- modeller_usage - salilab.org

problem with using chain identifiers ...
by gowthaman ramasamy 14 Apr '04

14 Apr '04

hello list, I tried so many times with all the combinations (listed bellow) to specify the residue identifiers in following top script. purpose of this script is to extract sequence from pdb files. following is base script which extracts all the chains from that pdb file. read_model FILE = '1PFZ', sequence_to_ali atom_files = '1PFZ', align_codes = 'gowtham' write_alignment file='outputmyseq.pir' I wanted to take out all residues of a particular chain say A. I used MODEL_SEGMENT = '79P:A' '329:A' and it works fine. But if I dont know start and end residue numbers of a particular chain, how should i extracts only its sequence. i tried the following and did not work: ' :A' ' :A' '.:A' '.:A' ':A' ':A' '@:A' '@:A' '@:A' '@:X' '@:A' '@:@' and many more ...... -- Ra. Gowthaman, Graduate Student, Bioinformatics Lab, Malaria Research Group, ICGEB , New Delhi. INDIA Phone: 91-9811261804 91-11-26173184; 91-11-26189360 #extn 314

1 0

Re: [modeller_usage] How to get various conformar for a modelled protein?
by Luis Rosales 14 Apr '04

14 Apr '04

Dear B.Nataraj, > For my modelled protein, I want to analyis various possible > conformare it can assume,In that connection I want to know what is the > command or in build routine to create all possible conformation for > my modelled protein ? Thank you in advance. To analyze possible conformers avalible to your model, you can run a molecular dynamics simulation with implicit or explicit solvent. On the latter case you first add a water shell to your model and minimize just the water shell, and after that you minimize the water-protein assambly. Finally you run a looooooooong dynamic, sample conformations at regular intervals of the simulation and voila!! You now have several conformers of your model!! You can do a search on NCBI Pubmed to get more info on this (software, parameters, etc). As always, what you do is defined by your needs and the computing resources available to you. I hope this helps, Kind regards, Luis.

2 1

dynamic restraints
by Thomas Duncan 13 Apr '04

13 Apr '04

I'd like to confirm the default and options for dynamic restraints. I believe the default is set, under the OPTIMIZE command, as DYNAMIC_SPHERE = on (all others off) and that this means that only soft-sphere overlap restraints are generated. Are all the other DYNAMIC_ options available (LENNARD, COULOMB, MODELLER, ACCESS) and, specifically, what type of nonbonded restraints are included if DYNAMIC_MODELLER is turned on? Thanks, Tom Duncan

2 1

How to get various conformar for a modelled protein?
by Nataraj Balkrishnan 13 Apr '04

13 Apr '04

Dear modellers, For my modelled protein, I want to analyis various possible conformare it can assume,In that connection I want to know what is the command or in build routine to create all possible conformation for my modelled protein ? Thank you in advance. yours truly, B.Nataraj --------------------------------- Yahoo! Messenger - Communicate instantly..."Ping" your friends today! Download Messenger Now

2 1

Regarding adding ligands to protein...
by Nataraj Balkrishnan 12 Apr '04

12 Apr '04

Dear Modellers, I have to add or define a new ligand to use it for modelling purpose. In this regard I want to know.... 1)Which liberary I have to change in modlib folder? 2)How it should be changed(I need here some sample of small molecule that you have changed in that liberary)? 3)Wheather we need to know all physical and chemical proterties of the ligand(small molecule),I mean, any of those details need to be incorporated as data inside liberary used for modeller. And things will be more appreciated if you could send me your complete input files for model building based on my this particular interested topic. Yours truly, B.Nataraj --------------------------------- Yahoo! Messenger - Communicate instantly..."Ping" your friends today! Download Messenger Now

