March 2006 - modeller_usage

Modeller usage with Python 2.4?
by Dow_Hurst 02 Apr '06

02 Apr '06

After perusing the archives for explanations of Modeller and Python interactions, it isn't apparent to me that Modeller couldn't use a later interpreter and modules if the paths are set correctly. I understand that Modeller can be made aware of standard python 2.3 modules with the PYTHONHOME variable. However, I haven't found a clear yes or no on using a Python 2.4 standard installation with Modeller. Is it possible to disable the internal Python 2.3 interpreter linked into Modeller and force Modeller to use a system's Python 2.4 installation? If not, then I could just compile/install Python 2.3. I use SUSE 9.3 and 10.0 mainly at the moment in our lab at UNCG on all the machines so I don't have a native install of the older Python. Uninstalling Python 2.4 breaks several packages so a side by side compile/install is probably easiest. Thanks for your help, Dow No sig.

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Problem in running Modeller 8v2
by Nagesh Chakka 30 Mar '06

30 Mar '06

Hi All, I have just installed Modeller version 8v2 and tried to run the following script. # Homology modelling by the allhmodel class from modeller.automodel import * # Load the automodel class log.verbose() # request verbose output env = environ() # create a new MODELLER environment to build this model in # directories for input atom files env.io.atom_files_directory = '/home/nagesh/modelling/structure' a = allhmodel(env, alnfile = 'inputAlignment_files/xenDpl.pir', # alignment filename knowns = '1I17', # codes of the templates sequence = 'xenopusDoppel') # code of the target a.starting_model= 1 # index of the first model a.ending_model = 1 # index of the last model # (determines how many models to calculate) a.make() # do the actual homology modelling Running the script is giving the following message. [nagesh@vogon ~/modelling]$ mod8v2 model_dpl_latest.top Traceback (most recent call last): File "<string>", line 1, in ? File "/usr/lib/modeller8v2/modlib/modeller/runtop.py", line 79, in run self.runlines(self.lines) File "/usr/lib/modeller8v2/modlib/modeller/runtop.py", line 129, in runlines self.set_top_vars(vars) File "/usr/lib/modeller8v2/modlib/modeller/runtop.py", line 256, in set_top_vars raise IndexError, "Variable name not recognized: %s" % varname.upper () IndexError: Variable name not recognized: MODELLER.AUTOMODEL What can be the probable reason for this problem. Thank you in advance. Nagesh

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About the topini.patch for 8v2 and the energy
by Zhiqiang Ye 29 Mar '06

29 Mar '06

Dear all, I have two questions about modeller. The first one is about the patch file topini.patch for 8v2 (http://salilab.org/modeller/wiki/Patches) Before the patching, I have run many modelling jobs with error message, do I need to rerun the jobs after the patching? I used python scripts to do my modelling job, not TOP scripts. The second question is the model.energy(). Can I compare the energy values between proteins of different size? If not, can I normalize them so that I can compare them? Thank you very much! -- Zhiqiang Ye

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Objective Function vs. Molecular PDF
by Leyla Celik 28 Mar '06

28 Mar '06

Hello, In the end of the log-file from a MODELLER (8v1) run there is a summation of the quality of the model: >> Summary of successfully produced models: Filename molpdf ---------------------------------------- A.B99990001.pdb 2355.08740 N.B99990002.pdb 2376.38696 ... ... My question now is if these values really are the molecular pdfs or if it is the objective function? The reason I am asking is, that we have built homology models of the same protein two times using the same sequence alignment and template pdb-files only changing the refinement level - one is the default the other is md_level = refine.slow_large. In the second run the values in the log-file range around 9000. If the value really represents the mol PDF this is good, but if it is the objective function, the first models (default refinement) with the lower values are much better... Another question: What is the default level of refinement actually? I have not been able to deduce this from the manual. I hope someone can help me with this:-) Thanks in advance Leyla -- Leyla Celik Ph.d. student Department of Chemistry University of Aarhus Langelandsgade 140 DK-8000 Aarhus C Denmark Tel: +45 8942 3869 e-mail: lc(a)chem.au.dk

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problem in running modeller8v0
by aneesh goyal 28 Mar '06

28 Mar '06

hello, i am trying to run modeller8v0 version on windows 2000. But i am getting these errors which i am unable to make out. D:\Data\Aneesh>mod8v0 model_JC1V2.py 'import site' failed; use -v for traceback Traceback (most recent call last): File "model_JC1V2.py", line 18, in ? a.make() # do the actual homology modelling File "C:\Program Files\Modeller8v0/modlib\modeller\automodel\automodel.py", li ne 88, in make self.homcsr(exit_stage) File "C:\Program Files\Modeller8v0/modlib\modeller\automodel\automodel.py", li ne 299, in homcsr aln = self.read_alignment() File "C:\Program Files\Modeller8v0/modlib\modeller\automodel\automodel.py", li ne 293, in read_alignment aln.append(file=self.alnfile, align_codes=self.knowns+[self.sequence]) File "C:\Program Files\Modeller8v0/modlib\modeller\alignment.py", line 36, in append return self.__int_append('alignment.append', io, vars) File "C:\Program Files\Modeller8v0/modlib\modeller\alignment.py", line 65, in __int_append return self.top.read_alignment(logname, aln=self.modpt, io=io.modpt, File "C:\Program Files\Modeller8v0/modlib\modeller\util\top.py", line 42, in r ead_alignment self.error_check() File "C:\Program Files\Modeller8v0/modlib\modeller\util\top.py", line 16, in e rror_check raise ModellerError modeller.error.ModellerError I will be very greatful if somebody can give me some hints. regads aneesh __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

