- modeller_usage - salilab.org

import pylab ImportError: No module named pylab
by 刘吉元 04 Aug '11

04 Aug '11

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using SALIGN-error
by Nava Moran 02 Aug '11

02 Aug '11

dear Modeller, I pasted a fasta-format sequence in the "window", hit the "upload" button and got the following: "Sorry, your request was not processed due to the following reason: * directory (/modbase5/home/salign/todo/1299736963_SA_230/upload/unzip/) Core(10)_Helices is still tainted at /usr/lib/perl5/5.8.8/File/Find.pm line 837." this is the stuff I pasted: >nt_just-seq YPDDRWYKIWEKFILIWAIYSSFFTPMEFAFFKGLPRKLFLLDICGQ IAFLVDIVVQFFVAYRDSQTYKMVHKRTPIALRYLKTHFILDFLSCMPWDNIYKAAGKKE GLRYLLWIRLSRVRRVNDFFQKMEKDIRINYLFTRILKLIV thanks in advance for an explanation how to use this "paste" nava *

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Regarding Optimal Alignment
by Ashish Runthala 02 Aug '11

02 Aug '11

Dear Modellers, Check out this alignment 3KIJA>------FLKPKINSFYAFEVKDAKGRTVSLEKYKGKVSLVVNVASDCQLT* 2P31A>------------QDFYDFKAVNIRGKLVSLEKYRGSVSLVVNVASECGFT* 2GS3A>TENLYFQSMRCARSMHEFSAKDIDGHMVNLDKYRGFVCIVTNVASQGGKT* 2OBIA>------DDWRCARSMHEFSAKDIDGHMVNLDKYRGFVCIVTNVASQCGKT* TARGET>---ENLYFQSMINSFYAFEVKDAKGRTVSLEKYKGKVSLVVNVASDCQLT* (I have given a space initially so that you can easily understand the alignment) Will somebody guide me how to incorporate the distant conserved chunk ENLYFQSM from "2GS3A" template without making the shifted alignments just to satisfy this constraint. Is there any way to use the chunk from it along with the other conserved aligned motifs. I know Sir Benn will definitely answer my query. Thanks Ashish Ashish Runthala, Lecturer, Structural Biology Cell, Biological Sciences Group, BITS, Pilani Rajasthan, INDIA

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Re: [modeller_usage] modeller_usage Digest, Vol 10, Issue 108
by Ashish Runthala 30 Jul '11

