User:Eric Martz/Cavities tests: Difference between revisions

Line 1:

<applet load='Dnac_from_2ggz_a.pdb' size='500' frame='true' align='right'

scene='User:Eric_Martz/Sandbox_4/Dnac_model_from_2ggz_a/3' />

scene='User:Eric_Martz/Sandbox_4/Dnac_model_from_2ggz_a/5' />

The following sequence was provided for DnaC from E. coli:

Line 16:

</tt>

This sequence was submitted to Swiss Model, which [http://tinyurl.com/4nek2q generated the homology model] shown here (<scene name='User:Eric_Martz/Sandbox_4/Dnac_model_from_2ggz_a/3'>restore initial scene</scene>) using [[2qgz]] chain A as a template, which has 18.6% sequence identity. Apparently Swiss Model used predicted secondary structure to help in the sequence alignment, but details are not clear to me. The homology model represents residues 55-237, shown in boldface in the above sequence.

This sequence was submitted to Swiss Model, which [http://tinyurl.com/4nek2q generated the homology model] shown here (<scene name='User:Eric_Martz/Sandbox_4/Dnac_model_from_2ggz_a/5'>restore initial scene</scene>) using [[2qgz]] chain A as a template, which has 18.6% sequence identity. Apparently Swiss Model used predicted secondary structure to help in the sequence alignment, but details are not clear to me. The homology model represents residues 55-237, shown in boldface in the above sequence.

Swiss Model has apparently used the [[temperature]] field in the PDB file to indicate regions that are highly unreliable, namely the regions that are red when the model is <scene name='User:Eric_Martz/Sandbox_4/Dnac_model_from_2ggz_a/4'>colored by temperature</scene>.

Swiss Model has apparently used the [[temperature]] field in the PDB file to indicate regions that are highly unreliable, namely the regions that are red when the model is <scene name='User:Eric_Martz/Sandbox_4/Dnac_model_from_2ggz_a/4'>colored by temperature</scene>. These regions are shown as '''translucent''' in the initial scene (using the Jmol command select temperature >50).

In order to find specific residues, or see other aspects of this homology model, please use:

@@ Line 1: / Line 1: @@
 <applet load='Dnac_from_2ggz_a.pdb' size='500' frame='true' align='right'
-scene='User:Eric_Martz/Sandbox_4/Dnac_model_from_2ggz_a/3' />
+scene='User:Eric_Martz/Sandbox_4/Dnac_model_from_2ggz_a/5' />
 The following sequence was provided for DnaC from E. coli:
@@ Line 16: / Line 16: @@
 </tt>
-This sequence was submitted to Swiss Model, which [http://tinyurl.com/4nek2q generated the homology model] shown here (<scene name='User:Eric_Martz/Sandbox_4/Dnac_model_from_2ggz_a/3'>restore initial scene</scene>) using [[2qgz]] chain A as a template, which has 18.6% sequence identity. Apparently Swiss Model used predicted secondary structure to help in the sequence alignment, but details are not clear to me. The homology model represents residues 55-237, shown in boldface in the above sequence.
+This sequence was submitted to Swiss Model, which [http://tinyurl.com/4nek2q generated the homology model] shown here (<scene name='User:Eric_Martz/Sandbox_4/Dnac_model_from_2ggz_a/5'>restore initial scene</scene>) using [[2qgz]] chain A as a template, which has 18.6% sequence identity. Apparently Swiss Model used predicted secondary structure to help in the sequence alignment, but details are not clear to me. The homology model represents residues 55-237, shown in boldface in the above sequence.
-Swiss Model has apparently used the [[temperature]] field in the PDB file to indicate regions that are highly unreliable, namely the regions that are <font color="red"><b>red</b></font> when the model is <scene name='User:Eric_Martz/Sandbox_4/Dnac_model_from_2ggz_a/4'>colored by temperature</scene>.
+Swiss Model has apparently used the [[temperature]] field in the PDB file to indicate regions that are highly unreliable, namely the regions that are <font color="red"><b>red</b></font> when the model is <scene name='User:Eric_Martz/Sandbox_4/Dnac_model_from_2ggz_a/4'>colored by temperature</scene>. These regions are shown as '''translucent''' in the initial scene (using the Jmol command <i>select temperature >50</i>).
 In order to find specific residues, or see other aspects of this homology model, please use: