April 2006 - modeller_usage

Loop bias
by Joel Tyndall 09 Apr '06

09 Apr '06

Hi folks, I'm looking at a group of templates where only one of them has an "extended" beta sheet / loop region. This single template is closer to the model sequence (in this region only) than the other templates. Is there a way to bias the construction of this particular "loop" towards only one template! I don't want to just build a model based on this structure alone however. Cheers Joel -- Joel Tyndall, PhD Lecturer National School of Pharmacy University of Otago PO Box 913 Dunedin New Zealand Pukenga Te Kura Taiwhanga Putaiao Te Whare Wananga o Otago Pouaka Poutapeta 913 Otepoti Aotearoa Ph / Waea +64 3 4797293 Fax / Waeawhakaahua +64 3 4797034

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Getting alignment positions fixed
by Paul Wilhelm Elsinghorst 09 Apr '06

09 Apr '06

Hi folks, I have a problem getting the alignment of two sequences the way I want it to be. Please have a look at this picture to see what I'm looking for: http://pwe.no-ip.org/other/modeller.jpg I'd like to set up my alignment file in a way that the alignment done by modeller gives exactly this result. I fiddeled with fixed_pos things but couldn't get it to work, actually I didn't figure out how it really works. This is the file I have for now: http://pwe.no-ip.org/other/modeller.txt If anyone could assist me a little or point me to the right direction I'd be glad. Thanks so far, Paul

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automodel optimization
by Alex Brown 07 Apr '06

07 Apr '06

Hi. Sorry for being such a nuisance, but I have a question concerning model optimization when using automodel. I would presume that automodel uses model.optimize when optimizing a model, with a default of a single pass, automodel.repeat_optimization having a default value of 1. However, according to the manual, the optimization_method parameter of model.optimize has default value of 999, whereas it should have a value of either 1 or 3. What default optimization method does automodel use, can it be changed, and what does the model.optimize default of 999 mean ? OK - that's three questions ! Many thanks, Alex

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model.pick_atoms problem
by Alex Brown 06 Apr '06

06 Apr '06

Hi. This may, or may not, be a problem, but I have found that using the selection_segment argument 'FIRST:A' , 'LAST:A' in model.pick_atoms doesn't appear to work properly. In fact, the whole molecule (all chains) is selected (i.e. the argument acts as if it were 'FIRST:', 'LAST:'). Correct selection does occur if discrete, numbered residues are used, as in '1:A', '100:A', selecting atoms in a segment from residues 1 to 100 in chain A. Is this correct, or have I stumbled across a bug. Cheers, Alex.

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Weighing the restraints differenlty on the modeller-fly
by Mehmet SEN 05 Apr '06

05 Apr '06

Hello I am running modeller8v2 to get the model of my protein. In this case, I do have the NMR experimental data (about 400 restraints). Now, I am able to run my structures with restraints I want to have from the NMR experiments. In this case, I would like to do following. I would like modeller restrains to be applied region for which I do not have any restrains, but for the region where I can define secondary structures via NMR experiment, I want to turn off modeller-derived restrains, or decrease weighing factor of the modeller-derived restraints, that is, I would like my restraints to weigh more then modeller-derived restraints. If you need make any comments on this subject, I would be so much pleased. If you have performed anything like that, and have any script available, I really want to get it. Mehmet Sen --------------------------------- New Yahoo! Messenger with Voice. Call regular phones from your PC for low, low rates.

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Modeller usage with Python 2.4?
by Dow_Hurst 02 Apr '06

02 Apr '06

After perusing the archives for explanations of Modeller and Python interactions, it isn't apparent to me that Modeller couldn't use a later interpreter and modules if the paths are set correctly. I understand that Modeller can be made aware of standard python 2.3 modules with the PYTHONHOME variable. However, I haven't found a clear yes or no on using a Python 2.4 standard installation with Modeller. Is it possible to disable the internal Python 2.3 interpreter linked into Modeller and force Modeller to use a system's Python 2.4 installation? If not, then I could just compile/install Python 2.3. I use SUSE 9.3 and 10.0 mainly at the moment in our lab at UNCG on all the machines so I don't have a native install of the older Python. Uninstalling Python 2.4 breaks several packages so a side by side compile/install is probably easiest. Thanks for your help, Dow No sig.

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