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Today's Topics:
1. Re: Multiple sequence alignment + modeling in one script
(Modeller Caretaker)
2. Re: Including ligand from template (Modeller Caretaker)
3. Re: Including ligand from template (James Starlight)
----------------------------------------------------------------------
Message: 1
Date: Tue, 15 Apr 2014 11:55:30 -0700
From: Modeller Caretaker <">>
To: James Starlight <">>, modeller_usage
<">>
Subject: Re: [modeller_usage] Multiple sequence alignment + modeling
in one script
Message-ID: <">>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
On 4/15/14, 12:11 AM, James Starlight wrote:
> I've forced with small problem during installation of the ModPipe: while
> running setup file it ask me
>
> You need to have a copy of MODELLER in the ext/mod/ directory.
> Please install it (see the documentation) then rerun this script.
>
> (here my modeller have been installed in the default dirs using
> sudo env KEY_MODELLER=***** dpkg -i modeller_9.13-1_amd64.deb
>
> how I could provide correct install path to dpkg?
See the documentation, like it suggests? ;) You need the .tar.gz
installer, as detailed at
http://salilab.org/modpipe/doc/install-ext.html#install-ext
> 2) Are there any usefull tutotials for the ModPipe besides presented in
> readme ?
See above...
Ben Webb, Modeller Caretaker
--
"> http://www.salilab.org/modeller/
Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage
------------------------------
Message: 2
Date: Tue, 15 Apr 2014 12:03:07 -0700
From: Modeller Caretaker <">>
To: James Starlight <">>, modeller_usage
<">>
Subject: Re: [modeller_usage] Including ligand from template
Message-ID: <">>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
On 4/15/14, 2:05 AM, James Starlight wrote:
> I've followed 1st modeller tutorial making alignment of my target
> against 1 template (with the inclusion of hetatm from the template). As
> the result I've obtained the below alignment
As pointed out already, you haven't told Modeller to put the ligand in
the model. Is it possible that you modified the 2rh1.pdb file? Your
template sequence doesn't match the one in 2rh1 from PDB (there's an
extra sequence in the official PDB from residue 1002:A to 1161:A that
isn't in yours). Maybe you removed the ligand by mistake too.
Ben Webb, Modeller Caretaker
--
"> http://www.salilab.org/modeller/
Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage
------------------------------
Message: 3
Date: Wed, 16 Apr 2014 10:40:08 +0400
From: James Starlight <">>
To: Modeller Caretaker <">>, modeller_usage
<">>
Subject: Re: [modeller_usage] Including ligand from template
Message-ID:
<">>
Content-Type: text/plain; charset="utf-8"
Thanks for suggestions again!
Could you tell me as well
1) what should I provide to the below ali.py script to copy HETATM from
the template to the model
env = environ()
aln = alignment(env)
# Read in HETATM records from template PDBs
env.io.hetatm = True
env.io.hydrogen= True
mdl = model(env, file='3eml', model_segment=('FIRST:A','LAST:A'))
aln.append_model(mdl, align_codes='3emlA', atom_files='3eml.pdb')
aln.append(file='od_r.ali', align_codes='od_r')
aln.align2d()
aln.write(file='result3.ali', alignment_format='PIR')
aln.write(file='result3.pap', alignment_format='PAP')
2) how salt bridges can be defined in the model taken from the template
with the homology cysteins in the same positions?
James
2014-04-15 23:03 GMT+04:00 Modeller Caretaker <">>:
> On 4/15/14, 2:05 AM, James Starlight wrote:
>
>> I've followed 1st modeller tutorial making alignment of my target
>> against 1 template (with the inclusion of hetatm from the template). As
>> the result I've obtained the below alignment
>>
>
> As pointed out already, you haven't told Modeller to put the ligand in the
> model. Is it possible that you modified the 2rh1.pdb file? Your template
> sequence doesn't match the one in 2rh1 from PDB (there's an extra sequence
> in the official PDB from residue 1002:A to 1161:A that isn't in yours).
> Maybe you removed the ligand by mistake too.
>
> Ben Webb, Modeller Caretaker
> --
> "> http://www.salilab.org/modeller/
> Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage
>
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