- modeller_usage - salilab.org

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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using different weights for spatial restraints
by Lillian Chong 02 Feb '07

02 Feb '07

Dear Modellers, I have created a chimera using the spatial restraints from the crystal structures of two domains. During the modelling process, I would like to weaken the spatial restraints in one of the domains relative to the other domain. Can you please tell me the best way to weaken the restraints? Thanks! Lillian

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Re: [modeller_usage] D-Proline problem
by N.Arun Prasanna 02 Feb '07

02 Feb '07

hello ben, i am facing a major problem. Template details: my template is a denova protein (PDB code: 1JY4). My main aim is to impose D-Proline on my sequence. when i aligned and ran iteration, it says protein structure not read in. The convention they followed for D-Proline is DPR i tried to change it to PRO in coordinate file since i need the D-Proline coordinate, but it is still not working. Please suggest me how to proceed this. Regards, Prasanna

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modeling a 2 domain protein with interdomain restraints
by Michel Seigneuret 02 Feb '07

02 Feb '07

Hi Modeller experts, Here is my problem. I would like to build a model of a 2 domain protein. I have templates for each domain as well as additional interdomain distance restraints from crosslinking data. As I understand it is possible to introduce these additionnal distance restraints in the input file. However I also notice from FAQ n°1 that in general :"...the relative orientation of the two domains the resulting model will probably have an incorrect relative orientation of the two domains ...". So I suspect there will be a conflict between my (correct) additionnal interdomain distance restraints and the (incorrect) interdomain distance restraints resulting from the initial arbitrary relative orientation of the 2 templates. How can I solve this. Is there a way to tell Modeller not to use these latter restraints or a way to remove these at some point ? Thank you in advance for your help. Best regards. Michel Michel Seigneuret Institut Cochin, U567-UMR8104 Département de Biologie Cellulaire 22 rue Méchain, 75014 Paris, France Tel: 33 (0)1 40 51 64 50 Fax: 33 (0)1 40 51 64 54

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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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