2 1

Re: FW: FAQ
by phanivijayg＠hotmail.com 12 Apr '04

12 Apr '04

Dear Modellers I have problem in my alignment file. i want to build structure for antibody. which has matching with the corresponding chains in the template. My first chain has nearly 110 aa which match with the 220aa template chainA and again my second chain has hit with the chain B. after chain A there are 100aa gapped and again hit with ChainB, again after that gap of 100aa. The problem is in template the two chains have seperate numbering. i dont want to build the chains individually. how can I then set my alignment file? I'm attaching alignment file with this. I already mailed to this address Modeller_usage(a)guitar.rockefeller.edu. but it was bounced back. so i'm sending u. sorry for the inconvenience. Thank you. with regards Phani Vijay

1 0

Regarding Optimization output ........
by Nataraj Balkrishnan 11 Apr '04

11 Apr '04

Dear modellers, I did optimization for my modelled protein using molecular dynamics "OPTIMIZATION_METHOD = 3". If I decrease the temperature from 300(modeller default value )to lower temperatue (eg., 200K,100K) the total energy of the optimized model decreases ,if I increase the temperature from 300 to higher temperature (eg., 400,500)the total energy of optimized model also increases. I do aware of that as the energy minimizes ,the model approaching its native nate or perfection. My question now is 1) wheather this behaviour happens with all protein (I mean increasing energy with initial temperature and vivevarsa)? 2) What are the useful conclution that I can derive out of this behaviour of my modeled protein ? Looking forward keenly to hear something from you. Yours truly, B.Nataraj --------------------------------- Yahoo! Messenger - Communicate instantly..."Ping" your friends today! Download Messenger Now

1 0

How to extract the backbone conformation alone from template?
by Nataraj Balkrishnan 11 Apr '04

11 Apr '04

Dear modellers, For my modelling process, I want to extract backbone conformation alone from the template to the target model.I mean,I want to restrict transformation of side chain to target model. Is it possible to achieve this in automatic modelling routine as given in "/example/tutorial-model/model-default.top" file. Otherwise may I have to write lengthier top file script to prevent this sidechain transformation from template to target? reply with example top script will be hightly appreciated. Let me know ... Thank you inadvance. Yours truly, B.Nataraj --------------------------------- Yahoo! Messenger - Communicate instantly..."Ping" your friends today! Download Messenger Now

1 0

karthik.
by kambhampati anjaneyulu 11 Apr '04

11 Apr '04

sir when i run modeller .it is showing error .how to run the modeller successfully 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, Windows_NT SSEDS x86 Family 15 Model 1 Stepping 3, GenuineIn Date and time of compilation : Jul 09 2002 16:21:30 Job starting time (YY/MM/DD HH:MM:SS): 2004/04/10 19:43:40.686 TOP_________> 105 705 SET ALNFILE = 'dd.ali' TOP_________> 106 706 SET KNOWNS = '1FFT' TOP_________> 107 707 SET SEQUENCE = '1EKH' TOP_________> 108 708 SET ATOM_FILES_DIRECTORY = './:../atom_files' TOP_________> 109 709 SET STARTING_MODEL = 1 TOP_________> 110 710 SET ENDING_MODEL = 1 TOP_________> 111 711 CALL ROUTINE = 'model' TOP_________> 112 399 CALL ROUTINE = 'getnames' TOP_________> 113 509 STRING_IF STRING_ARGUMENTS = MODEL 'undefined', OPERATI ON; = 'EQ', THEN = 'STRING_OPERATE OPERATION = CONCATENA; TE, STRING_ARGUMENTS = SEQUENCE .ini, RESULT = MODEL' TOP_________> 114 510 STRING_IF STRING_ARGUMENTS = CSRFILE 'undefined', OPERA TI; ON = 'EQ', THEN = 'STRING_OPERATE OPERATION = CONCATE; NATE, STRING_ARGUMENTS = SEQUENCE .rsr, RESULT = CSRFILE; ' TOP_________> 115 511 STRING_OPERATE OPERATION = 'CONCATENATE', ; STRING_ARGUMENTS = SEQUENCE '.sch', RESULT = SCHFILE TOP_________> 116 512 STRING_OPERATE OPERATION = 'CONCATENATE', ; STRING_ARGUMENTS = SEQUENCE '.mat', RESULT = MATRIX_FI; LE TOP_________> 117 513 SET ROOT_NAME = SEQUENCE TOP_________> 118 514 RETURN TOP_________> 119 400 CALL ROUTINE = 'homcsr' TOP_________> 120 106 READ_ALIGNMENT FILE = ALNFILE, ALIGN_CODES = KNOWNS SEQ UE; NCE Dynamically allocated memory at amaxseq [B,kB,MB]: 2205269 2153. 583 2.103 fullfn__230E> File not found: dd.ali Directories: Extensions : :.ali Prefixes : nothing, pdb recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 Dynamically allocated memory at finish [B,kB,MB]: 2205269 2153. 583 2.103 Starting time : 2004/04/10 19:43:40. 686 Closing time : 2004/04/10 19:43:42. 530 Total CPU time [seconds] : 1.72 --------------------------------- Do you Yahoo!? Yahoo! Tax Center - File online by April 15th

