- modeller_usage - salilab.org

FORTRAN runtime errors...and more
by Matthias 22 Mar '04

22 Mar '04

-- Hello, I'm Matthias! I have more then one question, so far: - How do I use the "user_after_singel_model" subroutine, for ex. to compare the model with an X-ray structure? Can you send me a sort of top.script, or at least, can you someone give me a hint? - Further, can you please check my top.script , please? I can't undestand why it sometimes doesn't work (.. it clashed more than once... and it appeared the message: FORTRAN runtime error: INQUIRE(UNIT=/usr/bin/mod6v2: line 38: 25355 segmentation fault (core dumped) $nice ${executable} $STEERF >$LOGF Can you explain me, what this mean? - I have some problems, in loop modelling, regard DEFINE_SYMMETRY.. my loops almost often aren't symmetric.. how can i solve it .. is it enough to call the 'def_sym' routine and fix SEG1 & SEG2? - At last but not least, how can i eliminate the error: "Array too small. Increase MPAIRS" or "Array too small. Increase MAXATM", and what's the reason for it? I know i'm askingyou a lot, but i hope someone can help me..... faithsfully Matthias Negri Diploma Student in Medicinal Chemistry at University of Bologna thias(a)scafrm.unibo.it P.S. i send you my tops: job.top --> JOB_28_125.pir, prova2.top, try.top --> Thias1.pir,

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Atom index is out of bounds error
by Han Choe 22 Mar '04

22 Mar '04

Dear All, I get the following error message and I don't understand how it arises. csrrng__299E> Atom index is out of bounds: 3015 3014 Cheers, Han

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problems with the MALIGN command
by Stefanie Offermann 19 Mar '04

19 Mar '04

hello, I would like to do another modeling procedure with two of my recent models as templates, so all the three sequences (2 structures, 1 sequence) in the aln-file are identical. to make a structural alignment of the 2 models I have used the command MALIGN with the following .top-script: ---------------------------------- # Read the sequences of structures from the specs in SEGFILE: READ_ALIGNMENT FILE = 'x.ali', ALIGN_CODES = 'all' # do a multiple sequence alignment of structures: MALIGN GAP_PENALTIES_1D = -600 -400 # do a multiple structural alignment of structures: MALIGN3D GAP_PENALTIES_3D = 0.0 3.0, WRITE_FIT = ON, WRITE_WHOLE_PDB = OFF, FIT_ATOMS = 'CA' # align the last sequence with the fixed alignment of structures: ALIGN GAP_PENALTIES_1D = -600 -400 # write the alignment to a file ALNFILE WRITE_ALIGNMENT FILE = 'out.aln', ALIGNMENT_FORMAT = 'ALN' ------------------------------------------------------------ after a few seconds the run stops with the following message in the log-file: --------------------------------------------------------------------------- Multiple dynamic programming alignment (MALIGN): Residue-residue metric : ${MODINSTALL6v2}/modlib//as1.sim.mat ALIGN_BLOCK : 1 Gap introduction penalty: -600.0000 Gap extension penalty : -400.0000 Length of alignment : 358 fndatmi_284E> Beginning atom index for a residue out of bounds: 0 0 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 ----------------------------------------------------------------- is there anybody who could explain me what I have to change ?? thank you! Steffi

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symmetrisation of models
by Binbin Liu 19 Mar '04

19 Mar '04

Hello there, My model is composed by several identical chains, but I find they are not really identical in 3D. How can I symmetrise them? Does anybody know any informatics? Many thanks. BinBin

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Search sequence in modeller not responding...!
by Nataraj Balkrishnan 18 Mar '04

18 Mar '04

Dear Modellers, I tried to search my sequence aganist the Modeller chain database. But my top file containing the search commands did not yield me any result after long time run. Here I pasted my topfile,alignment Top File SET SEARCH_RANDOMIZATIONS = 10 SET FILE = 'gam.ali' SEQUENCE_SEARCH ALIGN_CODES = 'gam' alignment file: >P1;gam sequence:gam:1 : :136 : : LNLLISIMGRTMGALGNLTFVLCIIIFIFAVMGMQLFGKNYVDNVD RFPDHDLPRWNFTDFMHSFMIVFRVLCGEWIESMWDCMLVGDVSCI PFFLATVVIGNLVVLNLFLALLLSNFGSSSLSAPTADNDTNKIA* The logfile did not contain any messages other than usual Heading that appear in all logfiles. Kindly help me. Yours, B.Nataraj --------------------------------- Yahoo! Messenger - Communicate instantly..."Ping" your friends today! Download Messenger Now

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Adding a ligand
by Shamshad Zarina 17 Mar '04

17 Mar '04

Dear All, I am interested in adding ligand like glucose to one particular residue in my protein (which is not present in my template). Any ideas? Thanks for any help. Best, Shamshad __________________________________ Do you Yahoo!? Get better spam protection with Yahoo! Mail. http://antispam.yahoo.com/tools

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Any thesis reg modeller project work
by Nataraj Balkrishnan 16 Mar '04

16 Mar '04

Dear modellers, Can any one send me the copy of Mr.A.Sali Ph.D. thesis, PDF file .If not could you please send me the link where I can download the same at free of cost. And more could you please send me the link where A.sali.et al.'s paper on 'comparative modelling of protein' (those are refered in Modeller6v2's manual ) is freely downloadable. And more any of yours thesis in modeller regarding protein modelling would be greatly appreciated for my thesis preparation work. Thank you in advance. yours truly, B.Nataraj ________________________________________________________________________ Yahoo! Messenger - Communicate instantly..."Ping" your friends today! Download Messenger Now http://uk.messenger.yahoo.com/download/index.html

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Why should add ourself ligand in protein?
by Nataraj Balkrishnan 16 Mar '04

16 Mar '04

Dear modeller, I want to know what is the purpose of adding ligand in protein by ourself in Modeller, what will be the useful outcome that we can expect by adding ligand in our model in Modeller? I mean is there any routein in Modeller6v2 to study the active site or interaction of our added ligands and protein? Please let me know. Yours truly, B.Nataraj --------------------------------- Yahoo! Messenger - Communicate instantly..."Ping" your friends today! Download Messenger Now

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ModWeb question
by alarcon＠lncc.br 15 Mar '04

15 Mar '04

Dear All When sending a query sequence to modweb, this will suggest a tridimensional model homology-related to a specific template (which has a experimental structure determined). The question is ; When using Modeller stand alone we can make an alignment between our query sequence and several templates in order to better define regions of structural similarity. ModWeb works also in this way ? I mean, the model contructed for the query sequence is based lonely in one template ? So, is correct to assume that the ModWeb procedure is less accurate than the modeller when used "manually" due the one-template basis of calculation? Thanks in advance Frank Alarcon ------------------------------------------------- This mail sent through IMP: http://horde.org/imp/

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pyroglutamate
by Han Choe 15 Mar '04

15 Mar '04

Dear Modellers, How do I denote pyroglutamate as one letter in the alignment file? I tried small "p" but it did not work. In three letter, I use "PCA". Cheers, Han

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