30 Jul '11

Dear Mustafa, As such energy can't discriminate between close decoys, Normalized_dope gives a better idea. You may see the effect of each of the Modeller assessment score through your modeling script this way. a = automodel(env, alnfile = '------', knowns = ('---', '---'), sequence = 'target', assess_methods=(assess.DOPE, assess.GA341,assess.normalized_dope)) Use a redirection operator > to save modeling result. Then use the trajectory of these values in your modeling. You will get your answer if you try modeling a known structure target, so that you can affirm model evaluation through GDT scores. Good Luck, Ashish Ashish Runthala, Lecturer, Structural Biology Cell, Biological Sciences Group, BITS, Pilani Rajasthan, INDIA ----- Original Message ----- From: "modeller usage-request" <modeller_usage-request(a)salilab.org> To: "modeller usage" <modeller_usage(a)salilab.org> Sent: Saturday, July 30, 2011 12:47:57 PM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi Subject: modeller_usage Digest, Vol 10, Issue 108 Send modeller_usage mailing list submissions to modeller_usage(a)salilab.org To subscribe or unsubscribe via the World Wide Web, visit https://salilab.org/mailman/listinfo/modeller_usage or, via email, send a message with subject or body 'help' to modeller_usage-request(a)salilab.org You can reach the person managing the list at modeller_usage-owner(a)salilab.org When replying, please edit your Subject line so it is more specific than "Re: Contents of modeller_usage digest..." Today's Topics: 1. Re: Good Quality Score (Modeller Caretaker) 2. Regarding Proper Alignment (Ashish Runthala) 3. Re: Regarding Proper Alignment (Modeller Caretaker) 4. Selection of Model (MUSTAFA BUGHIO) ---------------------------------------------------------------------- Message: 1 Date: Thu, 28 Jul 2011 17:18:07 -0700 From: Modeller Caretaker <modeller-care(a)salilab.org> Subject: Re: [modeller_usage] Good Quality Score To: Brian Tsui <btsui17(a)yahoo.com> Cc: "modeller_usage(a)salilab.org" <modeller_usage(a)salilab.org> Message-ID: <4E31FC3F.5010601(a)salilab.org> Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 7/26/11 8:33 PM, Brian Tsui wrote: > In the Madhusudhan paper, the cutoff was at least 70% for a SO of 3.5 A. Do you mean the SO was 70% for a cutoff of 3.5A? > What number does that correspond to in the salign output? The percentage of equivalent (i.e. within the cutoff) positions is the qscorepct member of the SalignData object returned by salign(). Set the cutoff with the rms_cutoff argument. And make sure you have QUALITY in the output argument. > For the quality score, is there an objective number that I can use for > every alignment to see whether it is good or not? As I said, only for structure alignments. > Lastly, for "iterative salign," is it recommended to run the regular > version first or just jump straight to using the iterative salign? The > Madhusudhan paper seems to forgo the use of iterative salign if the > alignment is 70% at a SO of 3.5 I'm assuming you're looking at fig 1 in the paper here. There are three iterative procedures within that flowchart; one of them is skipped if the first procedure (simpler alignment using a subset of features) found a reasonable starting guess for the last procedure (structural alignment). The second procedure is simply an attempt to improve this guess if the first failed. Ben Webb, Modeller Caretaker -- modeller-care(a)salilab.org http://www.salilab.org/modeller/ Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage ------------------------------ Message: 2 Date: Fri, 29 Jul 2011 12:19:49 +0530 (IST) From: Ashish Runthala <ashishr(a)bits-pilani.ac.in> Subject: [modeller_usage] Regarding Proper Alignment To: modeller <modeller_usage(a)salilab.org> Message-ID: <30722239.171381311922189682.JavaMail.root(a)mailserver.bits-pilani.ac.in> Content-Type: text/plain; charset=utf-8 Dear Modellers, May somebody tell me the logic of using rms_cutoff=3.5 while comparing and aligning multiple structures. Even when you alter, no difference come up in the generated model. Is this upper bound a relaxed in every modeling case. It may not be so, when same family proteins are aligned. So this strict upper bound on C? distance may leave several large chunks unaligned. Variable gap penalty makes the alignment correct through flexible allowed superposition, but why changing rms_cutoff didn't generate better models, not even 0.1 GDT_TS improvement was not observed. Thanks Ashish Ashish Runthala, Lecturer, Structural Biology Cell, Biological Sciences Group, BITS, Pilani Rajasthan, INDIA ------------------------------ Message: 3 Date: Fri, 29 Jul 2011 15:43:30 -0700 From: Modeller Caretaker <modeller-care(a)salilab.org> Subject: Re: [modeller_usage] Regarding Proper Alignment To: Ashish Runthala <ashishr(a)bits-pilani.ac.in> Cc: modeller <modeller_usage(a)salilab.org> Message-ID: <4E333792.1070802(a)salilab.org> Content-Type: text/plain; charset=UTF-8; format=flowed On 7/28/11 11:49 PM, Ashish Runthala wrote: > May somebody tell me the logic of using > rms_cutoff=3.5 while comparing and aligning multiple structures. Even > when you alter, no difference come up in the generated model. Changing rms_cutoff will not change the alignment. The cutoff is simply the distance below which two residues are considered to be structurally equivalent when aligned, so it will only affect measures such as the structural overlap (and quality score). Ben Webb, Modeller Caretaker -- modeller-care(a)salilab.org http://www.salilab.org/modeller/ Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage ------------------------------ Message: 4 Date: Sat, 30 Jul 2011 12:17:54 +0500 From: MUSTAFA BUGHIO <mustafab4(a)gmail.com> Subject: [modeller_usage] Selection of Model To: modeller_usage(a)salilab.org Message-ID: <CALHZR253S3mXhzH-=j4a8nM10__Tv+F+G2DNigfJHgZu=BEPjQ(a)mail.gmail.com> Content-Type: text/plain; charset="iso-8859-1" Dear Ben I wanna repeat the question already asked by some one regarding the selection of best model criterion. I have developed pentamer Structure using model-multichain.py command i want to know on what basis i should select the best model out of 20 models. I have checked both modeller objective function scores and also Dope score but there i could not observe any correlation between the two. Can i get your input in this regard Regards -- MUSTAFA BUGHIO Junior Research Fellow Lab # P-133 Computational Medicinal Chemistry and Drug Design Panjwani Center For Molecular Medicine and Drug Research, International Center for Chemical Sciences, University of Karachi, Karachi 75270 Pakistan, +923313425010

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Selection of Model
by MUSTAFA BUGHIO 30 Jul '11

