modeller care taker and users, I am new user to the modeler, I have started with the basic tutorial, I have difficulty with plotting the dope scores with GNU plot, when I plot the two dat files '1bdma_dope.dat','TVLDH_dope.dat'(from the tutorials folder) I get the graph plotted(Dope score vs Residue Index), but the two graphs are not aligned, as shown in the tutorial html file. how to align the graphs. hope someone could help me with this silly doubt. prabhakar Project Trainee, Bioinformatics and Data Management, National Institute of Virology, 20-A, Dr. Ambedkar Road, Pune-411 007 Maharastra India

On 10/5/05, modeller_usage-request@salilab.org < modeller_usage-request@salilab.org> wrote: > > Send modeller_usage mailing list submissions to > modeller_usage@salilab.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://salilab.org/mailman/listinfo/modeller_usage > or, via email, send a message with subject or body 'help' to > modeller_usage-request@salilab.org > > You can reach the person managing the list at > modeller_usage-owner@salilab.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of modeller_usage digest..." > > > Today's Topics: > > 1. Re: modeling of transmembrane proteins (Modeller Caretaker) > 2. Re: Modelling nucleic acids (nisha@ncbs.res.in) > 3. DOPE score (Leyla Celik) > 4. Re: DOPE score (Modeller Caretaker) > > > > ---------- Forwarded message ---------- > From: Modeller Caretaker modeller-care@salilab.org > To: Akansha Saxena asaxena17@yahoo.com > Date: Tue, 04 Oct 2005 11:02:18 -0700 > Subject: Re: [modeller_usage] modeling of transmembrane proteins > Akansha Saxena wrote: > > I used modeller to build a model for transmembrane > > protein (its an ion channel). The model is fine but > > has variations from the template structure. I wanted > > to know does modeller uses some different constraints > > for a transmembrane protein or it is similar to all > > other proteins. > > Modeller does not do anything special for transmembrane proteins; it > simply extracts restraints from the template structures. Note, however, > that Modeller's internal database of protein alignments, used to derive > statistics, include no transmembrane proteins, so it may not behave as > well as for globular systems. > > Ben Webb, Modeller Caretaker > -- > modeller-care@salilab.org http://www.salilab.org/modeller/ > Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage > > > > > ---------- Forwarded message ---------- > From: nisha@ncbs.res.in > To: modeller_usage@salilab.org > Date: Wed, 5 Oct 2005 15:40:36 +0530 (IST) > Subject: Re: [modeller_usage] Modelling nucleic acids > Hello Modeller Users > > Charlotte, thank you for your reply. However, I have included the number > of nucleic acid residues in the description line of the structure and > sequence. > > Actually, I have tried to model both the case of only nucleic acids, as > well as the case of protein+nucleic acids. > > (1) Modelling only nucleic acids - results in the following error: > rdpdb___303E> No atoms were read from the specified input PDB file, since > the starting residue number and/or chain id in MODEL_SEGMENT (or the > alignment file header) was not found; requested starting position: FIRST: > @ > > (2) Modelling protein+nucleic acid - results in the following error: > csrrng__299E> Atom index is out of bounds: 7621 7620 > nselat__596E> Atom index is out of range (iatm,natm): 7621 7620 > > I have a question: > Will Modeller allow for modelling only nucleic acids (without protein), or > does it need to have the nucleic acids modelled along with protein? > > I am still unable to model nucleic acids (either by itself or with > protein) using Modeller and would appreciate any suggestions on > corrections/changes to make. > > With thanks and regards > Nisha > > > > > Hello! > > > > Hopefully others will have more detailed responses, but here is > > something that might help you. > > > > In modelling my protein of interest with a ligand I obtained the same > error message as you have. What I had to do was to modifiy the sequence > headers in the alignment file. In the first description line for each > sequence and template, the total number of residues needs to include the > ligand residues. > > > > I am also trying to model a nucleic acid and have succeeded with a > simpler (ATP) ligand just within the last few days. > > > > I will be working on including a tRNA in my model in the next few > days/weeks and will share any useful info and tips. > > > > -Charlotte Habegger-Polomat > > > > > > > > > > nisha@ncbs.res.in wrote: > > > >>Hello Modeller Caretaker > >>I request your help with modelling nucleic acids using Modeller. Reading > through the archives, I have done the following: > >>(1) modified the restyp.lib file for Modeller to recognise my 1-letter > codes for the nucleic acids (ADE, THY, GUA, CYT), with the modified > contents of the file as below: > >>112 | ADE | ! | ADE | > >>114 | CYT | + | CYT | > >>120 | GUA | ^ | GUA | > >>136 | THY | & | THY | > >>(2) modified my pdb file to include the 3-letter pdb codes (ADE, CYT, > >> GUA, > >>THY) instead of 1-letter pdb codes (A,C,G,T,) in columns 18-20 of the > residue name, and > >>(3) have used the alignment of the modified nucleic acid codes (as > specified in restyp.lib) in my alignment file. > >>However, I still get a bunch of warnings and a couple of errors; and I > am > >>unable to understand what changes I need to make to model nucleic acids > using Modeller. > >>This is the final error although I cannot find any correction to make to > my alignment file: > >>rdpdb___303E> No atoms were read from the specified input PDB file, > since > >>the starting residue number and/or chain id in MODEL_SEGMENT (or the > alignment file header) was not found; requested starting position: > FIRST: > >>@. > >>I would appreciate your suggestions as to what I am doing incorrectly. > With thanks and regards > >>Nisha > >>_______________________________________________ > >>modeller_usage mailing list > >>modeller_usage@salilab.org > >>http://salilab.org/mailman/listinfo/modeller_usage > > > > > > > > > > > ---------- Forwarded message ---------- > From: Leyla Celik lc@chem.au.dk > To: modeller_usage@salilab.org > Date: Wed, 5 Oct 2005 17:39:37 +0200 > Subject: [modeller_usage] DOPE score > Hello, > > Does anyone out there know if it is possible to find a description of the > DOPE > score? I have been searching the manual, the MODELLER web-site and the > www... > > Thanks in advance > Leyla > > > > -- > Leyla Celik > Ph.d. student > Department of Chemistry > University of Aarhus > Langelandsgade 140 > DK-8000 Aarhus C > Denmark > Tel: +45 8942 3869 > e-mail: lc@chem.au.dk > > > > > ---------- Forwarded message ---------- > From: Modeller Caretaker modeller-care@salilab.org > To: Leyla Celik lc@chem.au.dk > Date: Wed, 05 Oct 2005 10:10:51 -0700 > Subject: Re: [modeller_usage] DOPE score > Leyla Celik wrote: > > Does anyone out there know if it is possible to find a description of > the DOPE > > score? I have been searching the manual, the MODELLER web-site and the > www... > > The description in the manual is at > http://salilab.org/modeller/manual/node155.html > > The method is still in development, so currently that is the only > documentation. A fuller description will be in the DOPE paper when it is > published. > > Ben Webb, Modeller Caretaker > -- > modeller-care@salilab.org http://www.salilab.org/modeller/ > Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage > > > > _______________________________________________ > modeller_usage mailing list > modeller_usage@salilab.org > http://salilab.org/mailman/listinfo/modeller_usage > > >

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