- modeller_usage - salilab.org

Re: Protein:DNA complexes in Modeller
by Andrej Sali 24 Aug '00

24 Aug '00

Mike Sierk wrote: > > Dr. Sali, > > We do not have Modeller installed here, and I was wondering how it does > modelling DNA-binding proteins. I have a structure of a protein:DNA > complex and would like to make a model of a related protein. Would it > work to just use the protein structure as a template, ignoring the DNA? Yes. > Could it model the unknown protein on the known DNA structure? Yes, but not with the default protocol. > Would it > model the unknown protein:DNA complex(with a different DNA sequence) > using the known complex? Yes, but not with the default protocol. The results are not likely to be overwhelming. Best, Andrej > > I found only two questions about DNA in the archive, with no answers to > either. > > Thank you, > Michael Sierk > > -- > > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > Michael Sierk email: mls5w(a)virginia.edu > Pharmacology Dept./Biophysics Program Phone(W): (804) 243-6725/924-1953 > Box 800735, Health Sciences Center (H): (804) 970-2268 > University of Virginia Fax: (804) 924-9057 > http://www.people.virginia.edu/~mls5w > GBS Homepage: http://www.med.virginia.edu/ed-programs/gpo/gbs/ > Grad Council Homepage: http://www.student.virginia.edu/~gsasc/ > ------------------------------------------------------------------------ > "If at first you do succeed, try not to act surprised." > - Anonymous. > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ -- 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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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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a problem
by Matteo Dal Peraro 16 Jun '00

16 Jun '00

in a modelling run I have this error during: 109 MAKE_RESTRAINTS RESTRAINT_TYPE = 'chi1_dihedral' ADD_RES; TRAINTS = ON Restraint type to be calculated: chi1_dihedral getpdf__E> your library requires all bins zero; nbinx: 4 what does it mean, I didn't find informations about it how can I resolve it? thanks matteo

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Average Coordinates
by giovannibottegoni＠libero.it 13 Jun '00

13 Jun '00

Dear Modeller users, I'd like to know if it's possible to give different weights to the templates when calculating the average coordinates to assign to the target sequence (TRANSFER_XYZ). Thank you in advance. Best regards, Giovanni ********************************** Giovanni Bottegoni Dip.Scienze Farmaceutiche Facoltà di Farmacia Università degli Studi di Bologna **********************************

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Segmentation fault
by Rafael Avila de Espindola 09 Jun '00

09 Jun '00

when I try to run the example of the tutorial in a Debian 2.2 system i get a segmentation fault, how do make it work?. Obs: I am runing the TINY version of modeller4

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libf2c.so.0
by Rafael Avila de Espindola 07 Jun '00

07 Jun '00

I want to use modeller with Debian GNU/Linux 2.2 but it needs libf2c.so.0 and Debian comes with libf2c.so.0, is there a moduller version compiled against this new version or should I get the old lib? >From where can I get one of then?

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