April 2010 - modeller_usage

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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Mutant models
by Alfonso Mendez 14 Apr '10

14 Apr '10

Hello: I am building a protein model using a script that has been cited several times. http://salilab.org/modeller/wiki/Mutate%20model I started to work on it using Modeller9v2 on a Windows XP machine. After some tries, I noted that I can use the script with the next command for example: mod9v7 mutar.py 1dxt 85 TYR A However, I needed to delete lines 2 and 165 of the script because the "import os" command is not recognized by the python version that is included with modeller. The script seems to work and autogenerates a log file and the mutant model of course. I am working with a model of hemoglobin (1DXT). However, after looking the log file there some messages that are intriging for me: a) Some atoms were not found in params file: generat_607W> Cannot find params in params file: CHARMM atoms : NPH FE NP1 CPA IUPAC atoms : NA FE NB C1B Atom indices : 4406 4405 4407 4414 Residues : HEME HEME HEME HEME As this is hemoglobin model HEME groups are important b) Serious non-bounded atoms contacts at the end of the script report______> Distribution of short non-bonded contacts: serious non-bonded atom clash: 650 4405 2.247 serious non-bonded atom clash: 1778 4448 2.197 serious non-bonded atom clash: 2850 4491 2.252 serious non-bonded atom clash: 3978 4534 2.101 c) The modelling was produced in few seconds. Can the model produced by this script be optimized even more? (even if the script takes more running time) Also I am interested in create a mutant model but without optimize it. Then I want to compare the energy of the mutant model before and after the optimization. How can I produce the mutant model without the optimization? I am attaching the log file of my previous model. Thanks Dr. Alfonso Méndez Tenorio

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Re: [modeller_usage] Alignment of the sequences
by Thomas Evangelidis 12 Apr '10

12 Apr '10

Your question is answered in the FAQs: http://salilab.org/modeller/FAQ.html#17 use that code to get the sequence from .pdb (as MODELLER reads it), and realign it with the rest of your sequences to generate a new .pir file. Otherwise just align it with the original sequence to spot discrepancies. Tom 2010/4/12 piyush diyora <yellow_piyu46(a)yahoo.co.in> > Hi, > I am new to modeller. > Before building a model, we have to first modify the sequence present in > the PIR file. PDB file and PIR file may have few different sequences. So is > there any way or software which can align both the sequences (from PDB file > and PIR file) so that the sequence present in PIR can be modified. > > Thank you, > Piyush Diyora > > > _______________________________________________ > modeller_usage mailing list > modeller_usage(a)salilab.org > https://salilab.org/mailman/listinfo/modeller_usage > >

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Alignment of the sequences
by piyush diyora 12 Apr '10

12 Apr '10

Hi, I am new to modeller. Before building a model, we have to first modify the sequence present in the PIR file. PDB file and PIR file may have few different sequences. So is there any way or software which can align both the sequences (from PDB file and PIR file) so that the sequence present in PIR can be modified. Thank you, Piyush Diyora

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