On 10/5/05, modeller_usage-request@salilab.org < modeller_usage-request@salilab.org> wrote:

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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

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