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starting Modeller program
by Dinah Farrington 27 Mar '06

27 Mar '06

Dear Caretaker, I am a brand new user of Modeller, and my question is very basic. I am not too familiar with DOS. I installed the Modeller version which works with Windows, and when I start, a black DOS screen opens up. It tells me to type 'mod8v2' to start. When this is typed in, I get a line starting "usage" . What should I do to have access to Modeller? I have tried some simple DOS commands but it does not help. If you have some suggestions for learning how to use DOS commands (like a manual, or tutorial) I would be glad to hear them. Thank you in advance, D. Farrington, ALBANY, NY ----------------------------------------- CONFIDENTIALITY NOTICE: This email and any attachments may contain confidential information that is protected by law and is for the sole use of the individuals or entities to which it is addressed. If you are not the intended recipient, please notify the sender by replying to this email and destroying all copies of the communication and attachments. Further use, disclosure, copying, distribution of, or reliance upon the contents of this email and attachments is strictly prohibited. To contact Albany Medical Center, or for a copy of our privacy practices, please visit us on the Internet at www.amc.edu.

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side chain packing issues
by teca calcagno galvao 27 Mar '06

27 Mar '06

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error saying max_pdf exceeded reg
by Bala Murugan 27 Mar '06

27 Mar '06

Hi modellers, I am new to this list and to modeller too. I was wondering that anybody faces the problem connected with max_pdf error. I have submitted modeller a job to model a protein of around 1200 residues. In the log it says that, >>summary of failed models 1fdx.B999900001.PDB obj.func. (109595.656) exceeded max_molpdf (100000.000). I don't know what is meant by max_molpdf. How should i proceed from this point? Thanks in advance. With best regards, P.Balamurugan Yours truly, P.BalaMurugan. -------------------------------------------------- "Science is built up of facts, as a house is built up of stones,but an accumulation of facts is no more a science than a heap of stones is a house"-Henri Poincare

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calculate RMSD
by Xia Jiang 22 Mar '06

22 Mar '06

Dear MODELLER developers/users, I have a question regarding caculating RMSD between residues. Using MODELLER command SUPERPOSE, we can get number of residues that within some cutoff (e.g. 3A).But how can we get which exact pairs of residues are within this cutoff? We also tried COMPARE command, but it does not give us detail of RMSD between residues given an alignment. Do you know what is the top command to do so? Thanks Xia Jiang ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Prof. Sjolander's Group BioEngineering Dept. UC Berkeley xiajiang(a)berkeley.edu ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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Please help me with tutorial error
by Claire Wei 21 Mar '06

21 Mar '06

Hi Modellers, I am pretty new using MODELLER. I met some problem with the tutorials. http://www.salilab.org/modeller/7v7/tutorial/basic.html I am using MODELLER 8v2. Thanks a lot if someone could tell me what might be wrong. Here is the seq_search.top file: SET SEARCH_RANDOMIZATIONS = 100 SET FILE = 'TvLDH.ali' READ_SEQUENCE_DB SEQUENCE_SEARCH ALIGN_CODES = 'TvLDH', DATA_FILE = ON Here is the seq_search.log file: --------- Kind, OS, HostName, Kernel, Processor: 4, Linux localhost.localdomain 2.6.9-22.ELsmp i686 Date and time of compilation : 02/28/2006 18:28:36 MODELLER executable type : i386-intel8 Job starting time (YY/MM/DD HH:MM:SS): 2006/03/21 11:52:24.775 SEQ_DATABASE_FILE : ${MODINSTALL8v2}/modlib//CHAINS_all.seq SEQ_DATABASE_FORMAT : PIR CHAINS_LIST : ${MODINSTALL8v2}/modlib//CHAINS_3.0_40_XN.cod CLEAN_SEQUENCES : T MINMAX_DB_SEQ_LEN : 0 999999 Number of sequences : 6869 Number of residues : 1543994 Length of longest sequence: 1491 sequenc_587E> Run alignment.append() or make alignment first. top_error__E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 Dynamically allocated memory at finish [B,kB,MB]: 5317486 5192.857 5.071 Starting time : 2006/03/21 11:52:24.775 Closing time : 2006/03/21 12:35:30.209 Total CPU time [seconds] : 2585.59 ------------ --------------------------------- Yahoo! Mail Use Photomail to share photos without annoying attachments.

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