Hi,
How do I build a PDB file containing more than 10 models?
Thank you.
Sam Kauba
On 10/31/2011 07:16 AM, junior wrote: > How do I build a PDB file containing more than 10 models?
If you really mean you want to make a single PDB file containing multiple models (which the PDB format allows, with a MODEL record at the start of each model and an ENDMDL record at the end) then you can't do that with MODELLER, for any number of models (10 or otherwise). The models produced by MODELLER are each in their own PDB file.
If you simply want to make more than 10 models, each in a *different* PDB file, then go with Mensur's suggestions. If you really want a single PDB file containing multiple models, you will have to first produce multiple PDB files, then stick them together manually, inserting MODEL and ENDMDL records, either with a text editor or with some simple scripting.
Ben Webb, Modeller Caretaker
There is no need for scripting in order to concatenate PDB files - and by the way, that is not how I understood the original question.
Theseus ( http://www.theseus3d.org/ ) will take a bunch of PDB files, align them structurally, and insert MODEL and ENDMDL records so that the final file will look like an NMR ensemble. A single command is all it takes:
theseus files.0???.pdb
This assumes we have lots of PDB files with files.0???.pdb names where ? stands for any character - those would be different numbers in case of MODELLER-made PDB files.
At 12:47 PM 11/1/2011, you wrote: >On 10/31/2011 07:16 AM, junior wrote: > > How do I build a PDB file containing more than 10 models? > >If you really mean you want to make a single PDB file containing >multiple models (which the PDB format allows, with a MODEL record at the >start of each model and an ENDMDL record at the end) then you can't do >that with MODELLER, for any number of models (10 or otherwise). The >models produced by MODELLER are each in their own PDB file. > >If you simply want to make more than 10 models, each in a *different* >PDB file, then go with Mensur's suggestions. If you really want a single >PDB file containing multiple models, you will have to first produce >multiple PDB files, then stick them together manually, inserting MODEL >and ENDMDL records, either with a text editor or with some simple scripting. > > Ben Webb, Modeller Caretaker >-- >modeller-care@salilab.org http://www.salilab.org/modeller/ >Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage >_______________________________________________ >modeller_usage mailing list >modeller_usage@salilab.org >https://salilab.org/mailman/listinfo/modeller_usage
========================================================================== | Mensur Dlakic, PhD | Tel: (406) 994-6576 | | Department of Microbiology | Fax: (406) 994-4926 | | Montana State University | | | 109 Lewis Hall, P.O. Box 173520 | http://myprofile.cos.com/mensur | | Bozeman, MT 59717-3520 | E-mail: mdlakic@montana.edu | ==========================================================================
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junior -
Mensur Dlakic -
Modeller Caretaker