- modeller_usage - salilab.org

Problem with MODELLER6v2
by Ludovic Pétain 12 Apr '06

12 Apr '06

Hello. Here is my script (for MODELLER6v2): INCLUDE SET ATOM_FILES_DIRECTORY='' SET ALNFILE='GPR43_ES_HSA#2.ali' SET KNOWNS='rhodo_1u19' SET SEQUENCE='GPR43_ES_HSA' SET OUTPUT_CONTROL=1 1 1 1 1 SET STARTING_MODEL=1 SET ENDING_MODEL=1 CALL ROUTINE='model' #Redefine the special_restraints routine to disable energy optimization on the residues 123 to 143 SUBROUTINE ROUTINE='special_restraints' DELETE_RESTRAINT RESIDUE_IDS='123' '124' END_SUBROUTINE #energy optimization ENERGY OUTPUT='SHORT' OPTIMIZE OPTIMIZATION_METHOD=1,MAX_ITERATIONS=10 But I when I run the script, here is the error message : No ":" in ATOM:RESID[CHAINID] atom identifier I have replaced several times the string after 'RESIDUE_IDS=' ( for example: '123 :','124 :' ), but it doesn't change anything. Thanks by advance. Ludovic PETAIN EUROSCREEN SA Tel +32 71 348 500 Fax +32 71 348 519 Direct +32 71 348 5XX http://www.euroscreen.com This message contains information that may be confidential and privileged and is intended solely for the use of the intended recipient. Unless you are the intended recipient (or authorized to receive for the intended recipient), you may not use, copy or disclose to anyone the message and any attachments or any information contained in the message. If you have received this message in error, please notify Euroscreen at +32 71 348 500 or by reply e-mail and destroy all copies of this message and any attachments.

3 3

Loop bias
by Joel Tyndall 09 Apr '06

09 Apr '06

Hi folks, I'm looking at a group of templates where only one of them has an "extended" beta sheet / loop region. This single template is closer to the model sequence (in this region only) than the other templates. Is there a way to bias the construction of this particular "loop" towards only one template! I don't want to just build a model based on this structure alone however. Cheers Joel -- Joel Tyndall, PhD Lecturer National School of Pharmacy University of Otago PO Box 913 Dunedin New Zealand Pukenga Te Kura Taiwhanga Putaiao Te Whare Wananga o Otago Pouaka Poutapeta 913 Otepoti Aotearoa Ph / Waea +64 3 4797293 Fax / Waeawhakaahua +64 3 4797034

2 1

Getting alignment positions fixed
by Paul Wilhelm Elsinghorst 09 Apr '06

09 Apr '06

Hi folks, I have a problem getting the alignment of two sequences the way I want it to be. Please have a look at this picture to see what I'm looking for: http://pwe.no-ip.org/other/modeller.jpg I'd like to set up my alignment file in a way that the alignment done by modeller gives exactly this result. I fiddeled with fixed_pos things but couldn't get it to work, actually I didn't figure out how it really works. This is the file I have for now: http://pwe.no-ip.org/other/modeller.txt If anyone could assist me a little or point me to the right direction I'd be glad. Thanks so far, Paul

2 1

automodel optimization
by Alex Brown 07 Apr '06

07 Apr '06

Hi. Sorry for being such a nuisance, but I have a question concerning model optimization when using automodel. I would presume that automodel uses model.optimize when optimizing a model, with a default of a single pass, automodel.repeat_optimization having a default value of 1. However, according to the manual, the optimization_method parameter of model.optimize has default value of 999, whereas it should have a value of either 1 or 3. What default optimization method does automodel use, can it be changed, and what does the model.optimize default of 999 mean ? OK - that's three questions ! Many thanks, Alex

2 1

model.pick_atoms problem
by Alex Brown 06 Apr '06

06 Apr '06

Hi. This may, or may not, be a problem, but I have found that using the selection_segment argument 'FIRST:A' , 'LAST:A' in model.pick_atoms doesn't appear to work properly. In fact, the whole molecule (all chains) is selected (i.e. the argument acts as if it were 'FIRST:', 'LAST:'). Correct selection does occur if discrete, numbered residues are used, as in '1:A', '100:A', selecting atoms in a segment from residues 1 to 100 in chain A. Is this correct, or have I stumbled across a bug. Cheers, Alex.

2 1

Weighing the restraints differenlty on the modeller-fly
by Mehmet SEN 05 Apr '06

05 Apr '06

Hello I am running modeller8v2 to get the model of my protein. In this case, I do have the NMR experimental data (about 400 restraints). Now, I am able to run my structures with restraints I want to have from the NMR experiments. In this case, I would like to do following. I would like modeller restrains to be applied region for which I do not have any restrains, but for the region where I can define secondary structures via NMR experiment, I want to turn off modeller-derived restrains, or decrease weighing factor of the modeller-derived restraints, that is, I would like my restraints to weigh more then modeller-derived restraints. If you need make any comments on this subject, I would be so much pleased. If you have performed anything like that, and have any script available, I really want to get it. Mehmet Sen --------------------------------- New Yahoo! Messenger with Voice. Call regular phones from your PC for low, low rates.

2 1

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.

3 2

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

3 3

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

2 2

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

2 2