30 Jul '11

Dear Ben I wanna repeat the question already asked by some one regarding the selection of best model criterion. I have developed pentamer Structure using model-multichain.py command i want to know on what basis i should select the best model out of 20 models. I have checked both modeller objective function scores and also Dope score but there i could not observe any correlation between the two. Can i get your input in this regard Regards -- MUSTAFA BUGHIO Junior Research Fellow Lab # P-133 Computational Medicinal Chemistry and Drug Design Panjwani Center For Molecular Medicine and Drug Research, International Center for Chemical Sciences, University of Karachi, Karachi 75270 Pakistan, +923313425010

1 0

Regarding Proper Alignment
by Ashish Runthala 29 Jul '11

29 Jul '11

Dear Modellers, May somebody tell me the logic of using rms_cutoff=3.5 while comparing and aligning multiple structures. Even when you alter, no difference come up in the generated model. Is this upper bound a relaxed in every modeling case. It may not be so, when same family proteins are aligned. So this strict upper bound on Cα distance may leave several large chunks unaligned. Variable gap penalty makes the alignment correct through flexible allowed superposition, but why changing rms_cutoff didn't generate better models, not even 0.1 GDT_TS improvement was not observed. Thanks Ashish Ashish Runthala, Lecturer, Structural Biology Cell, Biological Sciences Group, BITS, Pilani Rajasthan, INDIA

2 1

Good Quality Score
by Brian Tsui 28 Jul '11

28 Jul '11

Dear all, In the output for salign, there is a raw quality score, a percentage quality score, and many other values. What value should I focus on to make sure that I have a good alignment? Is there a cutoff that I should use? If so, are there references that I could cite? Thanks, Brian

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How to build customized salign result?
by Ashish Runthala 25 Jul '11

25 Jul '11

Dear Modellers, Tell me the solution to a query. Suppose I have 4 templates for a target sequence. And while using salign_multiple.py, I want to start the progressive alignment specifically from template 2 only, to let others follow this template2 alignment. Tell me the way to make salign force the progressive alignment starting on from a specific template only? Thanks in advance, Ashish -------- Ashish Runthala, Lecturer, Structural Biology Cell, Biological Sciences Group, BITS, Pilani Rajasthan, INDIA

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Dope profile of tetramer
by Matthias Schmidt 22 Jul '11

22 Jul '11

Hi, I have a model of a tetramer, and I would like to evaluate/show only the DOPE profile for one chain, because the tetramer is symmetric. Here is the script I used for calculating the DOPE profile: from modeller import * from modeller.scripts import complete_pdb log.verbose() # request verbose output env = environ() env.libs.topology.read(file='$(LIB)/top_heav.lib') # read topology env.libs.parameters.read(file='$(LIB)/par.lib') # read parameters # read model file mdl = complete_pdb(env, 'model.B99990001.pdb') # Assess with DOPE: s = selection(mdl) # all atom selection s.assess_dope(output='ENERGY_PROFILE NO_REPORT', file='model.profile', normalize_profile=True, smoothing_window=15) and for plotting: import pylab import modeller def get_profile(profile_file, seq): """Read `profile_file` into a Python array, and add gaps corresponding to the alignment sequence `seq`.""" # Read all non-comment and non-blank lines from the file: f = file(profile_file) vals = [] for line in f: if not line.startswith('#') and len(line) > 10: spl = line.split() vals.append(float(spl[-1])) # Insert gaps into the profile corresponding to those in seq: for n, res in enumerate(seq.residues): for gap in range(res.get_leading_gaps()): vals.insert(n, None) # Add a gap at position '0', so that we effectively count from 1: vals.insert(0, None) return vals e = modeller.environ() a = modeller.alignment(e, file='3zrs-align-nterm.ali') model = get_profile('3zrs-nterm.profile', a['3zrs-nterm']) template = get_profile('3zrs-nterm.profile', a['3zrs-nterm']) # Plot the template and model profiles in the same plot for comparison: pylab.figure(1, figsize=(10,6)) pylab.xlabel('Alignment position') pylab.ylabel('DOPE per-residue score') pylab.plot(model, color='red', linewidth=2, label='Model') pylab.plot(template, color='green', linewidth=2, label='Template') pylab.legend() pylab.savefig('dope_profile.png', dpi=65) These scripts are from the tutorial on the website. Best, Matthias

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SALIGN ERROR to clarify
by Nava Moran 21 Jul '11

21 Jul '11

dear Modeller, trying to upload a sequence in fasta mode to SALIGN I got this error: Sorry, your request was not processed due to the following reason: * directory (/modbase5/home/salign/todo/1299736963_SA_230/upload/unzip/) Core(10)_Helices is still tainted at /usr/lib/perl5/5.8.8/File/Find.pm line 837. *is this my fault? or something else? nava

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