Dear Junior, What you actually want to state? Do you need to build an average model based on the topology of 10 models? For this you may use them as templates without calling the chain identifiers.
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: Monday, October 31, 2011 7:46:24 PM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi Subject: modeller_usage Digest, Vol 10, Issue 132
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Today's Topics:
1. Re: What is the mistake in this set of lines? (Ashish Runthala) 2. Re: What is the mistake in this set of lines? (Ashish Runthala) 3. Build a model with multiple models (junior)
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Message: 1 Date: Sat, 29 Oct 2011 10:39:22 +0530 (IST) From: Ashish Runthala ashishr@bits-pilani.ac.in Subject: Re: [modeller_usage] What is the mistake in this set of lines? To: modeller modeller_usage@salilab.org Message-ID: 20822758.298281319864962852.JavaMail.root@mailserver.bits-pilani.ac.in Content-Type: text/plain; charset=utf-8
Is it possible that i can declare some variables in python similar to the standard default MODELLER variables atomfile, pdbfile and code. How these variables are declared in MODELLER?
Thanks Ashish
Ashish Runthala, Lecturer, Structural Biology Cell, Biological Sciences Group, BITS, Pilani Rajasthan, INDIA
----- Original Message ----- From: "Ashish Runthala" ashishr@bits-pilani.ac.in To: "modeller" modeller_usage@salilab.org Sent: Friday, October 28, 2011 8:17:00 AM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi Subject: What is the mistake in this set of lines?
Dear Modellers, I wrote a script to do three template modeling for a target sequence from all the templates present in the same folder. The script is expected to take 1SHW, 1SHX fixed and the third one should be iteratively taken from the current folder.
MODELLER defines atom as any PDB or .atm template file and pdbfile is the keyword defined for template with chain ID. So when i use pdbfile for both 1SHW, 1SHX why it only takes the one with the 2nd entry. Like a normal variable initial template name changes when it is assigned to some other template.
So what is the mistake in this set of lines? How should i solve this task.
for (code, code, atomfile, chain) in (('1SHWA','1SHXA','1SHX','A'), (pdbfile,pdbfile,fileName,'A')): mdl = model(env, file=atomfile, model_segment=('FIRST:'+chain, 'LAST:'+chain)) aln.append_model(mdl, atom_files=code, align_codes=atomfile)
Thanks, Ashish
Ashish Runthala, Lecturer, Structural Biology Cell, Biological Sciences Group, BITS, Pilani Rajasthan, INDIA
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Message: 2 Date: Sun, 30 Oct 2011 15:52:37 +0530 (IST) From: Ashish Runthala ashishr@bits-pilani.ac.in Subject: Re: [modeller_usage] What is the mistake in this set of lines? To: modeller modeller_usage@salilab.org Message-ID: 15487763.309941319970157647.JavaMail.root@mailserver.bits-pilani.ac.in Content-Type: text/plain; charset=utf-8
What nobody knows to declare such data types? Any guesses with anyone what it should be, as probably there in MODELLER modules and functional binaries.
Ashish Runthala, Lecturer, Structural Biology Cell, Biological Sciences Group, BITS, Pilani Rajasthan, INDIA
----- Original Message ----- From: "Ashish Runthala" ashishr@bits-pilani.ac.in To: "modeller" modeller_usage@salilab.org Sent: Saturday, October 29, 2011 10:39:22 AM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi Subject: Re: What is the mistake in this set of lines?
Is it possible that i can declare some variables in python similar to the standard default MODELLER variables atomfile, pdbfile and code. How these variables are declared in MODELLER?
Thanks Ashish
Ashish Runthala, Lecturer, Structural Biology Cell, Biological Sciences Group, BITS, Pilani Rajasthan, INDIA
----- Original Message ----- From: "Ashish Runthala" ashishr@bits-pilani.ac.in To: "modeller" modeller_usage@salilab.org Sent: Friday, October 28, 2011 8:17:00 AM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi Subject: What is the mistake in this set of lines?
Dear Modellers, I wrote a script to do three template modeling for a target sequence from all the templates present in the same folder. The script is expected to take 1SHW, 1SHX fixed and the third one should be iteratively taken from the current folder.
MODELLER defines atom as any PDB or .atm template file and pdbfile is the keyword defined for template with chain ID. So when i use pdbfile for both 1SHW, 1SHX why it only takes the one with the 2nd entry. Like a normal variable initial template name changes when it is assigned to some other template.
So what is the mistake in this set of lines? How should i solve this task.
for (code, code, atomfile, chain) in (('1SHWA','1SHXA','1SHX','A'), (pdbfile,pdbfile,fileName,'A')): mdl = model(env, file=atomfile, model_segment=('FIRST:'+chain, 'LAST:'+chain)) aln.append_model(mdl, atom_files=code, align_codes=atomfile)
Thanks, Ashish
Ashish Runthala, Lecturer, Structural Biology Cell, Biological Sciences Group, BITS, Pilani Rajasthan, INDIA
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Message: 3 Date: Mon, 31 Oct 2011 06:16:22 -0800 From: junior sam.kauba@gmail.com Subject: [modeller_usage] Build a model with multiple models To: modeller_usage@salilab.org Message-ID: CAEJMx6wtgQ8U6MAG+uepWiwwcvTHbCvqFZ824_jJJS3cM2jciQ@mail.gmail.com Content-Type: text/plain; charset=ISO-8859-1
Hi,
How do I build a PDB file containing more than 10 models?
Thank you.
Sam Kauba
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Ashish Runthala