- modeller_usage - salilab.org

how to create .ali file
by sankari thirumal 10 Oct '05

10 Oct '05

Dear all, Psiblast search could find a template for my protein sequence with low identity (19%). So i preferred mgenTHREADER. I got the alignment results form genthreader. Now i don't know how to create the .ali file i have a aligned text file and .aln file. Now what is command for creating the .ali file and what are the files i need to make changes in the files (scripts) with my own target sequence. But the psiblast hit and the mgentreader results are not the same. Can I trust the mgenthreader results.? thanks in advance sankari --------------------------------- Yahoo! Music Unlimited - Access over 1 million songs. Try it free.

1 0

Re: plotting with GNU
by Prabhakar. G. 07 Oct '05

07 Oct '05

Hi, 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

1 0

No optimization
by mathieu coincon 06 Oct '05

06 Oct '05

Hi, I had a structure where a 15-residues loop is missing. So I want to create it but without moving the other atoms. I tried a lot of things (md_level= None, and so...) but I wasn't able to obtain a model where the non-loop atoms stayed in place. I think that there is still an optimization I can't stop. After that I could try to optimize my loop with the refine_loop.py from the advanced tutorial but first I need my model. Can someone help me please? Mathieu Coincon PhD Student Universite de Montreal

3 3

Re: modeller_usage Digest, Vol 4, Issue 90
by Prabhakar. G. 05 Oct '05

05 Oct '05

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(a)salilab.org < modeller_usage-request(a)salilab.org> wrote: > > Send modeller_usage mailing list submissions to > modeller_usage(a)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(a)salilab.org > > You can reach the person managing the list at > modeller_usage-owner(a)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(a)ncbs.res.in) > 3. DOPE score (Leyla Celik) > 4. Re: DOPE score (Modeller Caretaker) > > > > ---------- Forwarded message ---------- > From: Modeller Caretaker <modeller-care(a)salilab.org> > To: Akansha Saxena <asaxena17(a)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(a)salilab.org http://www.salilab.org/modeller/ > Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage > > > > > ---------- Forwarded message ---------- > From: nisha(a)ncbs.res.in > To: modeller_usage(a)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(a)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(a)salilab.org > >>http://salilab.org/mailman/listinfo/modeller_usage > > > > > > > > > > > ---------- Forwarded message ---------- > From: Leyla Celik <lc(a)chem.au.dk> > To: modeller_usage(a)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(a)chem.au.dk > > > > > ---------- Forwarded message ---------- > From: Modeller Caretaker <modeller-care(a)salilab.org> > To: Leyla Celik <lc(a)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(a)salilab.org http://www.salilab.org/modeller/ > Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage > > > > _______________________________________________ > modeller_usage mailing list > modeller_usage(a)salilab.org > http://salilab.org/mailman/listinfo/modeller_usage > > > --

1 0

DOPE score
by Leyla Celik 05 Oct '05

05 Oct '05

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(a)chem.au.dk

2 1

Modelling nucleic acids
by nisha＠ncbs.res.in 05 Oct '05

05 Oct '05

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

2 2

modeling of transmembrane proteins
by Akansha Saxena 04 Oct '05

04 Oct '05

Hello Modeller caretaker, 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. Akansha __________________________________ Yahoo! Mail - PC Magazine Editors' Choice 2005 http://mail.yahoo.com

2 1

modelling of complexes
by Arnout Voet 04 Oct '05

04 Oct '05

dear modellers, I am wondering what the best approaches are to model complexes using modeller. How would a model best be modelled if: If you have the a pdb file with multiple chains and also multiple unknowns. Is the appropriate way then to make your knowns the different chains and your unknown query one chain separated by '\' Or can multiple unknown sequences be used? you have X different proteins with unknown 3D structure which are homologue with a big protein which has several domains (all in 1 connected chain crystallized). Would the best method be make 1 alligment of your unknown with the crystal and devide the chain by a '\' you have an unknown which is a complex in one amino acid chain and you have a homologue complex which is actually two different chains in the crystal structure. Is the best way in such a case to change the crystal structure to a one chain model? Or simply allign both chains with the one query chain? kind regards arnout voet Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm

1 0

Fwd: [modeller_usage] Python Modeller Script
by Ricardo Nicoluci 30 Sep '05

30 Sep '05

Hi, I thought that the script was woriking well but after running a while the modeller gives the following error: IOError: openf5__225E> File does not exist: file-not-found pdbnam__217W> Filename for PDB code not found: adsl.B99990001.pdb Directories: ./ Extensions : :.atm:.pdb:.ent:.crd openf5__224_> Open 11 OLD SEQUENTIAL file-not-found openf5__225E> File does not exist: file-not-found I checked the variable env.io.atom_files_directory and it is set to './' ...what am I doing wrong !? Any ideia !? Thanks, On 9/27/05, Modeller Caretaker <modeller-care(a)salilab.org> wrote: > > Ricardo Nicoluci wrote: > > Sorry, I really forgot to attach the script file. > > I was trying to put generate.transfer_xyz between quotations marks. > > > > Now, if someone could comment the script, I would appreciate... > > You call a.make() twice, so you'll build all your models twice, which is > inefficient. Get rid of the first a.make() call. > > a.loop.md_level is the same as a.md_level - i.e. you should remove the > quotes from ' refine.very_slow'. > > You don't need to pass topology_model, parlib, or toplib in the > loopmodel() constructor, since these are the defaults. > > Ben Webb, Modeller Caretaker > -- > modeller-care(a)salilab.org http://www.salilab.org/modeller/ > Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage > -- Ricardo de Paula Nicoluci PhD Student Medicinal Chemistry Laboratory IFSC - University of Sao Paulo Sao Carlos - SP - Brazil

1 0

symmetry in automodel
by Gordon Wells 27 Sep '05

27 Sep '05

Hi all Is it possible to impose symmetry restraints in automodel? I've tried the following: def defsym(mdl, aln, seg1, seg2): for (set,seg) in [(2,seg1), (3,seg2)]: mdl.pick_atoms(aln, pick_atoms_set=set,selection_segment=seg, atom_types='ALL',selection_status='INITIALIZE', selection_search='SEGMENT') mdl.symmetry.define(symmetry_weight=1.0,add_symmetry=(True,False)) segsize = 330 class symmodel(automodel): def special_restraints(self, aln): defsym(self,aln,seg1=('1',str(segsize)), seg2=(str(segsize+1),str(2*segsize))) defsym(self,aln,seg1=(str(segsize+1),str(2*segsize)), seg2=(str(2*segsize+1),str(3*segsize))) The commands are accepted, but have no effect on the final model. -- "FABRICATI DIEM, PVNC" -- Terry Pratchett, Guards! Guards! Gordon Wells Bioinformatics and Computational Biology Unit Department of Biochemistry University of Pretoria

2 1