2 1

Re: [modeller_usage] residue problem
by Eric Feyfant 07 Apr '04

07 Apr '04

Hermant; Extract your sequence from the pdb file and your problem will be solved. Eric >>> hemant kushwaha <ritturajhemant(a)yahoo.com> 4/7/2004 10:00:58 AM >>> respected sir, I am having a problem that my alignment file has some residues missing than in the pdb file. Therefore modeller is giving the following error: Read the alignment from file : alignmenttest.ali Total number of alignment positions: 970 # Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------------- 1 1BDG 440 1 1BDG undefined 2 1DGK 898 1 1DGK undefined 3 1CZA 898 1 1CZA undefined 4 1BG3 887 1 1BG3 undefined 5 1HKC 896 1 1HKC undefined 6 1IG8 458 1 1IG8 undefined 7 1Str 493 1 1Str Candida albicans TOP_________> 121 107 CHECK_ALIGNMENT check_a_343_> >> BEGINNING OF COMMAND openf5__224_> Open 11 OLD SEQUENTIAL ./1BDG.pdb rdabrk__291E> Sequence difference between alignment and pdb : STRUCTURE RES_IND ALN_ITYP ALN_RES X_ITYP X_RES -----*----- 1 1 10 LEU 14 GLN -----LFEKVV rdabrk__288W> Protein not accepted: 1 openf5__224_> Open 11 OLD SEQUENTIAL ./1DGK.pdb openf5__224_> Open 11 OLD SEQUENTIAL ./1CZA.pdb openf5__224_> Open 11 OLD SEQUENTIAL ./1BG3.pdb rdabrk__291E> Sequence difference between alignment and pdb : STRUCTURE RES_IND ALN_ITYP ALN_RES X_ITYP X_RES -----*----- 4 1 3 ASP 11 MET -----DDQVKK rdabrk__288W> Protein not accepted: 4 openf5__224_> Open 11 OLD SEQUENTIAL ./1HKC.pdb rdabrk__291E> Sequence difference between alignment and pdb : STRUCTURE RES_IND ALN_ITYP ALN_RES X_ITYP X_RES -----*----- 5 1 18 VAL 3 ASP -----VKKIDK rdabrk__288W> Protein not accepted: 5 openf5__224_> Open 11 OLD SEQUENTIAL ./1IG8.pdb rdabrk__291E> Sequence difference between alignment and pdb : STRUCTURE RES_IND ALN_ITYP ALN_RES X_ITYP X_RES -----*----- 6 1 9 LYS 12 ASN -----KELMQQ rdabrk__288W> Protein not accepted: 6 check_a_337E> Structure not read in: 1 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 How can this problem be solved, that modeller should read pdb file with respect to residue position in alignment regards hemant __________________________________ Do you Yahoo!? Yahoo! Small Business $15K Web Design Giveaway http://promotions.yahoo.com/design_giveaway/ _______________________________________________ modeller_usage mailing list modeller_usage(a)salilab.org http://salilab.org/mailman/listinfo/modeller_usage

1 0