January 2007 - modeller_usage

Disulfides
by Joel Tyndall 05 Feb '07

05 Feb '07

Hi folks (& Ben), I have been building some models with disulfide patches. One of the disulfides presents a model with basically bad geometry (cys66-cys40) which is troubling. I have attached model and top file. (I'm using 8.2 with old style formats). Any suggestions as to how to rectify this (fix the geometry)? I'm trying to gauge which is the appropriate disulfide connectivity between this model and another and this ain't helping the cause. Many thanks J -- 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 INCLUDE SET ALNFILE = 'MIS_rec_modelII.ali' SET KNOWNS = '2hlq_a' SET MD_LEVEL = 'refine_1' SET SEQUENCE = 'MIS_rec_modelII' SET STARTING_MODEL = 1 SET ENDING_MODEL = 5 SET DEVIATION = 4.000000 SET DO_LOOPS = 1 SET RADII_FACTOR = 0.915 SET LOOP_STARTING_MODEL = 1 SET LOOP_ENDING_MODEL = 5 SET LOOP_MD_LEVEL = 'refine_2' SET HETATM_IO = on CALL ROUTINE = 'model' STOP SUBROUTINE ROUTINE = 'special_patches' PATCH RESIDUE_TYPE = 'DISU', RESIDUE_IDS = '34' '58' PATCH RESIDUE_TYPE = 'DISU', RESIDUE_IDS = '3' '39' PATCH RESIDUE_TYPE = 'DISU', RESIDUE_IDS = '40' '66' RETURN END_SUBROUTINE

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Question
by Manuel Aguilar 26 Jan '07

26 Jan '07

Dear all: Could somebody please tell me how much the resulting models would be different if I install and run Modeller in comparison with using the ModWeb Modelling Server within the MODBASE web page. I would like to get a model of one sequence based on one target with known 3D structure. Thanks a lot in advance. Sincerely Manuel B. Aguilar Dr. Manuel B. Aguilar Ramírez Laboratorio de Neurofarmacología Marina Instituto de Neurobiología-UNAM Campus UNAM-UAQ Juriquilla km 15 Carr. Querétaro-S.L.P. Juriquilla, Qro. 76230 México Tel./Fax: + 52 442 2381043

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I am having problems to install the MODELLER
by gpereira＠lnls.br 26 Jan '07

26 Jan '07

Hi, i instaled the modeller 9v2 in Pentium D PC, when trying to twirl software it presents the following error: mod9v1 salign_fix_positions.py Could not find platform independent libraries <prefix> Could not find platform dependent libraries <exec_prefix> Consider setting $PYTHONHOME to <prefix>[:<exec_prefix>] 'import site' failed; use -v for traceback Thanks, Gustavo G. Pereira LNLS - Laboratori Nacional deLuz Sincroton - http://www.lnls.br

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loop modeling
by Mehdi Bagheri-Hamaneh 25 Jan '07

25 Jan '07

Hi all, I am very new to loop modelling using MODELLER. I have been reading the documentation to find the answer to my questions, but I didn't find anything. I have two questions about loop refinement: 1) How can refine more than one loop at the same time. I know how to model one loop, but how can I select more than one region to refine? 2) Is it a good idea to model several loops (say 10) at the same time? Any help will be appreciated. Yours, Mehdi

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Model evaluation question - DOPE
by Charlie Allerston 24 Jan '07

24 Jan '07

Hi, I have a couple of questions I hope someone has answers for please..... Using the model-profile.py script I can produce a .profile file which can be read by the dopeplot perl script to generate 2 .dat files and a .png image of the DOPE scores. Firstly, the .png that i get just plots the psudoenergy of the template against that of the target, instead of plotting both energies against residue number (attached). Has anyone else encountered this problem? When I try and just strip the energies from the final line of the .profile (s) and plot them using GNUPLOT, I can get a plot, but the problem (I think) is that my target and template are of different lengths, so I am unsure how to interpret the differences in the energies as i dont think the gaps in alignment are taken into account? I suppose I could add these gaps manually but I would hope there would be a better way of doing this? the dat files of the target and template are attached. thanks charlie _________________________________________________________________ Get Hotmail, News, Sport and Entertainment from MSN on your mobile. http://www.msn.txt4content.com/

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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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