modeller_usage

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modeller_usage@salilab.org

October 2002

30 participants
42 discussions

a bug?
by Kong Lesheng 02 Oct '02

02 Oct '02

Hi, When I use align2d to generate alignment, non-standard residues are always replaced by "G" even I have set "HETATM_IO=ON". So in the following modeling, the program will complain that sequence differences between structure and alignment. Everytime before I do modeling, I have to manually edit the alignment sequences. Could MODELLER automatically write non-standard residues as "." or other symbols which do not affect modeling? Thank you very much! With best regards, Lesheng

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Problems with modeling chimera
by Andersen, Kim Vilbour (KVA) 02 Oct '02

02 Oct '02

Hi I try to model a chimeric protein based on FAQ 4 To test the method I took a PDB file and cut it in two parts and then try to model the complete molecule again based on an FAQ 4 I get the error: fit2xyz_E> number of equivalent positions < 3: 0 recover__> ERROR_STATUS >= STOP_ON_ERROR: 1 1 As I understand it there are not enough overlapping residues in the alignment. But that is exactly the point, I try to model a chimeric protein based on the independent fragments exactly as in FAQ 4. What is wrong? Does the templates have to be overlapping, and is FAQ 4 wrong? All files are attached Thanks in advance Kim ------------------------------------------------------------------------ Kim Vilbour Andersen, PhD Senior Scientist Maxygen Agern Allé 1 DK-2970 Hørsholm Denmark <<model.top.gz>> <<align.pir.gz>> <<1GR3_A2.pdb.gz>> <<1GR3_A1.pdb.gz>> Tel: +45 7020 5550 Direct: +45 4517 8473 Mobile: +45 2637 3727 Fax: +45 7020 5530 E-mail: kva(a)maxygen.dk http://www.maxygen.dk/ ------------------------------------------------------------------------

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