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Today's Topics:

  1. Re: modeling different conformations of a protein from
      related structures (Modeller Caretaker)
  2. Regarding Constraints covered in the    Salign_Multiple_Struc.py
      (Ashish Runthala)
  3. Re: Regarding Constraints covered in the
      Salign_Multiple_Struc.py (Ashish Runthala)
  4. modeller.parallel.communicator.RemoteError (Xiao-Ping Zhang)


----------------------------------------------------------------------

Message: 1
Date: Mon, 07 May 2012 08:06:04 -0700
From: Modeller Caretaker <modeller-care@salilab.org>
To: EGY <mp.2egy@gmail.com>
Cc: modeller_usage@salilab.org
Subject: Re: [modeller_usage] modeling different conformations of a
    protein from related structures
Message-ID: <4FA7E4DC.7070200@salilab.org>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

On 5/7/12 7:35 AM, EGY wrote:
> Sorry, my question is much more elementary.

Your original question was addressed just last week on the mailing list:
http://salilab.org/archives/modeller_usage/2012/msg00152.html

> I see an example from the tutorial (Advanced Modeling, Modeling
> ligands in the binding site) on an alignment similar to what I want.
> However, I don't see the associated script to give this alignment

You make the alignment yourself, e.g. in a text editor. There is no
script to generate it for you automatically.

> In this example, only the binding pocket of the 1emd structure was
> included in the alignment. I would also need to know how not to
> include a region in one of the other sequences.

Either edit the PDB file to remove the region you don't want to include,
or see http://salilab.org/modeller/9.10/FAQ.html#2

    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: Wed, 9 May 2012 12:14:41 +0530 (IST)
From: Ashish Runthala      <ashishr@bits-pilani.ac.in>
To: modeller <modeller_usage@salilab.org>
Subject: [modeller_usage] Regarding Constraints covered in the
    Salign_Multiple_Struc.py
Message-ID:
    <2636755.831336545880971.JavaMail.root@mailserver.bits-pilani.ac.in>
Content-Type: text/plain; charset=utf-8

Dear Modellers,
Tell me a preliminary aspect of the script Salign_Multiple_Struc.py
If multiple local folds are present in the computed alignment of this script for different templates, something like this,

Template1>---AAAAAA---BBBBBBBB----*
Template2>--APPPAAA---BCBBBB------*
Template3>----AAA----BBBBBBBB-----*
Template4>----AA-------BB---------*

Elaborate the factors considered by MODELLER to put template2 close to the template1, and why template3 and 4 are kept away from template1 and closer to template2.

Is it minimal RMSD of local template chunks, equal chunk lengths or something else. Give me the complete list of the considered factors considered in MODELLER for such a computation.

Best Regards
Ashish



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


------------------------------

Message: 3
Date: Sun, 13 May 2012 20:06:23 +0530 (IST)
From: Ashish Runthala      <ashishr@bits-pilani.ac.in>
To: modeller <modeller_usage@salilab.org>
Subject: Re: [modeller_usage] Regarding Constraints covered in the
    Salign_Multiple_Struc.py
Message-ID:
    <27579291.59631336919783568.JavaMail.root@mailserver.bits-pilani.ac.in>
   
Content-Type: text/plain; charset=utf-8

Dear Modellers,
I sent this message a few days back too. What is the currently employed path to drive out of the reliable alignment mystery's vicious circle?
Tell me a preliminary aspect of the script Salign_Multiple_Struc.py
If multiple local folds are present in the computed alignment of this script for different templates, something like this,

Template1>---AAAAAA---BBBBBBBB----*
Template2>--APPPAAA---BCBBBB------*
Template3>----AAA----BBBBBBBB-----*
Template4>----AA-------BB---------*

Elaborate the factors considered by MODELLER to put template2 close to the template1, and why template3 and 4 are kept away from template1 and closer to template2.

Is it minimal RMSD of local template chunks, equal chunk lengths or something else. Give me the complete list of the considered factors considered in MODELLER for such a computation.

Best Regards
Ashish



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


------------------------------

Message: 4
Date: Tue, 15 May 2012 17:59:34 -0700
From: Xiao-Ping Zhang <xpzhang@ucdavis.edu>
To: Modeller Caretaker <modeller-care@salilab.org>
Cc: modeller_usage@salilab.org
Subject: [modeller_usage] modeller.parallel.communicator.RemoteError
Message-ID: <1337129974.5888.35.camel@localhost>
Content-Type: text/plain; charset="ISO-8859-1"

Hi,

I got the following error when trying to run a old python script (see
below) that worked very well before. A couple of days ago, I removed the
Java came from the system (Fedora 13) and installed Java from java.com
(jdk-7u4-linux-i586.rpm, jre-7u4-linux-i586.rpm) to fix a crash problem
of Jalview.

