- modeller_usage - salilab.org

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

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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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Re: [modeller_usage] modeller_usage Digest, Vol 10, Issue 104
by Ashish Runthala 21 Jul '11

21 Jul '11

Dear Sir Benn, You are absolutely correct about CA-CA distance deviations, but when you choose 2 templates with CA-CA distances 5, 6 angstroms, then it will give you a better model as compared to 5, 10 angstroms set. Secondly, precise sequence alignment is always neccessary, but correctly aligned incorrect templates will still give bad models and probably shifted residues as was the general case till CASP5 and CASP6. Iterative Structural alignment also forces mathematical satisfaction of alignment, with no justification of biological significance of optimally placed gaps. So we still need better alignments. Now I request your expert reply against these views. Ashish Runthala, Lecturer, Structural Biology Cell, Biological Sciences Group, BITS, Pilani Rajasthan, INDIA Message: 2 Date: Thu, 21 Jul 2011 08:36:05 -0700 From: Modeller Caretaker <modeller-care(a)salilab.org> Subject: Re: [modeller_usage] Multiple Sequence Alignment vs Single Alignment To: Daniel Li <leeyuhang(a)yahoo.com> Cc: modeller_usage(a)salilab.org Message-ID: <4E284765.1020106(a)salilab.org> Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 7/21/11 12:16 AM, Daniel Li wrote: > From reading it seems as if multiple templates should usually generate > better scores but running 3 trials of 600 with different sets of > templates for different proteins I still get better results from my > single template models. So is there something I have to manipulate with > the scripts and parameters? Multiple templates generally do give better models, but they are more sensitive to alignment errors - the templates have to be quite well aligned with each other, otherwise they will present conflicting information (e.g. one template says that a given CA-CA distance is 5 angstroms, and another 10 angstroms) which is difficult to satisfy. Ben Webb, Modeller Caretaker -- modeller-care(a)salilab.org http://www.salilab.org/modeller/ Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage ------------------------------ _______________________________________________ modeller_usage mailing list modeller_usage(a)salilab.org https://salilab.org/mailman/listinfo/modeller_usage End of modeller_usage Digest, Vol 10, Issue 104 ***********************************************

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Multiple Sequence Alignment vs Single Alignment
by Daniel Li 21 Jul '11

21 Jul '11

Hi, I have been reading about modeller usage for awhile and ran some tests with different models from the dual specificity phosphatase family. However, whenever I run the modelling with salign for multiple templates, my GA341 score is many folds lower (under 0.1) and the dope score/molpdf scores are lower as well compared to just a single template. The templates that I use all give me a decent 50%+ identity based on output from build profile and I generally use 3 templates for my multiple template modeling.From reading it seems as if multiple templates should usually generate better scores but running 3 trials of 600 with different sets of templates for different proteins I still get better results from my single template models. So is there something I have to manipulate with the scripts and parameters?I'm sorry for the vague question because I'm not too sure what kind of additional information to provide but I hope someone can provide me with more insight into this. Thank you! Daniel

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Re: [modeller_usage] modeller_usage Digest, Vol 10, Issue 103
by Ashish Runthala 21 Jul '11

