August 2009 - modeller_usage

validation
by Adriana Esteves 31 Aug '09

31 Aug '09

Dear all: I am new in this task of homology modeling and I want to know how can I validate my model. I heard about several programs on line like ANOLEA, Verify 3D and What_check. Any one knows about the utility of this programs? Thank you very much Adriana

1 0

MODELLER behaviour with non-standard residues / HETATM
by Thomas Juettemann 29 Aug '09

29 Aug '09

Dear all, could someone enlighten me how MODELLER treats non-standard residues. I am using Dunbrack's S2C as a source for ATOM sequences. In the PDB file 1M2W, I have several selenomethionine (MSE) residues, marked as HETATM. Running MODELLER, it seems to convert them to methionine (which I appreciate) and successfully produces a model. My question is: How does MODELLER check / replace HETATM that have a residue identifier that is in the permitted range (not 'X', '.' or '-')? I did not not set env.io.hetatm to true. My apologies if I missed this information in the manual or my question is not clear enough. Many thanks, Thomas Template: http://www.pdb.org/pdb/files/1M2W.pdb (e.g. residue 1,50 & 105) Alignment >P1;1M2W structureX:1M2W:FIRST:@ END:::::: MKLNKQNLTQLAPEVKLPAYTLADTRQGIAHIGVGGFHRAHQAYYTDALMNTGEGLDWSICGVGLRSEDRKARDDLAGQDYLFTLYELGDTDDTEVRVIGSISDMLLAEDSAQALIDKLASPEIRIVSLTITEGGYCIDDSNGEFMAHLPQIQHDLAHPSSPKTVFGFICAALTQRRAAGIPAFTVMSCDNLPHNGAVTRKALLAFAALHNAELHDWIKAHVSFPNAMVDRITPMTSTAHRLQLHDEHGIDDAWPVVCEPFVQWVLEDKFVNGRPAWEKVGVQFTDDVTPYEEMKIGLLNGSHLALTYLGFLKGYRFVHETMNDPLFVAYMRAYMDLDVTPNLAPVPGIDLTDYKQTLVDRFSNQAIADQLERVCSDGSSKFPKFTVPTINRLIADGRETERAALVVAAWALYLKGVDENGVSYTIPDPRAEFCQGLVSDDALISQRLLAVEEIFGTAIPNSPEFVAAFERCYGSLRDNGVTTTLKHLLKKP / MKLNKQNLTQLAPEVKLPAYTLADTRQGIAHIGVGGFHRAHQAYYTDALMNTGEGLDWSICGVGLRSEDRKARDDLAGQDYLFTLYELGDTDDTEVRVIGSISDMLLAEDSAQALIDKLASPEIRIVSLTITEGGYCIDDSNGEFMAHLPQIQHDLAHPSSPKTVFGFICAALTQRRAAGIPAFTVMSCDNLPHNGAVTRKALLAFAALHNAELHDWIKAHVSFPNAMVDRITPMTSTAHRLQLHDEHGIDDAWPVVCEPFVQWVLEDKFVNGRPAWEKVGVQFTDDVTPYEEMKIGLLNGSHLALTYLGFLKGYRFVHETMNDPLFVAYMRAYMDLDVTPNLAPVPGIDLTDYKQTLVDRFSNQAIADQLERVCSDGSSKFPKFTVPTINRLIADGRETERAALVVAAWALYLKGVDENGVSYTIPDPRAEFCQGLVSDDALISQRLLAVEEIFGTAIPNSPEFVAAFERCYGSLRDNGVTTTLKHLLKKP * >P1;P09424-P77260 sequence:P09424-P77260:::::::: MK---------------------ALHFGAGNIGRG----FIGKLL-ADAGIQLTFADV-----NQVVLDALNAR-HSYQVHVVGETEQ-----VDTVSGVNAVSSIGDDVVDLIAQ-----VDLVTTAVGPVV----------LERIAPAIAK------------GQVKRKEQGNESPLNIIACENMVR-GTTQLKGHVMNALPEDAK--AWVEEHVGFVDSAVDRIVPPSASA----------TNDPLEVTVETFSEWIVDKTQFKG--ALPNIPGMELTDNLMAFVERKLFTLNTGHAITAYLGKLAGHQTIRDAILDEKIRAVVKGAME-ESGAVLIKRYGFDADKHAAYIQKILGRFENPYLKDDVERV---GRQPLRKLSAG--DRLIKP-----------------LLGTLEYGL------PHKNLIEGIAAAMHFRSEDDPQAQELAALIADKGPQ--AALAQISGLDANSEVVSEAVTAYKAMQ / ---NLLSAKATLPVYDLNNLAPRIVHLGFGAFHRAHQGVYAD-ILATEHFSDWGYYEVNLIGGEQQI-ADLQQQDNLYTVAEMS-ADVWTARVVGVVKKALHVQIDGLETVLAAMCEPQIAIVSLTITEKGYFHSPATGQLMLDHPMVAADVQNPHQPKTATGVIVEALARRKAAGLPAFTVMSCDNMPENGHVMRDVVTSYAQAVDVKLAQWIEDNVTFPSTMVDRIVPAVTEDTLAKIEQLTGVRDPAGVACEPFRQWVIEDNFVAGRPEWEKAGAELVSDVLPYEEMKLRMLNGSHSFLAYLGYLAGYQHINDCMEDEHYRYAAYGLMLQEQAPTL-KVQGVDLQDYANRLIARYSNPALRHRTWQIAMDGSQKLPQRMLDSVRWHLAHDSKFDLLALGVAGWMRYVGGVDEQGNPIEISDPLLPVIQKAVQSSAEGKARVQSLLAIKAIFGDDLPDNSLFTARVTETYLSLLAHGAKATVAKYSVK--

2 1

database with PIR format, help
by Quiliano Mesa, Miguel Angel 27 Aug '09

27 Aug '09

Dear followers of Modeller I am a new user and I found me with a easy but tedious problem (doing it by hand). I have several sequences in FASTA format so I would like to do the same process such as the basic tutorial with the database "95.pir", my question is... how to convert to PIR format.. should I use a program for this? there is a program for this? anyone have a scritp? I would very grateful if someone can hel me. thanks in advance. Miguel Quiliano.

2 1

remove short helices
by Shawna Frazier 22 Aug '09

22 Aug '09

Hi, When I view my structural model as a cartoon, it contains several short 'helices', composed of only three residues each. The template pdb shows each of these regions as unstructured loops. Therefore, I would like to remove these short helices from my model. Is there a simple way to remove secondary structure? Note, I have tried loop refinement; it worked on a couple of my short helices, but has failed to fix my last one. Any suggestions are appreciated. Thanks.

3 2

Re: [modeller_usage] modeller_usage Digest, Vol 8, Issue 60
by carlos Prudencio 19 Aug '09

19 Aug '09

Hi, I need to do a de novo 3D model because I was't able to find any similar structural to compare. thanks, Carlos R. Prudencio MSN: crprudencio(a)hotmail.com Fone: +34645465174 (Spain) On Aug 19, 2009, at 1:53 AM, modeller_usage-request(a)salilab.org wrote: > 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: how to evaluate which is the best model in "multiple > template" example (Modeller Caretaker) > 2. Heme in P450 (Storbeck, K, Dr <storbeck(a)sun.ac.za>) > 3. Re: Heme in P450 (Modeller Caretaker) > 4. remove short helices (Shawna Frazier) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 06 Aug 2009 08:50:51 -0700 > From: Modeller Caretaker <modeller-care(a)salilab.org> > To: albumns <albumns(a)yeah.net> > Cc: modeller_usage <modeller_usage(a)salilab.org> > Subject: Re: [modeller_usage] how to evaluate which is the best model > in "multiple template" example > Message-ID: <4A7AFBDB.3040400(a)salilab.org> > Content-Type: text/plain; charset=UTF-8; format=flowed > > albumns wrote: >> how to evaluate which is the best model in "multiple template" >> example? In the tutorial, it just use the model number 1 for the >> final one. How to judge these models which is better than the left? > > You can evaluate the model quality with the DOPE score (the model with > the lowest DOPE score is most likely to be the best) in the same way > as > the single template example. It doesn't matter how many templates were > used to build the model - the evaluation is of the model itself, not > the > alignment. > >> my another question is that how can we draw the "basic model" and >> multiple templates in the same diagram with GUNplot? > > If you're referring to the plot of DOPE score profiles, shown at the > end > of the basic tutorial, such a plot is only qualitative at best. You > can > only plot a single profile in GNUPLOT, because with multiple > profiles you have to account for the gaps. This is done by the > plot_profiles script in the basic tutorial. To plot multiple > templates, > it should be straightforward to modify that script, adding extra calls > to get_profile() and pylab.plot(). > > 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: Tue, 18 Aug 2009 19:45:27 +0200 > From: "Storbeck, K, Dr <storbeck(a)sun.ac.za>" <storbeck(a)sun.ac.za> > To: "modeller_usage(a)salilab.org" <modeller_usage(a)salilab.org> > Subject: [modeller_usage] Heme in P450 > Message-ID: > <D698F2F3BBE7504AA43E6B2A7CFFD82D127FA65B14(a)STBEVS06.stb.sun.ac.za> > Content-Type: text/plain; charset="us-ascii" > > Hi, > > I am modeling a cytochrome P450, I am able to include the heme in my > model. However, in the templates the heme iron is bound to a cys > residue, but I loose this bond in the model. How can I go about > keeping it in my model? > > Thanks > Karl > > > ------------------------------ > > Message: 3 > Date: Tue, 18 Aug 2009 13:06:24 -0700 > From: Modeller Caretaker <modeller-care(a)salilab.org> > To: "Storbeck, K, Dr <storbeck(a)sun.ac.za>" <storbeck(a)sun.ac.za> > Cc: "modeller_usage(a)salilab.org" <modeller_usage(a)salilab.org> > Subject: Re: [modeller_usage] Heme in P450 > Message-ID: <4A8B09C0.5030203(a)salilab.org> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Storbeck, K, Dr <storbeck(a)sun.ac.za> wrote: >> I am modeling a cytochrome P450, I am able to include the heme in my >> model. However, in the templates the heme iron is bound to a cys >> residue, but I loose this bond in the model. How can I go about >> keeping it in my model? > > If you have a CYS residue in your model aligned with that template > residue, then Modeller should automatically keep that bond in your > model > (see the third bullet point at > http://salilab.org/modeller/9v7/manual/node65.html) This does, > however, > require Modeller 9v5 or later. The heuristic is a simple one though > - if > the bond is longer than 2.3A you could just add a simple distance > restraint to approximate this interaction. But really to do this > properly you need to tell Modeller that that CYS residue is not > really a > 'CYS' but is a modified residue (i.e. that it has a bond to your > iron). > For that you'd need to patch your topology using the model.patch() > command and some knowledge of how CHARMM patches work, which can be > gleaned from the CHARMM manual. > > 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: Tue, 18 Aug 2009 16:38:21 -0700 > From: Shawna Frazier <sfrazier(a)caltech.edu> > To: modeller_usage(a)salilab.org > Subject: [modeller_usage] remove short helices > Message-ID: <06A265F6-2F41-4968-86C3-C51B21041AA7(a)caltech.edu> > Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes > > Hi, > > When I view my structural model as a cartoon, it contains several > short 'helices', composed of only three residues each. The template > pdb shows each of these regions as unstructured loops. Therefore, I > would like to remove these short helices from my model. Is there a > simple way to remove secondary structure? > > Note, I have tried loop refinement; it worked on a couple of my short > helices, but has failed to fix my last one. > > Any suggestions are appreciated. > Thanks. > > > ------------------------------ > > _______________________________________________ > modeller_usage mailing list > modeller_usage(a)salilab.org > https://salilab.org/mailman/listinfo/modeller_usage > > > End of modeller_usage Digest, Vol 8, Issue 60 > *********************************************

2 1

Heme in P450
by Storbeck, K, Dr <storbeck＠sun.ac.za> 18 Aug '09

18 Aug '09

Hi, I am modeling a cytochrome P450, I am able to include the heme in my model. However, in the templates the heme iron is bound to a cys residue, but I loose this bond in the model. How can I go about keeping it in my model? Thanks Karl

2 1

how to evaluate which is the best model in "multiple template" example
by albumns 06 Aug '09

06 Aug '09

Dear all: how to evaluate which is the best model in "multiple template" example? In the tutorial, it just use the model number 1 for the final one. How to judge these models which is better than the left? my another question is that how can we draw the "basic model" and multiple templates in the same diagram with GUNplot? Thank you very much.

2 1

query about coil region!!
by Cool Hunk 05 Aug '09

05 Aug '09

Thanks alot Ben, i really got it, can you please make me one more thing sure that can i declare any part of my target a coil region irrespective of its alignment wth template region, if yes then how?? cuz in tht example its told about the helix n strand.... but not about coils... thanking in advance Muhammad

3 3

query!!!
by Cool Hunk 04 Aug '09

04 Aug '09

Dear Ben, Actually i want to ask about a very common concept about modelling.... for this alignment, the red color representing beta strands is aligned with gaps and its the template part wch is aligned wth gaps, my question is how would this part be modelled??? would it be modelled a strand in predicted model??? and what if any part of target is aligned wth gaps but was conserdered a helix????? how would it be modelled.. --------000000000000000--------------------22--------------- CEEEEECCEEEEEEEEEEEEEEECCCCCCCCCCCC--------EECCEEEEEEEEEEECC AEIYNKDGNKVDLYGKAVGLHYFSKGNGENSYGGN--------GDMTYARLGFKGETQIN | | | -------MKKLLKSVLVFAALSSASSLQALPVGNPAEPSLMIDGIL-------------- -------CCCCCEEEEEEEEEEECCCCCCCCCCCCCEEEEEEEEEE-------------- Albeit its a childish question, but it can clear my concept and i can edit the alignment to get a good model then.. thanking in advance Muhammad

2 1

refinement of model, but keeping close to templates
by Robert Jorissen 04 Aug '09

04 Aug '09

G'day I am modelling a complex of two proteins, each of which has moderately high sequence similarity to their respective template proteins. I wish to create a model that strongly resembles their targets. The idea being that I wish to demonstrate the plausibility of the interface between the two template proteins being conserved in the target proteins. What is the best way to go about this? Presently, I have created a number of models using the library_schedule autosched.fastest with a starting coordinate deviation of zero (i.e. no random displacement added to the initial set of coordinates) and taken the best scoring of these. Is there a better way that optimizes the MODELLER score, but that does not stray far from the template structure, particularly in the ungapped, high similarity regions? Kind regards, Rob Jorissen Ludwig Institute for Cancer Research, Melbourne branch ____________________________________________________________________________________ Access Yahoo!7 Mail on your mobile. Anytime. Anywhere. Show me how: http://au.mobile.yahoo.com/mail

2 1