- modeller_usage - salilab.org

Refine
by Dany Naranjo Feliciano 23 Oct '07

23 Oct '07

Hi, When I use this script some parts of my protein appears streched. Should I put water molecule for better refinment? Why I obtein worse models with refine option? #Modelación por homología con un ligando transferido desde el molde from modeller import * # Carga las clases del Modeller from modeller.automodel import * # Carga la clase automodel log.verbose() # Solicita una salida detallada env = environ() # Crea un nuevo ambiente para construir para construir el modelo # Directorio del fichero pdb/atm de entrada env.io.atom_files_directory = './‘ # Lectura de los heteroátomos en el pdb molde env.io.hetatm = True a = dopehr_loopmodel(env, alnfile = 'hetatm2.ali', # Fichero del alineamiento knowns = '1gmyAok2.pdb', # Código del molde sequence = 'Q8I7B2_sequence') # Código del blanco a.starting_model= 1 # Índice del primer modelo a.ending_model= 50 # Índice del último modelo # (determina el número de modelos a calcular) a.md_level = refine.very_slow # refinar modelo a.loop.starting_model = 1 a.loop.ending_model = 2 a.loop.md_level = refine.very_slow # refinar lazos a.make() # Hacer los modelo Dany Naranjo Feliciano Lic. Bioquímica Grupo Biología Molecular Centro Nacional de Sanidad Agropecuaria (CENSA) Apartado 10. San José de las Lajas. La Habana. CP 32700. Cuba Teléfono 53-47-863014 ext 28 "Participe en Universidad 2008 del 11 al 15 de febrero del 2008. Palacio de Convenciones. La Habana. Cuba. http: //www.universidad2008.cu".

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how to generate large number of models without using automodel class
by harpreet singh 23 Oct '07

23 Oct '07

Dear Sir, Using automodel it is very easy to generate large number of models both for entire protein as well as for loops. But, I am trying to generate large number of models using model class. Will you please guide me how to achieve that and if possible what functions can be used. Thanks & Regards _________________________________________________________________ Climb to the top of the charts! Play Star Shuffle: the word scramble challenge with star power. http://club.live.com/star_shuffle.aspx?icid=starshuffle_wlmailtextlink_oct

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RMSD based clustering of models
by csreddy＠ncbs.res.in 22 Oct '07

22 Oct '07

Hi, By using modeller, I have generated 100 models. My next task is to cluster these models based on RMSD. Is there any option in the modeller to cluster models based on RMSD? Please let me know. Thanks in advance Regards Chandu -------------------------------------------------- C.CHANDRA SEKHAR REDDY(Research Scholar) Dr.SOWDHAMINI'S LAB NATIONAL CENTRE FOR BIOLOGICAL SCIENCES TATA INSTITUTE OF FUNDAMENTAL RESEARCH UAS-GKVK CAMPUS BELLARY ROAD BANGALORE-560065 INDIA PHONE NO.#+91-(0)80- 2366 6251 E.MAIL# csreddy(a)ncbs.res.in chandubio(a)yahoo.co.in URL# http://www.ncbs.res.in/ --------------------------------------------------

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Reg. model_energies.py
by Saravanan 21 Oct '07

21 Oct '07

I am using modeller8v2 in linux environment. When i try to execute model_energies.py, i got a error. "complete_pdb not defined" How can i solve this prolem? with regards, P.Saravanan Please don't print this e-mail unless you really need to. Save Trees.. P.Saravanan __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

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ImportError: No module named socket (or math)
by Greipel.Joachim＠MH-Hannover.DE 21 Oct '07

21 Oct '07

Hi all, I just installed Modeller 9v2 on my linux box and ran the examples. Occasionally I got the Error Messages ImportError: No module named socket resp. ImportError: No module named math. Does anybody know how to cope with this? Regards, Joachim (Here is an example of the output) mod9v2 center_of_mass.py Traceback (most recent call last): File "center_of_mass.py", line 3, in ? import math ImportError: No module named math mod9v2 selection.py mod9v2 parallel-msg.py Traceback (most recent call last): File "parallel-msg.py", line 2, in ? from modeller.parallel import * File "/network/apps/share/modeller-9v2/modlib/modeller/parallel/__init__.py", line 1, in ? from job import job File "/network/apps/share/modeller-9v2/modlib/modeller/parallel/job.py", line 1, in ? import socket, random, os, select ImportError: No module named socket mod9v2 parallel-task.py Traceback (most recent call last): File "parallel-task.py", line 2, in ? from modeller.parallel import * File "/network/apps/share/modeller-9v2/modlib/modeller/parallel/__init__.py", line 1, in ? from job import job File "/network/apps/share/modeller-9v2/modlib/modeller/parallel/job.py", line 1, in ? import socket, random, os, select ImportError: No module named socket