21 Jul '11

Dear Daniel, Multiple templates do improve the prediction accuracy as compared to the single best templates. This has been published in several papers. This has been reviewed correctly here Anna Tramontano: Protein Struture Prediction: Concepts and Applications Wiley-VCH; 2006. But here is a trick too, first of all you didn't mention what you actually used. Please answer these queries to help you practically with the best possible answer. 1. Did you use salign_iterative/salign_multiple? 2. What was the length of your sequence? 3. Did you do increased sampling? All the Scores that you discussed won't allow you to rank templates and select their correct set. Hence, it is beneficial if you try to take the correct set of a few biologically related templates. 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: Thursday, July 21, 2011 12:59:26 PM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi Subject: modeller_usage Digest, Vol 10, Issue 103 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: ModWeb details -> Modeller? (Modeller Caretaker) 2. Re: Help with modeller 9.9 in windows (Modeller Caretaker) 3. Multiple Sequence Alignment vs Single Alignment (Daniel Li) ---------------------------------------------------------------------- Message: 1 Date: Mon, 18 Jul 2011 12:13:13 -0700 From: Modeller Caretaker <modeller-care(a)salilab.org> Subject: Re: [modeller_usage] ModWeb details -> Modeller? To: rbelew(a)ucsd.edu Cc: modeller_usage(a)salilab.org Message-ID: <4E2485C9.3040006(a)salilab.org> Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 7/17/11 10:57 PM, richard k belew wrote: > i've done a couple of runs using the ModWeb server, and i'm wondering > how to recapitulate its results using Modeller directly? ModWeb gives > a .pdb file as a result, with a header that tells the template it > selected, and regions in it that were used for modeling. but: > - what method is used for selecting this template? > - is it possible to get the alignment that was used? If you asked for your results to be uploaded into ModBase, you can download the alignment file for each model from that web interface. The header of the alignment file specifies the method that was used to find the template (e.g. sequence-sequence, sequence-profile). If you instead chose to have the models sent directly to you, the alignment file isn't available. But it might still be on our system somewhere - if you email modweb(a)salilab.org with your ModWeb job ID we can see if we can find it for you. 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: Mon, 18 Jul 2011 12:21:16 -0700 From: Modeller Caretaker <modeller-care(a)salilab.org> Subject: Re: [modeller_usage] Help with modeller 9.9 in windows To: "Greene, Brandon Lee" <blgree2(a)emory.edu> Cc: "modeller_usage(a)salilab.org" <modeller_usage(a)salilab.org> Message-ID: <4E2487AC.1000003(a)salilab.org> Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 7/18/11 7:22 AM, Greene, Brandon Lee wrote: > There are three inorganic residues in the first chain and one in the > second placed as "." in my ali file. Your alignment file does not match the PDB. Modeller reads the residues sequentially, so what it will see is - A chain amino acids - B chain amino acids - A chain ligands - B chain ligands So your sequence should also be in this order (XXXXXX/XXXXXX/.../.). Alternatively, you can edit the PDB file to place the A chain ligands immediately after the A chain amino acids and leave your alignment unchanged. > Using this structure and the template ali file to do the alignment (w/ > salign) I get poor alignment in the PAP file, but not in the PIR file??? > (P/---XXXX instead of P---/XXX in PAP). Those two alignments are identical. Since neither gaps nor chain breaks are "real" residues, their relative ordering is irrelevant - it only matters which "real" residues (amino acids or ligands) they come between. > "No aligned template residues for BLK residue; number of templates: 1 > Make sure that each BLK residue in your target sequence is aligned with > your templates..." Just like it says, a BLK (".") residue in the target sequence must be aligned with a residue in the template. Usually this means you need a "." residue in the template in the same place as the "." in the target. You can't align a "." with a chain break or gap, because "." means to copy the aligned residue directly from the template to the target, so it needs a "real" residue to copy from. 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: 3 Date: Thu, 21 Jul 2011 00:16:06 -0700 (PDT) From: Daniel Li <leeyuhang(a)yahoo.com> Subject: [modeller_usage] Multiple Sequence Alignment vs Single Alignment To: modeller_usage(a)salilab.org Message-ID: <1311232566.71184.YahooMailClassic(a)web161902.mail.bf1.yahoo.com> Content-Type: text/plain; charset="iso-8859-1" Hi, I have been reading about modeller usage for awhile and ran some tests with different models from the dual specificity phosphatase family. However, whenever I run the modelling with salign for multiple templates, my GA341 score is many folds lower (under 0.1) and the dope score/molpdf scores are lower as well compared to just a single template.?The templates that I use all give me a decent 50%+ identity based on output from build profile and I generally use 3 templates for my multiple template modeling.From reading it seems as if multiple templates should usually generate better scores but running 3 trials of 600 with different sets of templates for different proteins I still get better results from my single template models. So is there something I have to manipulate with the scripts and parameters?I'm sorry for the vague question because I'm not too sure what kind of additional information to provide but I hope someone can provide me with more insight into this. Thank you! Daniel

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Help with modeller 9.9 in windows
by Greene, Brandon Lee 18 Jul '11

