Re: [modeller_usage] What is the mistake in this set of lines
To:
Subject: Re: [modeller_usage] What is the mistake in this set of lines
From: Igor Dvortsov <>
Date: Mon, 31 Oct 2011 18:33:01 +0300
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)
it's python question, not modeller. your for-cycle executes 2 times, in
first run code=1SHWA, then code=1SHXA, atomfile=1SHX, chan=A and body of
for-cycle executed, in second run code=pdbfile,
atomfile=fileName,chain=A. if you have variables pdbfile and fileName as
strings defined, the body of for-cycle will be executed again. it seems,
this is not that you supposed. maybe, something like this
atomfile='1SHX'
for (code,chain) in (('1SHWA','A'),('1SHXA','A')):
aln.append_model(mdl, atom_files=code, align_codes=atomfile)
kind regards, Igor
пишет:
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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)
----------------------------------------------------------------------
Message: 1
Date: Sat, 29 Oct 2011 10:39:22 +0530 (IST)
From: Ashish Runthala <>
Subject: Re: [modeller_usage] What is the mistake in this set of
lines?
To: modeller <>
Message-ID:
<>
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" <>
To: "modeller" <>
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
------------------------------
Message: 2
Date: Sun, 30 Oct 2011 15:52:37 +0530 (IST)
From: Ashish Runthala <>
Subject: Re: [modeller_usage] What is the mistake in this set of
lines?
To: modeller <>
Message-ID:
<>
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" <>
To: "modeller" <>
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" <>
To: "modeller" <>
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
------------------------------
Message: 3
Date: Mon, 31 Oct 2011 06:16:22 -0800
From: junior <>
Subject: [modeller_usage] Build a model with multiple models
To:
Message-ID:
<CAEJMx6wtgQ8U6MAG+>
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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