or, via email, send a message with subject or body
'help' to
You can reach the person managing the list at
When replying, please edit your Subject line so it is
more specific
than "Re: Contents of modeller_usage digest..."
Today's Topics:
1. setting the DEVIATION (Ori Kalid)
2. Atom Index is out of bounds: (Amjad Farooq)
3. Re: setting the DEVIATION (Karsten Suhre)
4. Regarding modelling (rajesh rengaraj)
----------------------------------------------------------------------
Message: 1
Date: Sun, 20 Feb 2005 16:18:35 +0200
From: "Ori Kalid" <>
Subject: [modeller_usage] setting the DEVIATION
To: <>
Message-ID: <00f801c51757$176c6320$551b4684@W2000EPRO>
Content-Type: text/plain; charset="windows-1255"
Hi Everyone,
Does anyone know how to control the XYZ randomization
parameter DEVIATION?
I tried modifying its value using a simple SET DEVIATION
= 0.0, but nothing happens. The reasults are the same as
for the default value of 4.0.
Thanks,
Ori
-------------- next part --------------
An HTML attachment was scrubbed...
------------------------------
Message: 2
Date: Mon, 21 Feb 2005 09:21:17 -0700
From: Amjad Farooq <>
Subject: [modeller_usage] Atom Index is out of bounds:
To:
Message-ID:
<>
Content-Type: TEXT/plain; CHARSET=US-ASCII
Dear Modeller users,
I am trying to model the structure of a 300-residue
protein containing a
phospho-threonine (PTH). After writing the topology of
PTH in
top_heavy.lib and specifying PTH in restype.lib under
the modlib
subdirectory, I get this error upon running MODELLER:
csrrng__299E> Atom index is out of bounds: 2392
2391
recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1
1
As you can see MODELLER does not complain about PTH but
some general
error. Has anyone encountered something like this
before? How can this
be fixed? Interestingly, when I substitute PTH with THR,
MODELLER
generates no such error and models the structure nicely.
Any help will be greatly appreciated.
Many thanks,
Amjad
****************************************
AMJAD FAROOQ PhD
Assistant Professor
Dept of Biochemistry & Molecular Biology
Miller School of Medicine
University of Miami
Gautier Building, Rm 214
1011 NW 15th Street
Miami, FL 33136
tel 305-243-2429
fax 305-243-3955
http://farooqlab.ws
****************************************
------------------------------
Message: 3
Date: Mon, 21 Feb 2005 09:45:37 +0100
From: Karsten Suhre <>
Subject: Re: [modeller_usage] setting the DEVIATION
To: "Ori Kalid" <>,
<>
Message-ID:
<>
Content-Type: text/plain; charset="windows-1255"
Hi Ori,
Does anyone know how to control the XYZ randomization
parameter DEVIATION?
I tried modifying its value using a simple SET DEVIATION
= 0.0, but nothing
happens. The reasults are the same as for the default
value of 4.0.
Try to generate more than one models in one go by using
the following
commands:
SET STARTING_MODEL= 1 # index of the first
model
SET ENDING_MODEL = 10 # index of the last
model
Also, I understand that the initial random seed has to
be a negative value in
order to produce different models in different runs,
e.g. use
SET RAND_SEED = -42
I hope this helps,
Kind regards, Karsten.
PS: Don't set DEVIATION to zero if you want different
models.
PPS: You can also try different MD_LEVEL parameters to
get different models
(of course the models will be of different quality, but
in some applications,
i.e. for molecular replacement, this may be a good idea)
SET MD_LEVEL = 'refine_3'
------------------------------
Message: 4
Date: Mon, 21 Feb 2005 09:05:26 +0000 (GMT)
From: rajesh rengaraj <>
Subject: [modeller_usage] Regarding modelling
To:
Is it possible to model 1249 amino acids at a stretch
by using modeller, where the target sequence is having
less similarty with the template.
I found the template by using the fold recognition
method.
Please help me modellers.
---------------------------------
Do you Yahoo!?
Yahoo! Search presents - Jib Jab's 'Second Term'
-------------- next part --------------
An HTML attachment was scrubbed...
------------------------------
_______________________________________________
modeller_usage mailing list
http://salilab.org/mailman/listinfo/modeller_usage
End of modeller_usage Digest, Vol 4, Issue 19
*********************************************