User:Eric Martz/Cavities tests: Difference between revisions

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<applet load='Dnac_from_2ggz_a.pdb' size='500' frame='true' align='right'
<StructureSection load='' size='350' side='right' caption='' scene=''>
scene='User:Eric_Martz/Sandbox_4/Dnac_model_from_2ggz_a/6' />


The following sequence was provided for DnaC from E. coli:
*1 <scene name='31/319439/Surface_test/1'>Surface test 1</scene>: simple surface on chain A of 1d66. Colored translucent green. This surface was generated with the '''representations''' tab of the SAT.


<tt>
MKNVGDLMQR LQKMMPAHIK PAFKTGEELL AWQKEQGAIR SAALERENRA
<br>
MKMQ<b>RTFNRS GIRPLHQNCS FENYRVECEG QMNALSKARQ YVEEFDGNIA
<br>
SFIFSGKPGT GKNHLAAAIC NELLLRGKSV LIITVADIMS AMKDTFRNSG
<br>
TSEEQLLNDL SNVDLLVIDE IGVQTESKYE KVIINQIVDR RSSSKRPTGM
<br>
LTNSNMEEMT KLLGERVMDR MRLGNSLWVI FNWDSYR</b>SRV TGKEY
</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/6'>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.
*2 <scene name='31/319439/6zgi_translucen_backbone/1'>6zgi as translucent backbone, chain colors</scene> (no isosurfaces). After clicking this standard SAT-generated green link, then
<jmol>
<jmolButton>
<script>
isosurface delete; isosurface "http://proteopedia.org/wiki/images/6/67/6zgi-cavities.jvxl";
</script>
<text>Load isosurface cavities</text>
</jmolButton>
</jmol>
(From uploaded file http://proteopedia.org/wiki/images/6/67/6zgi-cavities.jvxl -- see [[Image:6zgi-cavities.jvxl]])


Swiss Model has apparently used the [[temperature value]] 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 white''' in the initial scene (using the Jmol command <i>select temperature >50</i>).


The [[evolutionary conservation]] pattern, revealed by ConSurf, is quite interesting, showing <scene name='User:Eric_Martz/Sandbox_4/Dnac_model_from_2ggz_a/7'>two conserved patches</scene>.<ref>ConSurf found only 10 sequences in SwissProt, with an Average Pairwise Distance of 1.6. The run shown here used 100 sequences from Uniprot, with an APD of 1.4.</ref>
*3 <jmol>
<jmolButton>
<script>
load "http://proteopedia.org/wiki/images/c/c6/6zgi-cavities.pngj";
</script>
<text>Load .PNGJ file</text>
</jmolButton>
</jmol>
(From uploaded file http://proteopedia.org/wiki/images/c/c6/6zgi-cavities.pngj -- see [http://proteopedia.org/wiki/index.php/Image:6zgi-cavities.pngj Image:6zgi-cavities.png])


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


[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=http%3A//proteopedia.org/wiki/images/3/3e/Dnac_from_2ggz_a.pdb View DnaC Homology Model in FirstGlance in Jmol]
*4 <jmol>
<jmolLink>
<script>
load "http://proteopedia.org/wiki/images/c/c6/6zgi-cavities.pngj";
</script>
<text>Green link loading uploaded PNGJ file</text>
</jmolLink>
</jmol>. SAT not involved. PNGJ file generated externally in the [[Jmol/Application|Jmol Java application]], then uploaded to Proteopedia as for the previous item above.


The template was <scene name='User:Eric_Martz/Sandbox_4/2qgz/3'>2qgz</scene>. The portion of the template used was Glu107-Arg300. Only the amino-terminal 6 residues were not used as template (translucent). Note that there are <scene name='User:Eric_Martz/Sandbox_4/2qgz/5'>three loops</scene> in this segment of the template that lack coordinates due to [[disorder]] in the crystal (marked with spacefilled alpha-carbon atoms).


The missing loops are 202-205 (NGSV), 226-231 (EQATSW), and 268-275 (TIKGSDET). These gaps, which occur between the residues marked /\ below, were apparently ignored in making the model, which has a continuous main chain.
*5 <scene name='31/319439/6zgi_cavities_from_pngj/1'>Test dropping pngj with cavities into SAT</scene>, then saving scene. (No molecule loaded with the SAT "load molecule" tab.)


