April 2004 - modeller_usage

secondary structure display
by gowthaman ramasamy 30 Apr '04

30 Apr '04

hello list, This is not a Modeller related question, so bear with me. But I wonder if some one knows about this. I would like to display the secondary structure of a protein models graphically along with their sequence (as seen in RCSB's pdb summary page). does any one know of some stand alone software which does it. many thanks in advance gowtham -- Ra. Gowthaman, Graduate Student, Bioinformatics Lab, Malaria Research Group, ICGEB , New Delhi. INDIA Phone: 91-9811261804 91-11-26173184; 91-11-26189360 #extn 314

2 1

READ_MODEL error: MODEL atom not classified
by Sascha Tayefeh 28 Apr '04

28 Apr '04

Dear community, I am trying to get warm with modeller-usage by checking out the official manual's examples. For some reason, the READ_MODEL command does not work. Here's my input/output: *************** INPUT ************************** READ_TOPOLOGY FILE = '/soft/modeller6v2/modlib/top.lib', TOPOLOGY_MODEL = 3 READ_PARAMETERS FILE = '/soft/modeller6v2/modlib/par.lib' READ_MODEL FILE = '1P7B' *************** OUTPUT ************************** iatmcls_286W> MODEL atom not classified: VAL:OT1 VAL iatmcls_286W> MODEL atom not classified: VAL:OT1 VAL Using different pdbs (eg. manual's suggested 1fas), I get the same error with different residues. *************** OUTPUT ************************** iatmcls_286W> MODEL atom not classified: TYR:OT1 TYR iatmcls_286W> MODEL atom not classified: TYR:OT2 TYR I have checked the pdbs for OT1 - there is simply no such entry, so: what's the problem? Also, I have tried modeller on different platforms (linux, irix etc). Thanx for any help in advance S. Tayefeh (Grad. Stud.) Technical University Darmstadt Dept. of Phys. Chemistry Germany

2 1

B-factor column after Loop refinement in v6
by Bissan Al-Lazikani,(4627) 22 Apr '04

22 Apr '04

Hi I have followed the loop refinement script given in the on-line manual, but all the atoms in all generated models have "999.99" in the B-factor column- instead of a useful score To make sure it was nothing wrong with my input, I built models using the alignment and top file examples given in the online manual but I get the same behaviour. The initial model (pre-loop refinement) is fine. What am I doing wrong? Thank you Bissan x __________________________________________________________________ >P1;5fd1 structureX:5fd1:1 : :106 : :ferredoxin:Azotobacter vinelandii: 1.90: 0.19 AFVVTDNCIKCKYTDCVEVCPVDCFYEGPNFLVIHPDECIDCALCEPECPAQAIFSEDEVPEDMQEFIQLNAELA EVWPNITEKKDPLPDAEDWDGVKGKLQHLER* >P1;1fdx sequence:1fdx:1 : :54 : :ferredoxin:Peptococcus aerogenes: 2.00:-1.00 AYVINDSC--IACGACKPECPVNIIQGS--IYAIDADSCIDCGSCASVCPVGAPNPED----------------- -------------------------------* __________________________________________________________________ INCLUDE # Include the predefined TOP routines SET OUTPUT_CONTROL = 1 1 1 1 0 SET ALNFILE = 'test.ali' # alignment filename SET KNOWNS = '5fd1' # codes of the templates SET SEQUENCE = '1fdx' # code of the target SET ATOM_FILES_DIRECTORY = './:../atom_files' # directories for input atom files # SET STARTING_MODEL= 1 # SET ENDING_MODEL = 1 # (determines how many models to calculate) SET DO_LOOPS = 1 # do loops extensively SET LOOP_STARTING_MODEL = 1 SET LOOP_ENDING_MODEL = 4 SET LOOP_MD_LEVEL = 'refine_1' SET MD_LEVEL = 'nothing' CALL ROUTINE = 'model' # do homology modelling ___________________________________________________________________

2 1

possibility of usage of two force feild at a time for a model building
by Nataraj Balkrishnan 21 Apr '04

21 Apr '04

Dear modellers, I modelled protein using modeller to get initial models,after evaluating, I made correction in models using the SPDBV Software,since it gives visulization option for interactive adjustment of the model. Now my question is # Is it theoreticaly correct to adopt differnet force feild for Energy minimization at various stage of the model building methadology ?(As I produced my initial model in modeller where the optimization used the CHARMM force field,but in SPDBV implements GROMOS96 as force filed. So I did energy minimization of the model in SPDBV for some sterochemical adustment made in the modeled structure.) Yours truly, B.Nataraj B.Nataraj, Final year M.Tech.(Bioinformatics), SASTRA Deemed University, (www.sastra.edu) Thanjavur, Tamil Nadu, India. Email:nataraj@biotech2.sastra.edu Email:natarajmtech@yahoo.co.uk --------------------------------- Yahoo! Messenger - Communicate instantly..."Ping" your friends today! Download Messenger Now