I wonder if the problem is related to the new Java or some other
problems.

Thank you.

XP

############ my script  ########################

# Homology modeling by the automodel class
from modeller import *              # Load standard Modeller classes
from modeller.automodel import *    # Load the automodel class
from modeller.parallel import *    # Load the parallel class,
                                    #to use  multiple processors


# Use 5 CPUs in a parallel job on this machine
j = job() # Cluster
j.append(local_slave())
j.append(local_slave())
j.append(local_slave())
j.append(local_slave())
j.append(local_slave())

log.verbose()    # request verbose output
env = environ()  # create a new MODELLER environment to build this model
in
env.io.hetatm = True


# directories for input atom files
env.io.atom_files_directory = ['.',
'/usr/share/doc/modeller-9v8/examples']


a = automodel(env,
              alnfile  = 'CC1295N.ali',    # alignment filename
              knowns  = ('1H6L', '1CVM1', '3AMR'),              # codes
of the templates
              sequence = 'CC1295N')              # code of the target
a.starting_model= 1                # index of the first model
a.ending_model  = 20                # index of the last model
                                    # (determines how many models to
calculate)
a.use_parallel_job(j)
a.make()                            # do the actual homology modeling



####################    Errors  ########################
Traceback (most recent call last):
  File "CC1295N_model.py", line 32, in ?
    a.make()                            # do the actual homologymodeling
  File "/usr/lib/modeller9.10/modlib/modeller/automodel/automodel.py",
line 107, in make
    self.multiple_models(atmsel)
  File "/usr/lib/modeller9.10/modlib/modeller/automodel/automodel.py",
line 208, in multiple_models
    self.parallel_multiple_models(atmsel)
  File "/usr/lib/modeller9.10/modlib/modeller/automodel/automodel.py",
line 228, in parallel_multiple_models
    self.outputs.extend(job.run_all_tasks())
  File "/usr/lib/modeller9.10/modlib/modeller/parallel/job.py", line
131, in run_all_tasks for task in self._finish_all_tasks():
  File "/usr/lib/modeller9.10/modlib/modeller/parallel/job.py", line
164, in _finish_all_tasks  task = self._process_event(obj, s)
  File "/usr/lib/modeller9.10/modlib/modeller/parallel/job.py", line
180, in _process_event task = obj.task_results()
  File "/usr/lib/modeller9.10/modlib/modeller/parallel/slave.py", line
61, in task_results r = self.get_data(allow_heartbeat=True)
  File "/usr/lib/modeller9.10/modlib/modeller/parallel/communicator.py",
line 89, in get_data (cmdtype, obj) = self._recv()
  File "/usr/lib/modeller9.10/modlib/modeller/parallel/communicator.py",
line 130, in _recv raise RemoteError(obj.exc, self)
modeller.parallel.communicator.RemoteError: IndexError: user_form__E>
Functional form 8195 out of range from <Slave on localhost>
#####################################################






-----Original Message-----
From: Modeller Caretaker <modeller-care@salilab.org>
To: modeller_usage@salilab.org
Subject: Re: [modeller_usage] Error: Ran out of slaves to run tasks
Date: Thu, 23 Feb 2012 10:54:11 -0800

On 2/21/12 9:39 AM, Modeller Caretaker wrote:
> On 02/21/2012 08:55 AM, Xiao-Ping Zhang wrote:
>> When I was refining loops for a model in parallel, I asked modeller to
>> generate 9999 models. But modeller stopped at 1245 with the following
>> error. The computer has six cores, modeller uses four of them. The other
>> two cores were free.
> ...
>> ValueError: Ran out of slaves to run tasks
>
> This means exactly what it says: all of the slaves died, so it had
> nowhere to run the loop model building tasks. Each slave generates its
> own output file (look for files ending in .slave). Look in there to see
> what the problem was with each slave.

To conclude: it turned out that each slave was running out of memory.
This is actually caused by a memory leak in Modeller that only affects
parallel loopmodel runs. A patch is available to fix the problem at
http://salilab.org/modeller/wiki/Patches

    Ben Webb, Modeller Caretaker




------------------------------

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