- modeller_usage - salilab.org

question about tutorial build_profile basic
by Knut J Bjuland 22 Apr '10

22 Apr '10

I have read through the basic tutorial and I have question about section 2 selecting template. Where I can I read what the other collums are used for and what kind of information do the provide. I is colloum 6 though 9 I am interest about. Best regards Knut J

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(no subject)
by Davide Pirolli 22 Apr '10

22 Apr '10

Hello, <style type="text/css"> </style>I'm a PhD student and I'm using modeller version 9. I'd very glad if you could explain to me which is the solvation model used by modeller in the various steps (in particular in the simulated annealing refinement procedure, CG_minimization, MD etc.) and the temperatures at which SA is carried out in the high optimization level procedure. Many thanks in advance. Davide Pirolli Grazie a un gesto semplice puoi aiutare i malati del Policlinico "A. Gemelli", soprattutto nel campo delle cure palliative e della radioterapia oncologica e sintomatica, e puoi contribuire in prima persona alle iniziative promosse dal Centro di Ateneo per la solidarieta' internazionale e alla formazione di giovani meritevoli provenienti dai Paesi piÃ¹ bisognosi. Con questo messaggio istituzionale l'Ateneo dei cattolici italiani chiede un segno di amicizia e generosita', di cui molti Ti saranno riconoscenti. Dona il Tuo "5 x mille" all'Universita' Cattolica: codice fiscale 02133120150. Info: www.unicatt.it/5permille --- Le informazioni trasmesse sono destinate esclusivamente alla persona o alla societa' in indirizzo e sono da intendersi confidenziali e riservate. Ogni trasmissione, inoltro, diffusione o altro uso di queste informazioni a persone o societa' differenti dal destinatario e' proibita. Se ricevete questa comunicazione per errore, contattate il mittente e cancellate le informazioni da ogni computer. The information transmitted is intended only for the person or entity to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use, of or taking of any action in reliance upon, this information by persons or entities other than the intended recipient is prohibited. If you recived this in error please contact the sender and delete the material from any computer. ---

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ERROR: Radii must all be greater than zero.
by Thomas Evangelidis 21 Apr '10

21 Apr '10

Dear Modellers, I want to build models of a protein with ATP with the dopehr_loopmodel method. The problem is when I include ATP in the alignmnet I get the following error: Traceback (most recent call last): File "./build_model_parallel.py", line 28, in <module> results = j.run_all_tasks() File "/usr/lib64/python2.6/site-packages/modeller/parallel/job.py", line 127, in run_all_tasks for task in self._finish_all_tasks(): File "/usr/lib64/python2.6/site-packages/modeller/parallel/job.py", line 160, in _finish_all_tasks task = self._process_event(obj, s) File "/usr/lib64/python2.6/site-packages/modeller/parallel/job.py", line 176, in _process_event task = obj.task_results() File "/usr/lib64/python2.6/site-packages/modeller/parallel/slave.py", line 61, in task_results r = self.get_data(allow_heartbeat=True) File "/usr/lib64/python2.6/site-packages/modeller/parallel/communicator.py", line 84, in get_data (cmdtype, obj) = self._recv() File "/usr/lib64/python2.6/site-packages/modeller/parallel/communicator.py", line 125, in _recv raise RemoteError(obj.exc, self) modeller.parallel.communicator.RemoteError: <class '_modeller.ModellerError'>: e_gbsa__234E> Atom 1795 (type 94) has GB/SA radius 0.0000. Radii must all be greater than zero. Please edit the library file (e.g. modlib/solv.lib) to set a correct radius for this atom type. I'm not sure what radii I have to set and to what values. Is there any workaround with this? thanks, Tom

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align3d python script
by saibal das 20 Apr '10

20 Apr '10

Dear all, i want to use the align3d.py script for aligning my created model with pdb models but the script given in the modeller commands examples is not working and ends up showing the error in windows:PYTHON EXE IS NOT WORKING. the available script is ok or could anyone provide me with proper script for align3d. i am using modeller 9v3 for my work Thanking you saibal das M.sc bioinformatics BIT mesra India

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saibal das has invited you to open a Google mail account
by saibal das 20 Apr '10

20 Apr '10

I've been using Gmail and thought you might like to try it out. Here's an invitation to create an account. ----------------------------------------------------------------------- saibal das has invited you to open a free Gmail account. To accept this invitation and register for your account, visit http://mail.google.com/mail/a-b542546c04-1097337a65-40d46c73c96e1307 Once you create your account, saibal das will be notified with your new email address so you can stay in touch with Gmail! If you haven't already heard about Gmail, it's a new search-based webmail service that offers: - Over 2,700 megabytes (two gigabytes) of free storage - Built-in Google search that instantly finds any message you want - Automatic arrangement of messages and related replies into "conversations" - Powerful spam protection using innovative Google technology - No large, annoying ads--just small text ads and related pages that are relevant to the content of your messages To learn more about Gmail before registering, visit: http://mail.google.com/mail/help/benefits.html And, to see how easy it can be to switch to a new email service, check out our new switch guide: http://mail.google.com/mail/help/switch/ We're still working every day to improve Gmail, so we might ask for your comments and suggestions periodically. We hope you'll like Gmail. We do. And, it's only going to get better. Thanks, The Gmail Team (If clicking the URLs in this message does not work, copy and paste them into the address bar of your browser).