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regarding N terminus region
by simran jeet 17 Oct '07

17 Oct '07

I have a protein sequence whose N terminus region does not matches with the template. Is it neccessary that N and C terminus regions of a protein should be fixed for homology modeling? The n terminus region contains 12 residues.  There are long gaps also within the alignment. Can these regions be modelled by loop modelling? I am also attaching the alignment file.

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Warning messages
by csreddy＠ncbs.res.in 17 Oct '07

17 Oct '07

Hi All, I recently installed modller9v2 on the linux (UBUNTU) machine. I could modeller successfully, but I am getting few warning messages at the beginning of the execution. Below I am pasting the warning messages. Could not find platform independent libraries <prefix> Could not find platform dependent libraries <exec_prefix> Consider setting $PYTHONHOME to <prefix>[:<exec_prefix>] 'import site' failed; use -v for traceback I am thankful if some one can help me to correct it. Thnks in advance Regards Chandu -------------------------------------------------- C.CHANDRA SEKHAR REDDY(Research Scholar) Dr.SOWDHAMINI'S LAB NATIONAL CENTRE FOR BIOLOGICAL SCIENCES TATA INSTITUTE OF FUNDAMENTAL RESEARCH UAS-GKVK CAMPUS BELLARY ROAD BANGALORE-560065 INDIA PHONE NO.#+91-(0)80- 2366 6251 E.MAIL# csreddy(a)ncbs.res.in chandubio(a)yahoo.co.in URL# http://www.ncbs.res.in/ --------------------------------------------------

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regarding N terminus region
by simran jeet 17 Oct '07

17 Oct '07

I have a protein sequence whose N terminus region does not matches with the template. Is it neccessary that N and C terminus regions of a protein should be fixed for homology modeling? The n terminus region contains 12 residues.  There are long gaps also within the alignment. Can these regions be modelled by loop modelling? I am also attaching the alignment file.

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Re: [modeller_usage] RE : Re: Class mymodel: How to randomize coordinates
by Modeller Caretaker 11 Oct '07

11 Oct '07

Baptiste Legrand wrote: > Thanks for your answer, I didn't know that the default deviation is 4.0. > Is it interessant to set it to 8.0 or more or the models will be too far > from the template? Is there a theorical (estimation) limit to explore > the conformationnal space without deviate totally from the template? The deviation parameter controls the spread of initial models, not the final optimized models - if the optimization is functioning correctly, the optimized models should look like the template anyway. (However, optimization is not a 'solved' problem, which is why the initial model is the sequence threaded onto the template structure rather than, say, the extended chain or randomly placed points.) So in practice changing deviation will not have a large effect on your model generation (unless you set it to 0, in which case no randomization is done). Ben Webb, Modeller Caretaker -- modeller-care(a)salilab.org http://www.salilab.org/modeller/ Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage

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Class mymodel: How to randomize coordinates
by Baptiste Legrand 10 Oct '07

10 Oct '07

Hi all, I try to make models from a template, with constraints (Helix) and a randomization of the coordinates for each models. I set deviation to 4.0 but MODELLER dont use it. A part of my script: # Add Helix class mymodel(automodel): def special_restraints(self, aln): rsr = self.restraints at = self.atoms rsr.add(secondary_structure.alpha(self.residue_range('2:', '13:'))) # Build models, and assess with both DOPE and GA341 a = mymodel(env, alnfile = 'f125-1s35.ali', # alignment filename (use default: 'a = automodel', 'loopmodel' for loop, 'allhmodel' to add protons) knowns = '1j18', # codes of the templates (for multiple template, just add codes: knowns = ('1s35', '1quu')) sequence = 'f3s5', # code of the target deviation = 4.0, assess_methods =(assess.DOPE, assess.GA341)) # assessment scripts #inifile = 'my-initial.pdb') # use my initial structure What should I do to randomize in this case? Thanks in advance, Regards Baptiste --------------------------------- Ne gardez plus qu'une seule adresse mail ! Copiez vos mails vers Yahoo! Mail

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