July 2000 - modeller_usage

Error using MALIGN3D
by Michael Buck 24 Jan '02

24 Jan '02

MALIGN3D Top files which worked well using Modeler 4 are giving me this error : fndatmi_284E> Beginning atom index for a residue out of bounds: 0 0 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 I am using the following script # MALIGN3D READ_ALIGNMENT FILE = 'pair.aa' SET ATOM_FILES = '1.pdb' '2.pdb' SET FIT_ATOMS = 'CA' MALIGN3D GAP_PENALTIES_3D= 0 2.0, WRITE_FIT = on, WRITE_WHOLE_PDB = off If anybody has seen this problem, please help. Thank you Michael Buck ************************************************ Michael Buck NCSU Genetics mjbuck(a)unity.ncsu.edu Phone (919)515-5759 Fax (919)515-3355 http://www4.ncsu.edu/~mjbuck *************************************************

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problem!
by Paola D'Alessio 15 Jun '01

15 Jun '01

Dear users, I am trying to produce a chimeric model for my protein. The first thing I want to do is to check the alignment I have. When I tell Modeller to execute the "check_alignment" command, I get the following message: rdpir___E> alignment sequence not found in PDB file: 1 ./pXXXX.pdb ####################################################################################################################################### The alignment I have is: >P1;pXXXX structureX:pXXXX:.::.::::: CKPMSNFRF-GENHAIMGVAFTWVMALACAAPPLVGWS--RYIPEGMQC-SCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTH--------QGSDFGPIFMTIPAFFAKTSAVYNPVIYIMM* >P1;pAveM structure:pAveM:2::211::::: -----------VRWAKLYSLVIWGCTLLLSSPMLV-----------------------------EVFTNMLLNVVGFLLPLSVITFCTMQ---------------------ERRATVLVLVVLLLFIICWLPFQISTFLDTL----------------VITQIASFMAYSNSCLNPLVYVIV* >P1;Ali2 sequence:Ali2:::::::: VKTMSMGRMRGVRWAKLYSLVIWGCTLLLSSPMLVFRTMKEYSDEGHNVTACVISYPSL---IWEVFTNMLLNVVGFLLPLSVITFCTMQIMQVLRNNEMQKFKEIQT---ERRATVLVLVVLLLFIICWLPFQISTFLDTLHRLGILSSCQDERIIDVITQIASFMAYSNSCLNPLVYVIV* ####################################################################################################################################### Perhaps, something is wrong with file names or PDB codes.(I stored the pdb files as pXXXX.pdb) Can somebody help me? Thank you very much, Paola -- dott. Paola D'Alessio (PhD student) Universita' degli Studi di Salerno Dipartimento Scienze Farmaceutiche via Ponte Don Melillo, 84084 Fisciano (Sa), Italy tel.+39 089 962822; e-mail: pdalessio(a)unisa.it

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IRIX 6.5 problems; install patch 3371
by Andrej Sali 21 Aug '00

21 Aug '00

Problems with Modeller under Irix6.5: Patch 3371 is absolutely necessary. -- Andrej Sali, Associate Professor The Rockefeller University, 1230 York Avenue, New York, NY 10021-6399 tel +1 212 327 7550; lab +1 212 327 7206 ; fax +1 212 327 7540 e-mail sali(a)rockefeller.edu; http://salilab.org

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residue type undefined
by J.U. Flanagan Biomedical Research Centre 18 Jul '00

18 Jul '00

Hi all, Could anyone tell me what this error message is indicative of, and how I can fix it? iup2crm_E> IUPAC atom not found in topology library: CG iup2crm_E> residue type undefined recover__> MODELLER_STATUS >= STOP_ON_ERROR: 1 1 Thanks in advance Jack

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Re: Modeler - adding more models
by Andras Fiser 07 Jul '00

