October 2004 - modeller_usage

calling subroutine defsym
by amc 20 Oct '04

20 Oct '04

Dear modellers, I am modelling a homotetramer protein and curious when or by what the subroutine 'defsym' is called. Cheers, Han

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Alignment file.
by bcur001＠ec.auckland.ac.nz 13 Oct '04

13 Oct '04

I'm doing something wrong, I'm a novice though, so I know what what. I'm using a fairly simple TOP script to generate a model a nitroreductase. I've used blast on NCBI to find a simialr protein to the one I have the pdb model for. The blast results look like this : Query: 1 MDIISVALKRHSTKAFDASKKLTPEQAEQIKTLLQYSPSSTNSQPWHFIVASTEEGKARV 60 MDIISVALKRHSTKAFDASKKLT E+AE+IKTLLQYSPSSTNSQPWHFIVASTEEGKARV Sbjct: 1 MDIISVALKRHSTKAFDASKKLTAEEAEKIKTLLQYSPSSTNSQPWHFIVASTEEGKARV 60 Query: 61 AKSAAGNYVFNERKMLDASHVVVFCAKTAMDDVWLKLVVDQEDADGRFATPEAKAANDKG 120 AKSAAG YVFNERKMLDASHVVVFCAKTAMDD WL+ VVDQE+ADGRF TPEAKAAN KG Sbjct: 61 AKSAAGTYVFNERKMLDASHVVVFCAKTAMDDAWLERVVDQEEADGRFNTPEAKAANHKG 120 Query: 121 RKFFADMHRKDLHDDAEWMAKQVYLNVGNFXXXXXXXXXXXXPIEGFDAAILDAEFGLKE 180 R +FADMHR DL DD +WMAKQVYLNVGNF PIEGFDAAILD EFGLKE Sbjct: 121 RTYFADMHRVDLKDDDQWMAKQVYLNVGNFLLGVGAMGLDAVPIEGFDAAILDEEFGLKE 180 Query: 181 KGYTSLVVVPVGHHSVEDFNATLPKSRLPQNITLTE 216 KG+TSLVVVPVGHHSVEDFNATLPKSRLP + +TE Sbjct: 181 KGFTSLVVVPVGHHSVEDFNATLPKSRLPLSTIVTE 216 How do I then transform this into a successful alignment file? My attempt looks something like this: >P1;1OO5 structureX:1OO5: 2 :A: 217 :D:undefined:undefined:-1.00:-1.00 mdiisvalkrhstkafdaskkltpeqaeqiktllqyspsstnsqpwhfivasteegkarvaksaagnyvfnerkml dashvvvfcaktamddvwlklvvdqedadgrfatpeakaandkgrkffadmhrkdlhddaewmakqvylnvgnfll gvaalgldavpiegfdaaildaefglkekgytslvvvpvghhsvedfnatlpksrlpq nitltev* >P1;1NEC sequence:1NEC: 2 :A: 216 :D:undefined:undefined:-1.00:-1.00 DIISVALKRHSTKAFDASKKLTAEEAEKIKTLLQYSPSSTNSQPWHFIVASTEEGKARVAKSAAGTYVFNERKML DASHVVVFCAKTAMDDAWLERVVDQEEADGRFNTPEAKAANHKGRTYFADMHRVDLKDDDQWMAKQVYLNVGNFL LGVGAMGLDAVPIEGFDAAILDEEFGLKEKGFTSLVVVPVGHHSVEDFNATLPKSRLPLSTIVTE* I've basically taken the Query sequence (1OO5) which I have the pdb file for and placed it in the sequence section, then taken the result sequence which has been matched to it (1NEC) and placed it in the second position of the alignment file with the sequence label. However, when I run it, in my mod.log file, I'm getting the error: Dynamically allocated memory at amaxseq [B,kB,MB]: 2205269 2153.583 2.103 openf5__224_> Open 11 OLD SEQUENTIAL 1OO5.ali Dynamically allocated memory at amaxbnd [B,kB,MB]: 5377489 5251.454 5.128 openf5__224_> Open 11 OLD SEQUENTIAL 1OO5.ali read_al_375E> Unknown residue type,position,sequence: m 1 1 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 As far as I can gatherThis means that it doesn't like the residue at position one. I don't however know what it doesn't like about the residue at that position. Am I creating the alignment file in the wrong manner? Is there something else wrong? In case it of any use, the top file looks like: INCLUDE # Include the predefined TOP routines SET OUTPUT_CONTROL = 1 1 1 1 1 # uncomment to produce a large log file SET ALNFILE = '1ICV.ali' # alignment filename SET KNOWNS = '1ICV' # codes of the templates SET SEQUENCE = '1NEC' # code of the target # SET HYDROGEN_IO = on SET HETATM_IO = on SET ATOM_FILES_DIRECTORY = '../pdb' # directories for input atom files SET STARTING_MODEL= 1 # index of the first model SET ENDING_MODEL = 10 # index of the last model # (determines how many models to calculate) SET PDB_EXT = '.modlr.pdb' SET MD_LEVEL = 'refine_5' SET LIBRARY_SCHEDULE = 1 CALL ROUTINE = 'model Thanks. Ben.

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bumps in model
by Marc Gasser 13 Oct '04

13 Oct '04

dear Modellers, I used MUTATE_MODEL to mutate ALA into ILE. now the ILE bumps into another residue. turning the dihedral of the ILE sidechain manually in a viewer will solve this. but I want to include an automatic minimization process in the mutate.top script, which will do it for me. In the FAQ section I saw the question 2. which describes a similar problem, it refers to examples/tutorial-model/model-segment.top . but it's not so clear to me how to merge the mutate.top and the model-segment.top in one both_steps.top, does it really need an alignment for doing this optimization of one residue? thank you for good tips. marc

1 1

PDB updates for Modeller
by Bruno Afonso 07 Oct '04

07 Oct '04

Dear modeller hackers :), I'm trying to use modeller to find good PDB templates and there is at least one structure that is missing from modeller's database, which is good since it was deposited Jun 2003 in PDB, released in august. Could it be because it is 3.3 A? Since I know this PDB is probably a good model and it won't come up in seq_search I was wondering how I could manually update CHAINS_all.seq or create my own sequence database. best, BA ps: I found in the archives a person asking a similar question regarding a PDB database update but no script or url was given to get a newer version, or without resolution cut-off. :-) -- Bruno Afonso http://brunoafonso.net http://dequim.ist.utl.pt/~bruno/sciTocs/ - Bruno's SciTocs! http://freebsd-pt.org/forum/ - Portuguese FreeBSD forum

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Markus Jaritz is out of the office.
by markus.jaritz＠pharma.novartis.com 04 Oct '04

04 Oct '04

I will be out of the office starting 10/04/2004 and will not return until 10/18/2004. I will answer your mail when I am back.

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Modeller 7v7 AIX binary: now available
by Modeller Caretaker 01 Oct '04

01 Oct '04

For those of you who wish to use the new Modeller release, 7v7, on AIX systems: an AIX binary is now available. This is distributed as part of the 'Other Linux/Unix' download, at: http://salilab.org/modeller/download_installation.html Ben Webb, Modeller Caretaker -- modeller-care(a)salilab.org http://www.salilab.org/modeller/ Modeller mailing list: http://salilab.org/mailman/listinfo/modeller_usage

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