[modeller_usage] regarding Dope score in optimize.py

-- 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 ------------------------------ _______________________________________________ modeller_usage mailing list modeller_usage@salilab.org https://salilab.org/mailman/listinfo/modeller_usage End of modeller_usage Digest, Vol 11, Issue 58 **********************************************