1 0

alignment seq not found in pdb
by IPSITA ACHARYA 21 Apr '04

21 Apr '04

sir, I have been trying to model a molecule but i am getting an error that "alignment sequence not found in pdb". so please help me in providing some possible reasons and solution against that. Thanking you, Ipsita acharya Yahoo! India Matrimony: Find your partner online.

2 1

regarding chain identifiers ...
by gowthaman ramasamy 21 Apr '04

21 Apr '04

sorry to bother u with this simple question ... I use following top script to extract sequences from pdb file '1PFZ'. works fine. But it reads all the different chain (A,B,C ..etc). what should i do if i want to get only sequence of chain A. read_model FILE = '1PFZ', sequence_to_ali atom_files = '1PFZ', align_codes = 'gowtham' write_alignment file='seq.pir' I tried the following and did not work read_model FILE = '1PFZ',MODEL_SEGMENT = '@:A' 'X:A' #this works but writes only a chain break and * (/*) as a third line in output file 'seq.pir' many thanks in advance .... i could not get answer from list archives. i am sorry to bother you guys. -- Ra. Gowthaman, Graduate Student, Bioinformatics Lab, Malaria Research Group, ICGEB , New Delhi. INDIA Phone: 91-9811261804 91-11-26173184; 91-11-26189360 #extn 314

2 1

some questions..
by Your Name 20 Apr '04

20 Apr '04

Hi Ben! I'm Matthias , i wonna know whether its possible or not, to generate a part of the model with 'gererate_xyz' and the other part with 'transfer_xyz' ROUTINES? I suggest it's could be possible with model-segment, but i haven't tryied jet.. Further, I can't understand why this BIG.top file doesn't work (I think i' gonna have to add a READ ALIGNMENT, but where? Thxs for awhile, Matthias

1 0

model a tetramer with Modeller
by lgan＠smail.uni-koeln.de 20 Apr '04

20 Apr '04

Hi, everyone, I'm trying to model a tetramer with modeller. It seems that a simple automatic run works well. The strange problem I met is that the output structure is less symmetric than the input structure. Does somebody have experience with such kind of problem? Thanks in advance! lgan

1 0

Superposition of many model segments
by Toni Hermoso Pulido 19 Apr '04

19 Apr '04

Hello, I'm trying to superpose two model structures in order to get a RMS value using more than one segment for each structure. For exemple for model1 = '342:A' '343:A' and '348:A' '349:A' and for model2 = '1:' '2:' and '6:' '7:'. Is it possible to do with Modeller SUPERPOSE subroutine? Thanks! -- 000000000000 Toni Hermoso Pulido 111111111111 * Unitat de Bioinformàtica - Institut de Biotecnologia i Biomedicina | Universitat Autònoma de Barcelona @ email: flipe(a)bioinf.uab.es & pgp_public_key_id: 11749A26 111111111111 ATG <-LINRLS-> STOP 000000000000

1 0

Fwd: problem reading alignment file
by Clemens Steegborn 16 Apr '04

16 Apr '04

Hi everybody, thanks for all the suggestions how to solve my problem with reading an alignment file (see below). The solution was to remove all spaces from the alignment! Clemens >Date: Tue, 30 Mar 2004 16:55:59 -0500 >To: modeller_usage(a)salilab.org >From: Clemens Steegborn <cls2001(a)med.cornell.edu> >Subject: problem reading alignment file > > >Hi, > >I'm using the WINDOWS version of MODELLER6v2 > >I get the following error when reading the template and alignment files: > > > > >TOP_________> 121 107 CHECK_ALIGNMENT > > > >check_a_343_> >> BEGINNING OF COMMAND > >openf5__224_> Open 11 OLD SEQUENTIAL myt.atm > >rdabrk__290E> Number of residues in the alignment and pdb files are > different: 433 392 > > For alignment entry: 1 > >recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 > > > >the problem seems to be that MODELLER doesn't understand the gap residue >'-', as it also >doesn't understand '/' (using '/' gives an error stating it doesn't know >this residue)! > >I tried including a link called RESTYP_LIB to restyp.lib in the libs.lib >file, but that didn't help. > >Any suggestions would be appreciated! > >Clemens

1 0