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modelling a large protein of 664 amino acids with its domain specific templates
by saibal das 19 Apr '10

19 Apr '10

hi all, i have a large protein of 664 amino acids long to model but a dont have a significant template matching sequence length but i do got all the domain specific model templates. if i want to model the entire sequence based on this templates which scripts to use. thank you saibal das m.sc bioinformatics India

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coulomb energy
by abdullah ahmed 19 Apr '10

19 Apr '10

Dear Modeller users, I am working on two structures where the insides of the structure do not have access to water. One structure contains a charged Lysine and a charged Glutamic acid residue facing each other, with distances favorable for electrostatic interactions. The other contains a negatively charged residue only. There are no other charges in either molecule, but there are a large number of Glutamines. The dielectric constant is set to 1. Theoretically, the structure with two opposite charges should have a higher coulomb energy. However, this is not the case after optimization (the single charge has a higher energy value). I would like to know if this is because: 1) I haven't used the coloumb energies properly? (I used the following line in the optimization.py script to switch it on: "env.edat.dynamic_coulomb= True") 2) Modeller calculates the electrostatic energies in a different way to what I has excepting? Thank you in advance for your reply, Abdullah Ahmed _________________________________________________________________ Hotmail: Free, trusted and rich email service. https://signup.live.com/signup.aspx?id=60969

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coulomb energy
by abdullah ahmed 19 Apr '10

19 Apr '10

Dear modeller users, I incorrectly wrote, "However, this is not the case after optimization (the single charge has a higher energy value)" in my previous mail. This should have been "the single charge has a lower energy value." Sorry about the inconvenience, Abdullah From: abdullah_renk_ahmed(a)hotmail.com To: modeller_usage(a)salilab.org; andrey.kajava(a)crbm.cnrs.fr Subject: coulomb energy Date: Mon, 19 Apr 2010 16:11:58 +0600 Dear Modeller users, I am working on two structures where the insides of the structure do not have access to water. One structure contains a charged Lysine and a charged Glutamic acid residue facing each other, with distances favorable for electrostatic interactions. The other contains a negatively charged residue only. There are no other charges in either molecule, but there are a large number of Glutamines. The dielectric constant is set to 1. Theoretically, the structure with two opposite charges should have a higher coulomb energy. However, this is not the case after optimization (the single charge has a higher energy value). I would like to know if this is because: 1) I haven't used the coloumb energies properly? (I used the following line in the optimization.py script to switch it on: "env.edat.dynamic_coulomb= True") 2) Modeller calculates the electrostatic energies in a different way to what I has excepting? Thank you in advance for your reply, Abdullah Ahmed Hotmail: Free, trusted and rich email service. Get it now. Your E-mail and More On-the-Go. Get Windows Live Hotmail Free. Sign up now. _________________________________________________________________ Your E-mail and More On-the-Go. Get Windows Live Hotmail Free. https://signup.live.com/signup.aspx?id=60969

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model with ligand
by Knut J Bjuland 15 Apr '10

15 Apr '10

I am useing modeller to do modell protein. There are some point that I do not get in adding the ligand. Is it possible to add the lign in the alignment witouth adding manual to the aln file. How do I instruct t saling to add the ligand. I have tried add env.io.hydrogen = True env.io.water = True env.io.hetatm=True with out much success. Knut J _________________________________________________________________ Hotmail: Powerful Free email with security by Microsoft. https://signup.live.com/signup.aspx?id=60969

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question about unusual bond length, bond angle, Chirality deviations
by Song, Hyundeok (songhk) 15 Apr '10

15 Apr '10

Dear Modeller users I generated the dimer by Modeller. Fasta sequence number of model(400) is 70 less than Fasta sequence number of template(470). Sequence identity between template and model is 24%. after selecting the template, I aligned them, and then I did loop modeling. (I attached the code at the bottom.) Finally I got final pdb structure, but when I checked my model, I found the below warning message. "Unusual bond length, unusual bond angle, Chirality deviations " I am a beginner, so I don't what should I do to correct above warning message. Please help me, Any suggestions or comments are welcomed. Thanks. Hyun. ---align2d.py---- from modeller import * env = environ() aln = alignment(env) mdl = model(env, file='****', model_segment=('FIRST:A','LAST:B')) aln.append_model(mdl, align_codes='******', atom_files='*****') aln.append(file='******.ali', align_codes='*****') aln.align2d() aln.write(file='**************.ali', alignment_format='PIR') aln.write(file='**************.pap', alignment_format='PAP') ---model-loop.py----- # Homology modeling by the automodel class from modeller import * from modeller.automodel import * # Load the automodel class log.verbose() env = environ() # directories for input atom files env.io.atom_files_directory = ['.', '../atom_files'] a = loopmodel(env, alnfile = '***************.ali', # alignment filename knowns = '*******', # codes of the templates sequence = '******') # 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.md_level = None # No refinement of model a.loop.starting_model = 1 # First loop model a.loop.ending_model = 50 # Last loop model a.loop.md_level = refine.fast # Loop model refinement level a.make() # do homology modeling

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