- modeller_usage - salilab.org

plotdope problem
by jacques deruchoud 29 Oct '07

29 Oct '07

hello, I have some problem using plotdope, as I understand the perl script extract not the correct column from the .profile file, so I get only 0 value in the .dat file did anyone experience the same problems ? could anyone run correctly the plotdope script ? thanks for the info jacques dumont __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

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help
by simran jeet 24 Oct '07

24 Oct '07

After modeling a protein using modeller some residues remain in the disallowed regions of ramachandran plot. Is that model incorrect ? Is there any way to remove bad contacts and residues in disallowed regions after modeling? I tried to overcome this problem using Deepview by selecting two or more residues and building loop. Though the residues in disallowed regions and bad contacts become zero by this procedure but structure is affected. What should I do please guide me.

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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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