- modeller_usage - salilab.org

using restraints from saxs data
by Christian Meesters 24 Jan '07

24 Jan '07

Hi, Just worked myself through the tutorials and now I would like to do some modelling using SAXS data as restraints. As far as I could google there is the possibility of doing so, presumably using the saxsdata class, but I've no idea how. Are there any examples around? Or anything specific in the documentation (which I must have overlooked)? Any pointer is welcome. Thanks a lot in advance Christian

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Modeller 9v1 release
by Modeller Caretaker 22 Jan '07

22 Jan '07

The new version of Modeller, 9v1, is now available for download! Please see the download page at http://salilab.org/modeller/ and the release notes at http://salilab.org/modeller/release.html for information. If you have a license key for Modeller 8, there is no need to reregister for Modeller 9v1 - the same license key will work. (It won't do any harm to reregister if you want to, though!) What's new in 9v1? (For a full list, see http://salilab.org/modeller/release.html#new ) # Modeller is now distributed as a shared library, allowing it to be used with other Python-based applications, or to be extended by the user. # New DOPE-HR assessment method, and DOPE-based loop modeling. # Speed improvements for profile searches. # HDF5 format now used for all binary files. # Much more flexible Python objects used for atom selections, model optimizations, schedules, symmetry, pseudo atoms, and restraints. # Improved handling of multi-chain models. # Quasi-Newton minimization, self-guided dynamics, and rigid bodies. If you encounter bugs in Modeller 9v1, please see http://salilab.org/modeller/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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help about evaluate_model.log
by Purzelfrau＠gmx.de 19 Jan '07

19 Jan '07

Hello everybody, i have a question about the output-file evaluate_model.log. I looked in the basic_example from the Modellers Homepage and also in my own output files. In the most of the cases there is the following message: report______> Distribution of short non-bonded contacts: serious non-bonded atom clash: 1 2 1.480 serious non-bonded atom clash: 2 3 1.539 serious non-bonded atom clash: 2 7 1.493 serious non-bonded atom clash: 3 4 1.528 serious non-bonded atom clash: 4 5 1.817 serious non-bonded atom clash: 5 6 1.816 .... Can everybody explain what does it exactly mean? Is for example the number 1 the first atom in the template and 2 the second in the model or what does it mean? And what can i do that this message never comes? Thanks for all answers! Verena -- Der GMX SmartSurfer hilft bis zu 70% Ihrer Onlinekosten zu sparen! Ideal für Modem und ISDN: http://www.gmx.net/de/go/smartsurfer

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(no subject)
by Purzelfrau＠gmx.de 19 Jan '07

19 Jan '07

-- Der GMX SmartSurfer hilft bis zu 70% Ihrer Onlinekosten zu sparen! Ideal für Modem und ISDN: http://www.gmx.net/de/go/smartsurfer

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forrtl Error using the "/." construct
by Schmid, Dr R. 12 Jan '07

12 Jan '07

Dear all, I am trying to model a protein with a ligand using the "/." construct in the alignment and I am getting the following error: [ralf@localhost models]$ mod8v2 tens1.top forrtl: severe (64): input conversion error, unit -5, file Internal Formatted Read Image PC Routine Line Source mod8v2_i386-intel 0837011A Unknown Unknown Unknown mod8v2_i386-intel 0836E555 Unknown Unknown Unknown mod8v2_i386-intel 0834064D Unknown Unknown Unknown ... mod8v2_i386-intel 080811C6 Unknown Unknown Unknown mod8v2_i386-intel 08080D81 Unknown Unknown Unknown libc.so.6 006F179A Unknown Unknown Unknown mod8v2_i386-intel 08080CC1 Unknown Unknown Unknown [ralf@localhost models]$ [ralf@localhost models]$ tail -20 tens1.log read_al_374_> Non-standard residue type,position,sequence: . 324 1 read_al_374_> Non-standard residue type,position,sequence: . 324 2 Read the alignment from file : tens1.ali Total number of alignment positions: 324 # Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------------- 1 1d5r 308 2 1d5r . 2 tensin1 309 2 tensin1 . TOP_________> 129 113 STRING_IF STRING_ARGUMENTS = TOP_VERSION 'accelrys', OPER; ATION = 'EQ' TOP_________> 130 117 CHECK_ALIGNMENT check_a_343_> >> BEGINNING OF COMMAND openf5__224_> Open 11 OLD SEQUENTIAL 1d5r.pdb Dynamically allocated memory at amaxstructure [B,kB,MB]: 2652691 2590.519 2.530 openf5__224_> Open 11 OLD SEQUENTIAL 1d5r.pdb [ralf@localhost models]$ I should mention that the modelling process without ligand runs smoothly. I am using Modeller 8v2 on Linux RHE, 2.4.21-47.0.1.ELsmp kernel. Thanks in advance for any hints, Ralf

