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Today's Topics:
1. file name problem (Starr Hazard)
2. Re: file name problem (Modeller Caretaker)
3. Re: To Model missing domains in the content of the rest
(Shirley Li)
4. To use separate templates for different region of a protein
(Shirley
Li)
----------------------------------------------------------------------
Message: 1
Date: Thu, 08 Dec 2005 13:53:38 -0500
From: Starr Hazard
Subject: [modeller_usage] file name problem
To: modeller_usage@salilab.org
Message-ID:
Content-Type: text/plain; charset=us-ascii; format=flowed
Folks,
The following lines:
mdl.assess_dope(output='ENERGY_PROFILE NO_REPORT',
file=code+'.profile',
normalize_profile=True, smoothing_window=15)
are producing output files with a question mark in the name string.
ABC31_HUMAN.BL09950001.pdb?.profile
The question mark renders cp, mv and rename incapable of doing anything
with the file. Is there a way to prevent modeller from
appending the question mark to the created files?
Thanks,
Starr
------------------------------
Message: 2
Date: Thu, 08 Dec
2005 11:17:16 -0800
From: Modeller Caretaker
Subject: Re: [modeller_usage] file name problem
To: Starr Hazard
Cc: modeller_usage@salilab.org
Message-ID: <439886BC.6050700@salilab.org>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Starr Hazard wrote:
> mdl.assess_dope(output='ENERGY_PROFILE NO_REPORT',
> file=code+'.profile',
> normalize_profile=True, smoothing_window=15)
>
> are producing output files with a question mark in the name string.
>
> ABC31_HUMAN.BL09950001.pdb?.profile
If this is from your earlier script, you're getting 'code' from the
following bit of Python:
code = in_file.readline()
Note that readline() does not remove the line-end character(s), and
that's probably confusing Modeller. Try putting in
code = code.rstrip('\r\n')
after you read the line from your file.
> The question mark renders cp,
mv and rename incapable of doing anything
> with the file.
You can just quote the filename, or escape the ? with a \ character, to
make cp, mv and friends work with it.
Ben Webb, Modeller Caretaker
--
modeller-care@salilab.org http://www.salilab.org/modeller/
Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage
------------------------------
Message: 3
Date: Thu, 8 Dec 2005 13:15:23 -0800 (PST)
From: Shirley Li
Subject: [modeller_usage] Re: To Model missing domains in the content
of the rest
To: modeller_usage@salilab.org
Message-ID: <20051208211523.94416.qmail@web53801.mail.yahoo.com>
Content-Type: text/plain; charset="iso-8859-1"
Dear MODELLER experts,
I have a target protein, whose X-ray structure is PARTIALLY available (the middle part, named domain B). There are two big regions missing (domain A & C) in the crystal structure, with more than 50
residues in each I would like to use MODELLER to model domain A & C, and there are templates available. I wonder if it is possible to include THE CONTENT OF domain B. in another word, to create a complete model of A-B-C while keep the coordinates of B domain fixed.
Any help/information will be greatly appreciated.
hi
its possible, just include the sequence of domain B in the ali file along with the seqence of domains A and B . the program will definitely orient the known structure with the calculated structure, but still u have to minimize it later on to infer the proper alignment
with regards
rathankar
Shirley
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Message: 4
Date: Thu, 8 Dec 2005 14:03:57 -0800 (PST)
From: Shirley Li
Subject: [modeller_usage] To use separate templates for different
region of a protein
To: modeller_usage@salilab.org
Message-ID: <20051208220357.23940.qmail@web53808.mail.yahoo.com>
Content-Type: text/plain; charset="iso-8859-1"
Dear All,
With MODELLER, I wonder if it is possible to use different template(s) for different region of one target protein. For example, One protein has domain 1, 2 and 3. I would like to construct a complete model of this protein, with templates A and B for domain 1, templates C,D,and E for domain 3, and domain 2 already has coordinates/structure, which need to be preserved in the complete model.
Is there any way to do the above? If so, how? I tried to use the
"inifile" feature and use the existing coordinate file of domain 2 as "inifile". while I got error message of " Atom index is out of range (iatm,natm)".
Any help/information will be very much appreciated.
Shirley
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