[modeller_usage] Re: modeller_usage Digest, Vol 4, Issue 75

hi all

i am facing a problem in modelling a chimeric protein. i need only certain regions of the protein to be modelled by one template and not the rest of them . so dont know what is wrong with my code, plz help me. i have enclosed the .ali , .top and .log files

with regards

rathankar

wrote:

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Today's Topics:

1. Re: Internal error: array too small (Modeller Caretaker)
2. Tutorial for beginners? (Antonio Arroyo Luque)
3. Re: Tutorial for beginners? (Modeller Caretaker)
4. Re: Tutorial for beginners? (Karsten Suhre)

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Message: 1
Date: Thu, 01 Sep 2005 16:58:09 -0700
From: Modeller Caretaker <>
Subject: Re: [modeller_usage] Internal error: array too small
To: hchoe <>
Cc: Modeller <>
Message-ID: <>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

hchoe wrote:
> I've got this error message.
>
> dihdisn_223E> Internal error: array too small:
> current maximum, current need: 100 101
>
> What should be fixed? Thanks in advance..

Modeller has an internal limit of 100 on the number of Cys residues
(which it uses while building disulfide bridge tables), which you have
exceeded due to the large size of your system (do you really intend to
model 31000 residues?). I don't think I'll be able to reproduce your
problem here, because your input sequence doesn't appear to correspond
to 1lp1 in the PDB. There is unfortunately no way that this limit can be
circumvented, short of modeling a smaller protein, or waiting for us to
release a new version of Modeller without this limit.

Ben Webb, Modeller Caretaker
--
http://www.salilab.org/modeller/
Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage

------------------------------

Message: 2
Date: Mon, 05 Sep 2005 13:57:44 +0200
From: Antonio Arroyo Luque <>
Subject: [modeller_usage] Tutorial for beginners?
To: Modeller <>
Message-ID: <>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

Hello everyone,
I try to lunch and run Modeller8v1 without any success. I use either the
Windows or the Mac version of the program. The problem I have is that I
don't know anything about Informatics but I want to learn. The tutorial
of Modeller I've found assumes certain knowledge of Informatics. For
instance, how do I launch Modeller? From the prompt of a OS terminal?
How to say to the program where my files are located? I have this
problem since version 6 of Modeller (more than 2 years ago) and since
that I've been downloading new versions of the program but as I said
without any success.
Is there any basic, basic, basic (something like Modeller for Dummys -
as I am) tutorial to start with? I will very appreciate your help. Also,
any Spanish people working with Modeller?
Thank you very much
Antonio

------------------------------

Message: 3
Date: Mon, 05 Sep 2005 10:12:16 -0700
From: Modeller Caretaker <>
Subject: Re: [modeller_usage] Tutorial for beginners?
To: Antonio Arroyo Luque <>
Cc: Modeller <>
Message-ID: <>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

Antonio Arroyo Luque wrote:
> I try to lunch and run Modeller8v1 without any success. I use either
> the Windows or the Mac version of the program. The problem I have is
> that I don't know anything about Informatics but I want to learn. The
> tutorial of Modeller I've found assumes certain knowledge of
> Informatics. For instance, how do I launch Modeller? From the prompt
> of a OS terminal?

There are many other resources available for learning informatics, and
it's really outside the scope of the Modeller tutorial to rehash them.
There is a step-by-step guide to installing and using Modeller itself in
the release notes at http://salilab.org/modeller/release.html

You will also find running instructions in the manual at
http://salilab.org/modeller/manual/node15.html

To summarise these notes: for Windows, the installer adds a "Modeller"
shortcut to your Start Menu, which opens a terminal for you. For Mac,
you need to open the Terminal application. Then you just type 'mod8v1'
and the name of your input file to run Modeller.

> How to say to the program where my files are located?

As with any other program, the files are in the directory which you run
'mod8v1' in, unless you give a full path name. See step 2 at that page
in the manual I mentioned above.

For PDB files, you may have them in a different directory, in which case
it's useful to set the env.io.atom_files_directory variable. See the
example in the manual.

> Is there any basic, basic, basic (something like Modeller for Dummys
> - as I am) tutorial to start with? I will very appreciate your help.

I'm really not sure how the manual example could be any more
straightforward, so if there are still points that aren't clear, feel
free to follow up with me directly.

> Also, any Spanish people working with Modeller?

If anybody wants to add Spanish pages (in fact, pages in any language)
for other Modeller users, there is a user-editable wiki available at
http://salilab.org/modeller/wiki/

Ben Webb, Modeller Caretaker
--
http://www.salilab.org/modeller/
Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage

------------------------------

Message: 4
Date: Tue, 6 Sep 2005 10:33:13 +0200
From: Karsten Suhre <>
Subject: Re: [modeller_usage] Tutorial for beginners?
To:
Message-ID: <>
Content-Type: text/plain; charset="iso-8859-1"

On Monday 05 September 2005 19:12, Modeller Caretaker wrote:
> > Is there any basic, basic, basic (something like Modeller for Dummys
> > - as I am) tutorial to start with? I will very appreciate your help.
>
> I'm really not sure how the manual example could be any more
> straightforward, so if there are still points that aren't clear, feel
> free to follow up with me directly.

You might try "Bioinformatics for Dummies" ...

http://www.dummies.com/WileyCDA/DummiesTitle/productCd-0764516965,page-1.html

Kind regards,

Karsten.

------------------------------

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