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Cómo instalar MODELLER
by Carlos Lozano 11 Jan '07

11 Jan '07

Hola a todos de la comunidad, la primer pregunta que me surge, es que no tengo ni idea de cómo instalar MODELLER en mi ibook. Sí alguién puede recomendarme algún tip, se lo agradecería. Carlos

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origin of blosum62.sim.mat and as1.sim.mat
by Joshua A. Speidel 11 Jan '07

11 Jan '07

Hello, I am curious about the origin of the blosum62.sim.mat and as1.sim.mat. When I look at the blosum62.sim.mat, I can't figure out the relationship between the numbers there, and the original blosum62 matrix. Initially, I thought that the Henikoff & Henikoff values were just scaled to between 0 and 1000, but that didn't seem to work. I can't find a reference for ALBASE3 mentioned in as1.sim.mat. Finally, if I wanted to use my own matrix, is it necessary for me to scale it to between 0 and 1000? Your help in understanding this is greatly appreciated, Josh

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Re: [modeller_usage] Ligands
by Esben Jannik Bjerrum 09 Jan '07

09 Jan '07

Hi Joel Have you tried to include an @ in your alignment file?according to restyp.lib (in mollib directory) it should correspond to ATP. I dont know how about the quality of the parameters are, but its a starter. And theres a starter for tweaking in top_heav.lib. If theres no ATP (or similat molecule) in you template You'll need to add some constraints to some atoms between your protein and ATP to restrict it to a position near the binding site. Happy Modelling Esben Bjerrum __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

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Ligands
by Joel Tyndall 08 Jan '07

08 Jan '07

Hi all, I'm wanting to add in an ATP molecule based on my template to my modelled structure. I have looked at the FAQ and it does seem a laborious task to write the CHARM topology files etc. I was wondering if there was a database of ligands (wiki? type thing) or a web based converter ( i have already looked at Prodrg in dundee) or if someone wants to share their top files for ATP. ...Or any alternative methods out there? I'm currently using 8v2 but with old scripts and will upgrade soon. Cheers joel -- Joel Tyndall, PhD Lecturer National School of Pharmacy University of Otago PO Box 913 Dunedin 9054 New Zealand Pukenga Te Kura Taiwhanga Putaiao Te Whare Wananga o Otago Pouaka Poutapeta 913 Otepoti 9054 Aotearoa Ph / Waea +64 3 4797293 Fax / Waeawhakaahua +64 3 4797034

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modeller model and modbase model
by hori koshii 07 Jan '07

07 Jan '07

Hi all, Has anyone come across with the models on MODBASE? How does that compare to our own models built by using "MODELLER"? (I know they are both using MODELLER, but the protein I am working on, have very different "insertion" loops from my results and modbase's) I have been trying to build a protein model using MODELLER8, but recently come across with one already available on the MODBASE. I think there is actually only one good template (over 30%) for my target. I used MODELLER 8 to build 1000 models and pick out the ones with lower DOPE scores. The loop conformations in my model and the one on MODBASE are quite different. I am curious espeically about the loop insertions. So, I am wondering how come they are very different? Could anyone from this forum give me any comment about this please? Thank you :) Sincerely yours, __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

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