Difference between revisions of "Assignment 5 fallback data"
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==LGA superposition== | ==LGA superposition== | ||
| − | The resulting output produced by the LGA server for the 1DUX_ABC and 1MB1 superposition consists of two parts: the superposition report explains which residues were matched and what their RMSD after superposition was. The coordinates contain the rotated coordinates of the entire 1DUX file superimposed on 1MB1. In order to use this for as RasMol, the following | + | The resulting output produced by the LGA server for the 1DUX_ABC and 1MB1 superposition consists of two parts: the superposition report explains which residues were matched and what their RMSD after superposition was. The coordinates contain the rotated coordinates of the entire 1DUX file superimposed on 1MB1. In order to use this for as RasMol, the following manual edits were performed. |
:#LGA created several <code>END </code> records in the middle of the file. These prevent the following lines to be read in. They were simply deleted. Since the protein chans of the Mbp1 and Elk-1 domains are closely superimposed, RasMol tries to draw multiple bonds between the residues that have close contacts. This was addressed by bracketing the chains in <code>MODEL</code> and <code>ENDMDEL</code>, which prevents bonds between being drawn. | :#LGA created several <code>END </code> records in the middle of the file. These prevent the following lines to be read in. They were simply deleted. Since the protein chans of the Mbp1 and Elk-1 domains are closely superimposed, RasMol tries to draw multiple bonds between the residues that have close contacts. This was addressed by bracketing the chains in <code>MODEL</code> and <code>ENDMDEL</code>, which prevents bonds between being drawn. | ||
:*[[Assignment_5_LGA_Results| '''LGA superposition report''']] | :*[[Assignment_5_LGA_Results| '''LGA superposition report''']] | ||
:*[[Assignment_5_1DUX_1MB1| '''1DUX_1MB1 Coordinates''']] | :*[[Assignment_5_1DUX_1MB1| '''1DUX_1MB1 Coordinates''']] | ||
| + | |||
| + | ==Protein-DNA complex model== | ||
| + | |||
| + | The DNA coordinates (chain A and B) from the LGA superimposed coordinate file were copied, and pasted into the SwissModel coordinate file, thus generating a homology model of a Protein / DNA complex. | ||
| + | |||
| + | :*[[Assignment_5_Model_DNA| '''Model/DNA complex Coordinates''']] | ||
Revision as of 06:35, 6 December 2006
Contents
Target sequence
>MBP1_CHAGL XP_001224558:8..108 AGIYSATYSGIPVYEYQFGPDMKEHVMRRREDNWINATHILKAAGFDKPARTRILERDV QKDVHEKIQGGYGKYQGTWIPLEQGRALAQRNNIYDRLRPIF
CLUSTALW formatted alignment
CLUSTAL alignment 1MB1 NQIYSARYSGVDVYEFIHSTG---SIMKRKKDDWVNATHILKAANFAKAKRTRILEKEV MBP1_CHAGL AGIYSATYSGIPVYEYQFGPDMKEHVMRRREDNWINATHILKAAGFDKPARTRILERDV 1MB1 LKETHEKVQGGFGKYQGTWVPLNIAKQLAEKFSVYDQLKPLF MBP1_CHAGL QKDVHEKIQGGYGKYQGTWIPLEQGRALAQRNNIYDRLRPIF
SwissModel response
Four e-mails are sent by SwissModel after submission of the modeling request. Two of the received files are welcome and help messages. Two other e-mail messages conatin the program output and the model.
LGA superposition
The resulting output produced by the LGA server for the 1DUX_ABC and 1MB1 superposition consists of two parts: the superposition report explains which residues were matched and what their RMSD after superposition was. The coordinates contain the rotated coordinates of the entire 1DUX file superimposed on 1MB1. In order to use this for as RasMol, the following manual edits were performed.
- LGA created several
ENDrecords in the middle of the file. These prevent the following lines to be read in. They were simply deleted. Since the protein chans of the Mbp1 and Elk-1 domains are closely superimposed, RasMol tries to draw multiple bonds between the residues that have close contacts. This was addressed by bracketing the chains inMODELandENDMDEL, which prevents bonds between being drawn.
- LGA created several
Protein-DNA complex model
The DNA coordinates (chain A and B) from the LGA superimposed coordinate file were copied, and pasted into the SwissModel coordinate file, thus generating a homology model of a Protein / DNA complex.
