Dear Mustafa, Don't fall in multichain scripts etc. Specify chains in model_mult.py or model_multiple.py from all of your n chains using n different copies of your template, available in the same folder. This will solve purpose for alignment too.

Good Luck Ashish

Ashish Runthala, Lecturer, Structural Biology Cell, Biological Sciences Group, BITS, Pilani Rajasthan, INDIA

----- Original Message ----- From: "modeller usage-request" modeller_usage-request@salilab.org To: "modeller usage" modeller_usage@salilab.org Sent: Wednesday, July 13, 2011 1:46:00 PM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi Subject: modeller_usage Digest, Vol 10, Issue 98

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Today's Topics:

1. Re: optimize.py (Modeller Caretaker) 2. Re: Modelling of multi-domain protein from oligomeric template (Modeller Caretaker) 3. Multi-chain modeling (MUSTAFA BUGHIO) 4. Disulphide patch (MUSTAFA BUGHIO)

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Message: 1 Date: Wed, 06 Jul 2011 12:18:04 -0700 From: Modeller Caretaker modeller-care@salilab.org Subject: Re: [modeller_usage] optimize.py To: MUSTAFA BUGHIO mustafab4@gmail.com Cc: modeller_usage@salilab.org Message-ID: 4E14B4EC.5060207@salilab.org Content-Type: text/plain; charset=ISO-8859-1; format=flowed

On 07/06/2011 06:58 AM, MUSTAFA BUGHIO wrote: > I am trying to do energy minimization step by running optimize.py script > file but it does not execute every time i tried to run and got the > following error, i will be thankful if you help me get this problem > resolved. > > IOError: pdbnam_____E> Filename for PDB code not found: hGLR > Directories: ../atom_files > Extensions : :.atm:.pdb:.ent:.crd > (Also tried prepending 'pdb', looking for .Z, .gz, .bz2, > .7z, .xz, > and trying PDB-style subdirectories - e.g. ab for > pdb1abc.ent)

Just like it says, you asked it to open a PDB file called "hGLR" and told it to look for it in the ../atom_files directory, and it can't find it in there. Set env.io.atom_files_directory to the directory containing your PDB file (or remove that line entirely if it's in the same directory as the script).

Ben Webb, Modeller Caretaker