQ number 6, define additional disulphides not in template, with appropriate changes, see top file below. any ideas what I am doing wrong? cheers Dan top file: # Homology modelling by the MODELLER TOP routine 'model'. INCLUDE # Include the predefined TOP routines SET OUTPUT_CONTROL = 1 1 1 1 1 # uncomment to produce a large log file SET ALNFILE = 'loop1.ali' # alignment filename SET KNOWNS = '4DPV' # codes of the templates SET SEQUENCE = 'lop1' # code of the target SET ATOM_FILES_DIRECTORY = './:../atom_files' # directories for input atom files SET STARTING_MODEL= 1 # index of the first model SET ENDING_MODEL = 1 # index of the last model # (determines how many models to calculate) CALL ROUTINE = 'model' STOP # Redefine the special_patches routine to include the additional disulfides # (this routine is empty by default): SUBROUTINE ROUTINE = 'special_patches' # A disulfide between residues 226 and 234 in chain A: PATCH RESIDUE_TYPE = 'DISU', RESIDUE_IDS = '226:A' '234:A' # A disulfide between residues 228 and 232 in chain A: PATCH RESIDUE_TYPE = 'DISU', RESIDUE_IDS = '228:A' '232:A' RETURN END_SUBROUTINE log file: Kind, OS, HostName, Kernel, Processor: 4, Linux modeling.bio.jyu.fi 2.6.8-1.521 i686 Date and time of compilation : 09/14/2004 11:06:39 Job starting time (YY/MM/DD HH:MM:SS): 2004/10/12 15:04:54.106 rdactio_534E> Command not recognized: recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 Dynamically allocated memory at finish [B,kB,MB]: 56755 55.425 0.054 Starting time : 2004/10/12 15:04:54.106 Closing time : 2004/10/12 15:04:55.092 Total CPU time [seconds] : 0.94 ali file: >P1;4DPV-CPVVP-withDNAZ structure:4DPV:22 :Z:593 :Z:::: GSGNGSGGGGGGGSGGVGISTGTFNNQTEFKFLENGWVEITANSSRLVHLNMPESENYRR VVVNNMDKTAVNGNMALDDIHAQIVTPWSLVDANAWGVWFNPGDWQLIVNTMSELHLVSF EQEIFNVVLKTVSE----PPTKVYNNDLTASLMVALDSNNTMPFTPAAMRSETLGFYPWK PTIPTPWRYYFQWDRTLIPSHTGT---------SGTPTNIYHGTDPDDVQFYTIENSVPVHLLRTGDEF ATGTFFFDCKPCRLTHTWQTNRALGLPPFLNSLPQSEGATNFGDIGVQQDKRRGVTQMGN TNYITEATIMRPAEVGYSAPYYSFEASTQGPFKTPIAAGRGGAQTDENQAADGNPRYAFG RQHGQKTTTTGETPERFTYIAHQDTGRYPEGDWIQNINFNLPVTNDNVLLPTDPIGGKTG INYTNIFNTYGPLTALNNVPPVYPNGQIWDKEFDTDLKPRLHVNAPFVCQNNCPGQLFVK VAPNLTNEYDPDASANMSRIVTYSDFWWKGKLVFKAKLRASHTWNPIQQMSINVDNQFNY VPSNIGGMKIVYEKSQLAPRKLY* >P1;COAT_PAVC2_VP2 sequence:lop1:22 :A:593 : :A::: GSGNGSGGGGGGGSGGVGISTGTFNNQTEFKFLENGWVYITANSSRLVHLNMPESENYRR VVVNNMDKTAVNGNMALDDIHAEIVTPWSLVDANAWGVWFNPGDWQLIVNTMSELHLVSF EQEIFNVVLKTVSESATQPPTKVYNNDLTASLMVALDSNNTMPFTPAAMRSETLGFYPWK PTIPTPWRYYFQWDRTLIPSHTGTCDCRGDCFCSGTPTNIYHGTDPDDVQFYTIENSVPVHLLRTGDEF ATGTFFFDCKPCRLTHTWQTNRALGLPPFLNSLPQSEGATNFGDIGVQQDKRRGVTQMGN TNYITEATIMRPAEVGYSAPYYSFEASTQGPFKTPIAAGRGGAQTDENQAADGNPRYAFG RQHGKKTTTTGETPERFTYIAHQDTGRYPEGDWIQNINFNLPVTNDNVLLPTDPIGGKTG INYTNIFNTYGPLTALNNVPPVYPNGQIWDKEFDTDLKPRLHVNAPFVCQNNCPGQLFVK VAPNLTNQYDPDASANMSRIVTYSDFWWKGKLVFKAKLRASHTWNPIQQMSINVDNQFNY VPSNIGGMKIVYEKSQLAPRKLY* Dr. Daniel James White BSc. (Hons.) PhD Cell Biology, Ambiotica C242 Department of biological and environmental science PO Box 35 University of Jyväskylä Jyväskylä FIN 40014 Finland +358 14 260 4183 (work) +358 468102840 (mobile) http://www.chalkie.org.uk dan(a)chalkie.org.uk white(a)cc.jyu.fi

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where can I get file.crv file.cav by write_date
by Shu-Qun Liu 21 Oct '04

21 Oct '04

Dear Modeller Users and Developers, The WRITE_DATA command can write the selected types of data (such as PSA DIH NGH SSM CRV CAV CROSS-SECTIONS) about the MODEL to a corresponding file. The example script write_data.top in the path 'modeller7v7/example/commands' is: # Example for: WRITE_DATA # This will calculate solvent accessibility, dihedral angles, and # residue-residue neighbors for a structure in the PDB file. SET OUTPUT_CONTROL = 1 1 1 1 1 # Get topology library for radii and the model without waters and # HETATMs: READ_TOPOLOGY FILE = '$(LIB)/top_heav.lib' SET HETATM_IO = off, WATER_IO = off READ_MODEL FILE = '1fas' # Calculate residue solvent accessibilities, dihedral angles, and # residue-residue neighbors: SET RADII_FACTOR = 1.0 # The default is 0.82 (for soft-sphere restraints) WRITE_DATA FILE = '1fas', OUTPUT = 'PSA DIH NGH SSM CRV' After I run this script, I can get corresponding files: 1fas.dih 1fas.ngh 1fas.psa 1fas.sol 1fas.ssm. However, when I changed the last line "WRITE_DATA FILE = '1fas', OUTPUT = 'PSA DIH NGH SSM CRV'" into "WRITE_DATA FILE = '1fas', OUTPUT = 'ALL'" or "WRITE_DATA FILE = '1fas', OUTPUT = 'CRV CAV CROSS-SECTIONS'", I can not find 1fas.crv, 1fas.cav in the ouput directory. And there is no information on writing 1fas.crv and 1fas.cav in write_data.log file. Where can I get these two files or information about mainchain curvatures and protein internal cavity volums? is it a bug? Best regards Shuqun Liu

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hetatms placed far away from the backbone
by Michael Knoll 20 Oct '04

20 Oct '04

Dear Modellers, I'm trying to model a ZN-containing (two zn ions) protein with modeller6v2. I used : 'SET HETATM_IO = on' in the .top file and the following syntax in the .ali file : ------------------------------------------ >P1;template structure:template:2:A: :A: : : : ANHD...VGN---LYPE-/zz* >P1;target sequence:target: : : : : : : : ANHD...VGNPL-LYR-G/zz* --------------------------------------------- I renamed the ZN in the template pdb file to ZN2 and the residue numbers are continuous. The model building results in a model where the overall structure of the model looks almost good, but the zn atoms are PLACED FAR AWAY from the model backbone. I tried to solve this problem many times without success so far. So, I would be very happy if anybody could help me. Thanks to all in advance, Michael ******************************************** Michael Knoll email : michael.knoll(a)itb.uni-stuttgart.de ********************************************

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Modeller stopped with no specific error message
by 서주현 20 Oct '04

20 Oct '04

3 2