07 Jul '00

Hi Randa, OK, unless you set a different random start you will always have the same set of models i.e.. include in your top file e.g.: SET RAND_SEED = -10973 see, default: RAND_SEED = <integer:1> -8123 random seed from -50000 to -2 Andras RATHNACHALAM_RADHAKRISHNAN(a)Lilly.com wrote: > > Dear Andras, > > May be I was not clear when I asked my question. Initially I have made 5 > models. I wanted to make more models. > So I made the changes that I had indicated in my earlier message. Now I do > get models from 6 to 10. They are > named correctly. Only thing is the model 6 was the same as model 1, model > 7 was the same as model 2 and like wise. > How can I save time without redoing everything again? Thanks for your > reply. > > radha > > Andras Fiser <andras(a)tuba.rockefeller.edu>@mail.rockefeller.edu on > 07/07/2000 02:06:28 PM > > Please respond to fisera(a)rockefeller.edu > > Sent by: andras(a)mail.rockefeller.edu > > To: RATHNACHALAM_RADHAKRISHNAN(a)lilly.com > cc: modeller_usage(a)salilab.org > > Subject: Re: Modeler - adding more models > > It should work as you suggested, I suspect some trivial syntax problem. > > Andras > > RATHNACHALAM_RADHAKRISHNAN(a)lilly.com wrote: > > > > Hello: > > > > If I have already made say 5 models using Modeler, and if I would like > > to make models say from 6 to 10 what should I do. I tried to edit the > top > > file > > and changes the STARTING_MODEL and ENDING_MODEL TO 6 and 10. > > It seems the output files are the same. Is there another control to let > > the program > > take a different path to get more models? Thanks > > > > radhakrishnan -- , Andras Fiser, PhD # phone: (212) 327 7206 The Rockefeller University # fax: (212) 327 7540 Box 270, 1230 York Avenue # e-mail:fisera@rockefeller.edu New York, NY 10021-6399, USA # http://salilab.org/~andras

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Modeler - adding more models
by RATHNACHALAM_RADHAKRISHNAN＠LILLY.COM 07 Jul '00

07 Jul '00

Hello: If I have already made say 5 models using Modeler, and if I would like to make models say from 6 to 10 what should I do. I tried to edit the top file and changes the STARTING_MODEL and ENDING_MODEL TO 6 and 10. It seems the output files are the same. Is there another control to let the program take a different path to get more models? Thanks radhakrishnan

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Re: Modeller - Chain IDs
by Andras Fiser 02 Jul '00

02 Jul '00

Hi Thorsten, Once you are done with modeling, make another top file like this one: ######### READ_MODEL file='LONGSEQ.pdb' RENAME_SEGMENTS SEGMENT_IDS = 'A' 'B' 'C' , RENUMBER_RESIDUES = 1 3 3 WRITE_MODEL FILE='SEGMENTED.pdb' ########### This will take the resulting model with 1000+ residues (LONGSEQ.pdb: continuously numbered and no chain IDs), but TER records included as you defined in the alignment file by '/'. Next, in the above top file I assumed that there are 3 segments, they will be labeled as A, B, C and each segment will be renumbered and start with the specified starting numbers, in this case with 1, 3 and 3 respectively. So, look at the RENAME_SEGMENT command for details. Andras If you do not mind I am sending this reply to the list as well, since this question was not discussed so far. > Dear Andras, > > I have a question concerning the modelling of my hexamer > with the modeller version you gave me: > > I used the hint on the mailinglist concerning modelling > hetero-trimers in 1998 - to use the slash / to identify a > new chain - it works fine, but Modeller does not insert > any chain IDs... (there are IDs in the template). > This means the aa-id-numbers increase to over 1000, and > in the PDB-format, only three numbers are allowed for one > chain, so the visualization programs cut off the first number > and start again with 000... > > How do I get the chain-IDs and a correct aa-numbering? > > Thanks, > Thorsten -- , Andras Fiser, PhD # phone: (212) 327 7206 The Rockefeller University # fax: (212) 327 7540 Box 270, 1230 York Avenue # e-mail:fisera@rockefeller.edu New York, NY 10021-6399, USA # http://salilab.org/~andras

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