18 Jul '11

Hey, having an issue modelling inorganic ligands in a large dimer protein. My pdb file is a vmd cut-up of a larger pdb that looks as follows.. ATOM 1 N ALA A 3 -60.617 -12.474 -31.114 1.00 43.43 N ATOM 2 CA ALA A 3 -59.796 -11.349 -30.513 1.00 46.97 C ATOM 3 C ALA A 3 -59.651 -11.332 -28.938 1.00 48.20 C ATOM 4 O ALA A 3 -60.595 -11.655 -28.205 1.00 47.64 O ATOM 5 CB ALA A 3 -60.235 -9.947 -31.052 1.00 48.47 C ATOM 6 N ARG A 4 -58.445 -10.979 -28.485 1.00 44.79 N ... TER 2039 ATOM 2040 N GLU B1003 -60.710 -26.975 -64.326 1.00 44.60 N ... ATOM 6402 OXT HIS B1561 -32.057 -14.269 -58.556 1.00 23.80 O ANISOU 6402 OXT HIS B1561 3054 3146 2843 -160 47 -56 O TER 6403 HIS B1561 HETATM25650 FE1 SF4 A2001 -31.581 -9.338 -45.929 1.00 15.82 FE HETATM25651 FE2 SF4 A2001 -34.045 -9.711 -44.672 0.50 17.11 FE ... HETATM25689 O4 NFV B2005 -32.416 -23.476 -49.460 1.00 19.96 O END There are three inorganic residues in the first chain and one in the second placed as "." in my ali file. >P1;TrHyd sequence:TrHyd:::::::0.00: 0.00 AKRPSVIWLSFQECTGCTESLTRSHAPTLEDLILDVISLDYHHTLQAAAGDAAEHAREQAMAANPGEYLVIVDGSIPGPDSNPGYSTVAGHSNYAMLMETVENAAAVIAVGTCATFGGLPGANPNPTGAMSVMDLVKDKPVINVSGCPPIPMVITGVIAHYLTFGRLPELDAYNRPMAFFGQSIHDRCYRRPFYDKGLFAKTFDDEGARLGWCLYELGCKGPTTYNACATMRWNDGTSWPVEAGHPCLGCSEPRFWDAGGFYNTVSVP.../ERIVVDPVTRIEGHLRIEAQMDGENIAQAYSSGTSVRGLETILKGRDPRDAWAFAQRICGVCTLVHGIASVRSVEDALKIELPPNAQLIRNLMISSQFVHDHVMHFYHLHALDWVDVVSALSADPKATSDLAQSISSWPKSSPGYFADTQKRIKTFVESGQLGIFANGYWGHPAYKLPPEANLMAVAHYLEALAWQRDVARLHAIFGGKNPHPNFVVGGVPSPIDIDSDSAINAKRLAEVQQILQSMQTFVDQVYVPDTLAIASFYKDWGERGEGLGNFMSYGDLPATGTMDPAQFLFPRGVILNRDLSTIHEIDLHDAGQIQEYVAHSWYEYSGGNDQGLHPYDGETNLEYDARGGVKPPYTQLDVNDGYSWMKAPRWKGHAMEVGPLARVLLLYASGHEQTKELVEMTLTTLDLPVRALYSTLGRTAARTLETKILTDTAQDWYNQLIANIKAGDSRTFNETLWEPSSWPAEARGAGYMEAPRGALGHWIVIKDRKIANYQAVVPSTWNAGPRDPSDQPGAYEAALQDNHQLVDVKQPIEILRTIHSFDPCIACAVH.* Using this structure and the template ali file to do the alignment (w/ salign) I get poor alignment in the PAP file, but not in the PIR file??? (P/---XXXX instead of P---/XXX in PAP). I figured this wasn't a huge issue since modeller doesn't use the PAP file but it is odd. Anyway my alignment looks like this... >P1;Avfull structureX:Avfull.pdb: 3 :A:+827 :B:::-1.00:-1.00 ARRPSVIWLSFQECTGCTESLTRAHAPTLEDLILDFISLDYHHTLQAASGEAAEAARLQAMDENRGQYLVIVDGS IPGPDANPGFSTVAGHSNYSILMETVEHAAAVIAVGTCAAFGGLPQARPNPTGAMSVMDLVRDKPVINVPGCPPI PMVITGVIAHYLVFGRLPELDGYGRPLAFYGQSIHDRCYRRPFYDKGLFAESFDDEGAKQGWCLYRLGCKGPTTY NACATMKWNDGTSWPVEAGHPCLGCSEPQFWDAGGFYEPVSVP---/ERIVVDPITRIEGHLRIEAQMDGATIAQ AYSSGTMVRGIETILKGRDPRDAWAFVQRICGVCTLVHGIASVRAVEDALRIELPLNAQLIRNLMIGAQYIHDHV