Dear James,

you have to define it with alignment file.

like you have template sequence for example...

>P1;xyz structureX:xyz.pdb: 11 :A:+364 :A LGDTNLFKPIKIGNNELLH.*

>P1;ABC sequence:ABC: : : : ::: 0.00: 0.00 MSDSRLFKPLKVGSIELL.*

here . defines the Heteroatom

then use ali.py script and don't forget ligand must be present in template pdb file

with regards, Rajesh Kumar Gazara

On Wed, Apr 16, 2014 at 9:40 AM, modeller_usage-request@salilab.org wrote:

> Send modeller_usage mailing list submissions to > modeller_usage@salilab.org > > To subscribe or unsubscribe via the World Wide Web, visit > https://salilab.org/mailman/listinfo/modeller_usage > or, via email, send a message with subject or body 'help' to > modeller_usage-request@salilab.org > > You can reach the person managing the list at > modeller_usage-owner@salilab.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of modeller_usage digest..." > > > 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 modeller-care@salilab.org > To: James Starlight jmsstarlight@gmail.com, modeller_usage > modeller_usage@salilab.org > Subject: Re: [modeller_usage] Multiple sequence alignment + modeling > in one script > Message-ID: 534D80A2.5090504@salilab.org > 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 > -- > modeller-care@salilab.org 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 modeller-care@salilab.org > To: James Starlight jmsstarlight@gmail.com, modeller_usage > modeller_usage@salilab.org > Subject: Re: [modeller_usage] Including ligand from template > Message-ID: 534D826B.6060002@salilab.org > 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 > -- > modeller-care@salilab.org 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 jmsstarlight@gmail.com > To: Modeller Caretaker modeller-care@salilab.org, modeller_usage > modeller_usage@salilab.org > Subject: Re: [modeller_usage] Including ligand from template > Message-ID: > < > CAALQopx1nYLFQAGxct_5SGeMJDMLpwBx2t2_b44Oy38esCxeuQ@mail.gmail.com> > 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 modeller-care@salilab.org: > > > 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 > > -- > > modeller-care@salilab.org http://www.salilab.org/modeller/ > > Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage > > >