May 2008 - modeller_usage

multiple templates
by Petr Danecek 30 May '08

30 May '08

Hello, I am attempting to build a model from multiple templates, but I am getting very bad results. After doing some tests I have discovered that the problem lies most probably in the unwanted 3D orientation of the blocks which the model is built from. To test this, I took a single PDB file and splitted it into three chunks aligned as: aaaaaaaaa------------------------- ------aaaaaaaaaaa----------------- --------------aaaaaaaaaaaaaaaaaaaa aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa In this test, I would like to reconstruct the original structure. Is it possible? I tried to set the variable a.initial_malign3d=1, but the modeller ends with the error "_modeller.ModellerError: fit2xyz_296E> Number of equivalent positions < 3: 0" Any help would be greatly appreciated. Best regards, Petr Danecek

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Post - problem with modelling a chain using another chain as template
by plmallip＠mail.uh.edu 29 May '08

29 May '08

Is it possible to re-orient chains in a pentameric way after using one of those chains as template to build others? I have a pentameric protein. The protein and the nearest template miss some residues at a particular position in all the chains, except one chain. So, I carried out homology modeling using modeller9v3 as follows: 1. I modelled the pentamer at a time using the nearest available pdb file as template (~85% similarity). 2. Each of the chains are about 70% similar to each other. I built a model of chain C Using chain A of available pdb file 3. Then, I overlapped chain C from step 3 and step 1, using VMD "RMSD tool". Saved both pdb's in this orientation. Copied the "region of missing residues (14) only" to chain C of step 1. 4. Similarly I did for chain B. 5. When, I reassembled chains B and C with other 3 subunits from step 1, Chains B and C are overlapping with chain A. Imagine, its like a trimer now, with 3 chains overlapping at one place. I tried both VMD, InsightII using Chains from the pentamer as reference and overlay the modelled chains. But, there is no change in orientation. Is there any way I can do this? Is this a plausible way to build missing residues, when there is not at all any template available for that region in the entire family of this protein? I would be grateful for your suggestions in this regard. warm regards, Prema, plmallip(a)mail.uh.edu

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Searching the PDB for sequence with structure
by Florian Odronitz 28 May '08

28 May '08

Hi Modelleros, I am in the process of modeling ~100 similar structures. I have a bunch of templates that cover most of the sequence of the targets. However, there are some gaps. Most gaps are loop regions or contain loops, sometimes comprising ~30 aas, so ab initio modeling is not an option. So I go to the PDB and BLAST with my missing sequence as a query. I get a great number of hits but for most of the PDBs, the large parts of the sequence have no _structure_. Downloading each of those PDBs and looking at them is not an option since its hundreds. I am looking for a tool to BLAST (or otherwise search) the sequences in the PDB that have _structure_. The people at the PDB told me there is no such option and they are not aware of such an resource. I figure I am not the first person to encounter such a difficulty. How would you handle this? Is there such a resource? Thanks and best regards, Florian

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how add sidechains
by matziast＠med.uth.gr 28 May '08

28 May '08

Hi, I have a problem with the model building. Specifically, I have the coordinates of the backbone and I want to add its sidechains but I can't find the appropriate script. If someone knows the name of the script, tell me. Thank you in advance, Maria.

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Re: [modeller_usage] Searching the PDB for sequence with structure
by Florian Odronitz 28 May '08

28 May '08

Hi Christian, > If no one will come up with a better solution, you might want to build > this tool yourself: That sounds like fun! > > All you need to do is to download the PDB files and check whether the > sequences in question are contained. The thing is that the sequence might be there but with gaps. It would be nice to have that be matched by BLAST, since regular expressions are not suited for this. If I am not the only one who has this problem I might do something like: - Download all PDB Structures. - Extract the sequences of the proteins as well as the sequences that have ATOM records. - Make a quick alignment between each of those two sequences. - Put the two sequences and the PDB ID in a database. - Make a BLAST database file witch the full sequences. - Make BLAST accessible on a web server. The search results could be presented as an alignment of the sequence that was searched for and the sequence that actually has structure. It would be easy to implement queries like "search for sequence X and return only results where more than 30% has structure". > checks) is contained in the biopython project ( http:// > biopython.org/ ). I would prefer to do it in ruby, but same same. > MD is not an option for you? I think the stretches are too long (several dozen aas) and to numerous (~100 structures * several gabs/structure). I would also feel better if I could use experimental data. Cheers, Florian

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one question,please answer
by Maryam Nikoosaleh 27 May '08

27 May '08

Hi all! My question is about Modeller restraints. Have you ever used of special_restraints or add_rsr to add your own restraints? Or to build conserved part of your target protein (such as ligand binding site or binding state of ligand)?Did Modeller build a model without any violation of your restraints? My target protein has a conserved ligand binding site.But even when I give it the restraints ,it doesn't work exactly.(e.g. I gave it distance restraints with mean=2.3 Åand std=0.03 Åand one of pair_atom were in 3.7 Å from each other) Is it common?Even about conserved parts of structure? Thanks Maryam

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PDB gap fill
by Anna Marabotti 23 May '08

23 May '08

Dear all, I tried to use the script shown in Wiki "Missing residue" section to automatically fill a gap of 12 residues in a file PDB. However, the application stops with the error message: "No loops detected for refinement: you must redefine select_loop_atoms". I had a look at the archive and found that 12 residues is the upper limit for loop detection and refinement, therefore I don't know why Modeller 9v4 does not work in my case. Does anyone have suggestions? Many thanks and best regards Anna ______________________________________________ Anna Marabotti, Ph.D. Laboratorio di Bioinformatica e Biologia Computazionale Istituto di Scienze dell'Alimentazione, CNR Via Roma 52 A/C 83100 Avellino (Italy) Tel: +39 0825 299651 Fax: +39 0825 781585 Skype: annam1972 E-mail: amarabotti(a)isa.cnr.it Web page: http://bioinformatica.isa.cnr.it/anna.htm ____________________________________________________ "If you think you are too small to make a difference, try sleeping with a mosquito"

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Re: [modeller_usage] modeller_usage Digest, Vol 7, Issue 30
by salam pradeep 22 May '08

22 May '08

How do I installed Pylab for plotting the plot_profiles.py On Thu, May 22, 2008 at 10:00 PM, <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. EM density maps for building models? (Juan Chang) > 2. Re: EM density maps for building models? (Modeller Caretaker) > 3. Modeller 9v4 release (Modeller Caretaker) > 4. multiple template model (deepti nayar) > 5. Re: multiple template model (Modeller Caretaker) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 13 May 2008 12:49:35 -0400 > From: Juan Chang <juan.chang(a)bcm.edu> > Subject: [modeller_usage] EM density maps for building models? > To: modeller_usage(a)salilab.org > Message-ID: <4829C69F.6000108(a)bcm.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Hello, > > The density.grid_search() function outputs a 'bestCC_targ' file which > contains the CCF. Is there a way to use this information for model > building? A web tutorial or Python code on how to use electron > microscope density maps for model building would be helpful. > > Thanks! > > > ------------------------------ > > Message: 2 > Date: Tue, 13 May 2008 12:28:44 -0700 > From: Modeller Caretaker <modeller-care(a)salilab.org> > Subject: Re: [modeller_usage] EM density maps for building models? > To: Juan Chang <juan.chang(a)bcm.edu> > Cc: modeller_usage(a)salilab.org > Message-ID: <4829EBEC.2030603(a)salilab.org> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Juan Chang wrote: > > The density.grid_search() function outputs a 'bestCC_targ' file which > > contains the CCF. Is there a way to use this information for model > > building? A web tutorial or Python code on how to use electron > > microscope density maps for model building would be helpful. > > grid_search is for static fitting of models into density maps, e.g. for > model assessment. It is not suitable for guiding the model building > procedure itself. You could, however, check out Flex-EM at > http://salilab.org/Flex-EM/ and check out the referenced paper to see if > that is helpful 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: 3 > Date: Thu, 15 May 2008 09:17:30 -0700 > From: Modeller Caretaker <modeller-care(a)salilab.org> > Subject: [modeller_usage] Modeller 9v4 release > To: modeller_announce(a)salilab.org, modeller_usage(a)salilab.org > Message-ID: <482C621A.5030005(a)salilab.org> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > The new version of Modeller, 9v4, is now available for download! Please > see the download page at http://salilab.org/modeller/ for more > information. > > If you have a license key for Modeller 8 or 9, there is no need to > reregister for Modeller 9v4 - the same license key will work. (It won't > do any harm to reregister if you want to, though!) > > 9v4 is primarily a bugfix release relative to the last public release > (9v3). Major user-visible changes include: > > # The speed of GB/SA calculations has been dramatically increased. > # io_data.atom_files_directory is now a Python list of directories, > rather than a colon-separated string. (This is so that everything > works on Windows, where ':' is a valid character in directory names.) > Old scripts that use colon-separated strings should still work, but > will trigger a warning. > # When reading or writing compressed files, the uncompressed versions of > these files are now written into writeable local storage. Previously, > these files were written into the same directory as the compressed > versions, which is problematic when that directory is read-only or is > on network storage. > # Update PDB files used in the examples (remediated PDBs are now used). > > See the Modeller manual for a full change log: > http://salilab.org/modeller/9v4/manual/node38.html > > If you encounter bugs in Modeller 9v4, please see > http://salilab.org/modeller/9v3/manual/node10.html for information on > how to report them. > > 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: Thu, 22 May 2008 12:24:33 +0530 > From: "deepti nayar" <deeptinayar(a)gmail.com> > Subject: [modeller_usage] multiple template model > To: modeller_usage(a)salilab.org > Message-ID: > <630ea2870805212354k4c5b5e5bmcb4cde2b08be5ca5(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hi all > > I am new to modeller. I am using modeller 9v2. I am trying to model > structure for a protein using two templates. Can anyone tell me > whethermodeller first builds its own alignment among the templates and then > build a model??? > > Is there a way by which we can get the model based on our wished alignment. > I tried this but it seems it doesnt work. > > thanks > > -- > Regards > > Deepti Nayar > Research Assistant > Bioinformatics Centre > National Institute of Immunology > New Delhi - 110067 > e-mail: deeptinayar(a)gmail.com >

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multiple template model
by deepti nayar 22 May '08

22 May '08

Hi all I am new to modeller. I am using modeller 9v2. I am trying to model structure for a protein using two templates. Can anyone tell me whethermodeller first builds its own alignment among the templates and then build a model??? Is there a way by which we can get the model based on our wished alignment. I tried this but it seems it doesnt work. thanks -- Regards Deepti Nayar Research Assistant Bioinformatics Centre National Institute of Immunology New Delhi - 110067 e-mail: deeptinayar(a)gmail.com

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Modeller 9v4 release
by Modeller Caretaker 15 May '08

15 May '08

The new version of Modeller, 9v4, is now available for download! Please see the download page at http://salilab.org/modeller/ for more information. If you have a license key for Modeller 8 or 9, there is no need to reregister for Modeller 9v4 - the same license key will work. (It won't do any harm to reregister if you want to, though!) 9v4 is primarily a bugfix release relative to the last public release (9v3). Major user-visible changes include: # The speed of GB/SA calculations has been dramatically increased. # io_data.atom_files_directory is now a Python list of directories, rather than a colon-separated string. (This is so that everything works on Windows, where ':' is a valid character in directory names.) Old scripts that use colon-separated strings should still work, but will trigger a warning. # When reading or writing compressed files, the uncompressed versions of these files are now written into writeable local storage. Previously, these files were written into the same directory as the compressed versions, which is problematic when that directory is read-only or is on network storage. # Update PDB files used in the examples (remediated PDBs are now used). See the Modeller manual for a full change log: http://salilab.org/modeller/9v4/manual/node38.html If you encounter bugs in Modeller 9v4, please see http://salilab.org/modeller/9v3/manual/node10.html for information on how to report them. Ben Webb, Modeller Caretaker -- modeller-care(a)salilab.org http://www.salilab.org/modeller/ Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage

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