MHFYHLHALDWVDVVSALSADPRATSELAQSISAWPKSSPGYFADTQKRIKTFVESGQLGIFANGYWGHPAYRLP PEANLMAVAHYLEALAWQRDTAKFHAIFGGKNPHPNFVVGGVPSPIDLDSDSALNAKRLAEVRNLIQSMRTFVDQ VYVPDTLAIAGFYKDWGERGEGLGNFLCYGDLPTGASLDPATFLFPRGAILDRDLSTIHEVDLEATGEIQEFVNH SWYEYSVGNDRGLHPYEGQTNLEYDRRGGVAPPYKQLDVSDGYSWLKAPRWKGRSVEVGPLARVLMLYATGHDQA RELVDSTLSRLDLPVDALYSTLGRTAARALESKILVDAMQGWYDGLIANVKSGDTKTFNETLWEPSSWPSRAQGV GIMEAPRGALGHWIVIEDGRIANYQAVVPSTWNAGPRDGRGQAGAYEAALQDNHQLVDVKQPIEILRTIHSFDPC IACAVH-* >P1;TrHyd sequence:TrHyd: : : : ::: 0.00: 0.00 AKRPSVIWLSFQECTGCTESLTRSHAPTLEDLILDVISLDYHHTLQAAAGDAAEHAREQAMAANPGEYLVIVDGS IPGPDSNPGYSTVAGHSNYAMLMETVENAAAVIAVGTCATFGGLPGANPNPTGAMSVMDLVKDKPVINVSGCPPI PMVITGVIAHYLTFGRLPELDAYNRPMAFFGQSIHDRCYRRPFYDKGLFAKTFDDEGARLGWCLYELGCKGPTTY NACATMRWNDGTSWPVEAGHPCLGCSEPRFWDAGGFYNTVSVP.../ERIVVDPVTRIEGHLRIEAQMDGENIAQ AYSSGTSVRGLETILKGRDPRDAWAFAQRICGVCTLVHGIASVRSVEDALKIELPPNAQLIRNLMISSQFVHDHV MHFYHLHALDWVDVVSALSADPKATSDLAQSISSWPKSSPGYFADTQKRIKTFVESGQLGIFANGYWGHPAYKLP PEANLMAVAHYLEALAWQRDVARLHAIFGGKNPHPNFVVGGVPSPIDIDSDSAINAKRLAEVQQILQSMQTFVDQ VYVPDTLAIASFYKDWGERGEGLGNFMSYGDLPATGTMDPAQFLFPRGVILNRDLSTIHEIDLHDAGQIQEYVAH SWYEYSGGNDQGLHPYDGETNLEYDARGGVKPPYTQLDVNDGYSWMKAPRWKGHAMEVGPLARVLLLYASGHEQT KELVEMTLTTLDLPVRALYSTLGRTAARTLETKILTDTAQDWYNQLIANIKAGDSRTFNETLWEPSSWPAEARGA GYMEAPRGALGHWIVIKDRKIANYQAVVPSTWNAGPRDPSDQPGAYEAALQDNHQLVDVKQPIEILRTIHSFDPC IACAVH.* Using the template code in advanced modeling with similar for loops for all constraints of the inorganic ligand connections to the protein backbone through side chains modeller begins to compute the model and quickly returns this error... "No aligned template residues for BLK residue; number of templates: 1 Make sure that each BLK residue in your target sequence is aligned with your templates..." So my question is, is there a problem with my alignment that I am not seeing or is it some formating issue in the pdb that needs to be resolved? Any ideas would be much appreciated! ________________________________ This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited. If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments).

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ModWeb details -> Modeller?
by richard k belew 18 Jul '11

18 Jul '11

i've done a couple of runs using the ModWeb server, and i'm wondering how to recapitulate its results using Modeller directly? ModWeb gives a .pdb file as a result, with a header that tells the template it selected, and regions in it that were used for modeling. but: - what method is used for selecting this template? - is it possible to get the alignment that was used? thanks for any leads, Rik

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