Below is the alignment produced by Swiss Model, used in making the 3D model. Vertical bars for identity were inserted by hand.
<pre>
                                                |    | |  |    ||
TARGET    55            R TFNRSGIRPL HQNCSFENYR VECEGQMNAL SKARQYVEEF
2qgzA    100  qkqaais--e riqlvslpks yrhihlsdid vnnasrmeaf saildfveqy
                                                                     
TARGET                    sssss    h h            hhhhhhh hhhhhhhhh
2qgzA              hhh  h  sss    h h            hhhhhhh hhhhhhhhh


                            |        | ||  ||    | |              |
Tested in Firefox (current version) on macOS Mojave, mid-2014 MacBook Pro, 2.2 GHz Intel Core i7.
TARGET    96    DGN-IASFIF SGKPGTGKNH LAAAICNELL L-RGKSVLII TVADIMSAMK
2qgzA    148  psaeqkglyl ygdmgigksy llaamahels ekkgvsttll hfpsfaidvk
                                                                     
TARGET                ssss ss    hhh hhhhhhhhhh h h  ssss sshhhhhhh
2qgzA                ssss ss    hhh hhhhhhhhhh hh    ssss sshhhhhhh


                                  ||  |  | ||                |
*6 <scene name='31/319439/6zgi_cavities/1'>Cavities in coronavirus spike protein 6zgi</scene>. It took 8.5 min to generate the cavity isosurfaces after I entered the command "isosurface minset 100 interior cavity 3.0 10.0" into the command slot in the SAT. (This command takes ~45 sec in the Jmol Java app which is therefore 11-fold faster for this operation.) After clicking this green link, I waited 11 min and the scene still did not appear. So I think the isosurfaces are being generated again when the green link is clicked.
TARGET    144  DTFRNSGTSE EQLLNDLSNV DLLVIDEIGV QTESKYEKVI INQIVDRRSS
2qgzA    198  naiske---- --eidavknv pvlilddiga vrde-----v lqvilqyrml
                  /\                          / \
TARGET                        hhh    ssssss              hhhhhhhhhh
2qgzA                        hh  h    ssssss              hhhhhhhhhh


                  |    |                ||| |  |              |
TARGET    194  SKRPTGMLTN SNMEEMTKLL ---GERVMDR MRLGNSLWVI FNWDSYR 
2qgzA    247  eelptfftsn ysfadlerkw awqakrvmer vr-ylarefh leganrr- 
                                      /\
TARGET          h  ssssss    hhhhh          hhhh hh  ssssss s       
2qgzA          h  ssssss    hhhh          hhhh hh hh ssss s
</pre>


Below is the sequence with ATOM records (coordinates) from 2QGZ, numbered 100-300, showing the gaps as "...". This sequence listing was used to locate the positions marked /\ above.
<pre>
    1 .......... .......... .......... .......... ..........
  51 .......... .......... .......... .......... .........Q
  101 KQAAISERIQ LVSLPKSYRH IHLSDIDVNN ASRMEAFSAI LDFVEQYPSA
  151 EQKGLYLYGD MGIGKSYLLA AMAHELSEKK GVSTTLLHFP SFAIDVKNAI
  201 S....KEEID AVKNVPVLIL DDIGA..... .VRDEVLQVI LQYRMLEELP


  251 TFFTSNYSFA DLERKWA... .....WQAKR VMERVRYLAR EFHLEGANRR
</StructureSection>
</pre>
(Copied from Protein Explorer's sequence display.)

Latest revision as of 18:59, 13 August 2020


  • 1 : simple surface on chain A of 1d66. Colored translucent green. This surface was generated with the representations tab of the SAT.


  • 2 (no isosurfaces). After clicking this standard SAT-generated green link, then

(From uploaded file http://proteopedia.org/wiki/images/6/67/6zgi-cavities.jvxl -- see File:6zgi-cavities.jvxl)


  • 3

(From uploaded file http://proteopedia.org/wiki/images/c/c6/6zgi-cavities.pngj -- see Image:6zgi-cavities.png)


  • 4 . SAT not involved. PNGJ file generated externally in the Jmol Java application, then uploaded to Proteopedia as for the previous item above.


  • 5 , then saving scene. (No molecule loaded with the SAT "load molecule" tab.)


Tested in Firefox (current version) on macOS Mojave, mid-2014 MacBook Pro, 2.2 GHz Intel Core i7.

  • 6 . It took 8.5 min to generate the cavity isosurfaces after I entered the command "isosurface minset 100 interior cavity 3.0 10.0" into the command slot in the SAT. (This command takes ~45 sec in the Jmol Java app which is therefore 11-fold faster for this operation.) After clicking this green link, I waited 11 min and the scene still did not appear. So I think the isosurfaces are being generated again when the green link is clicked.



Drag the structure with the mouse to rotate
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