str_bio_2.htm

Student HSE, 29.09.2017 16:56

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506
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510
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515
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531
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538
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540
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542
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617
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619
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625
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629
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635
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636
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637
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639
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645
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647
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649
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655
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657
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659
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660
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663
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664
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680
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682
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        mso-gram-e:yes;}
744
.MsoChpDefault
745
        {mso-style-type:export-only;
746
        mso-default-props:yes;
747
        font-size:10.0pt;
748
        mso-ansi-font-size:10.0pt;
749
        mso-bidi-font-size:10.0pt;
750
        font-family:"Calibri",sans-serif;
751
        mso-ascii-font-family:Calibri;
752
        mso-ascii-theme-font:minor-latin;
753
        mso-fareast-font-family:Calibri;
754
        mso-fareast-theme-font:minor-latin;
755
        mso-hansi-font-family:Calibri;
756
        mso-hansi-theme-font:minor-latin;
757
        mso-bidi-font-family:"Times New Roman";
758
        mso-bidi-theme-font:minor-bidi;
759
        mso-fareast-language:EN-US;}
760
@page WordSection1
761
        {size:595.3pt 841.9pt;
762
        margin:2.0cm 42.5pt 2.0cm 3.0cm;
763
        mso-header-margin:35.4pt;
764
        mso-footer-margin:35.4pt;
765
        mso-paper-source:0;}
766
div.WordSection1
767
        {page:WordSection1;}
768
-->
769
</style>
770
<!--[if gte mso 10]>
771
<style>
772
 /* Style Definitions */
773
 table.MsoNormalTable
774
        {mso-style-name:"??????? ???????";
775
        mso-tstyle-rowband-size:0;
776
        mso-tstyle-colband-size:0;
777
        mso-style-noshow:yes;
778
        mso-style-priority:99;
779
        mso-style-parent:"";
780
        mso-padding-alt:0cm 5.4pt 0cm 5.4pt;
781
        mso-para-margin:0cm;
782
        mso-para-margin-bottom:.0001pt;
783
        mso-pagination:widow-orphan;
784
        font-size:10.0pt;
785
        font-family:"Calibri",sans-serif;
786
        mso-ascii-font-family:Calibri;
787
        mso-ascii-theme-font:minor-latin;
788
        mso-hansi-font-family:Calibri;
789
        mso-hansi-theme-font:minor-latin;
790
        mso-bidi-font-family:"Times New Roman";
791
        mso-bidi-theme-font:minor-bidi;
792
        mso-fareast-language:EN-US;}
793
</style>
794
<![endif]--><!--[if gte mso 9]><xml>
795
 <o:shapedefaults v:ext="edit" spidmax="1026"/>
796
</xml><![endif]--><!--[if gte mso 9]><xml>
797
 <o:shapelayout v:ext="edit">
798
  <o:idmap v:ext="edit" data="1"/>
799
 </o:shapelayout></xml><![endif]-->
800
</head>
801

    
802
<body lang=RU link="#0563C1" vlink="#954F72" style='tab-interval:35.4pt'>
803

    
804
<div class=WordSection1>
805

    
806
<p class=MsoNormal>??????? ?2. ?????????? ?????</p>
807

    
808
<p class=MsoNormal><span class=SpellE>load</span> 1lmp.pdb </p>
809

    
810
<p class=MsoNormal><span class=GramE><span lang=EN-US style='mso-ansi-language:
811
EN-US'>remove</span></span><span lang=EN-US style='mso-ansi-language:EN-US'>
812
solvent<o:p></o:p></span></p>
813

    
814
<p class=MsoNormal><span class=GramE><span lang=EN-US style='mso-ansi-language:
815
EN-US'>extract</span></span><span lang=EN-US style='mso-ansi-language:EN-US'> <span
816
class=SpellE>ligands,het</span><o:p></o:p></span></p>
817

    
818
<p class=MsoNormal><span class=GramE><span lang=EN-US style='mso-ansi-language:
819
EN-US'>as</span></span><span lang=EN-US style='mso-ansi-language:EN-US'>
820
surface, 1lmp<o:p></o:p></span></p>
821

    
822
<p class=MsoNormal><span class=GramE><span lang=EN-US style='mso-ansi-language:
823
EN-US'>set</span></span><span lang=EN-US style='mso-ansi-language:EN-US'>
824
transparency,0.5<o:p></o:p></span></p>
825

    
826
<p class=MsoNormal><span class=GramE><span lang=EN-US style='mso-ansi-language:
827
EN-US'>as</span></span><span lang=EN-US style='mso-ansi-language:EN-US'>
828
sticks, ligands<o:p></o:p></span></p>
829

    
830
<p class=MsoNormal><span class=GramE><span lang=EN-US style='mso-ansi-language:
831
EN-US'>show</span></span><span lang=EN-US style='mso-ansi-language:EN-US'>
832
stick, byres(1lmp w. 4 of ligands)<o:p></o:p></span></p>
833

    
834
<p class=MsoNormal><span class=GramE><span lang=EN-US style='mso-ansi-language:
835
EN-US'>center</span></span><span lang=EN-US style='mso-ansi-language:EN-US'>
836
ligands<o:p></o:p></span></p>
837

    
838
<p class=MsoNormal><span class=GramE><span lang=EN-US style='mso-ansi-language:
839
EN-US'>origin</span></span><span lang=EN-US style='mso-ansi-language:EN-US'>
840
ligands<o:p></o:p></span></p>
841

    
842
<p class=MsoNormal><span class=GramE><span lang=EN-US style='mso-ansi-language:
843
EN-US'>zoom</span></span><span lang=EN-US style='mso-ansi-language:EN-US'>
844
ligands<o:p></o:p></span></p>
845

    
846
<p class=MsoNormal><span class=SpellE><span lang=EN-US style='mso-ansi-language:
847
EN-US'>h_add</span></span><span lang=EN-US style='mso-ansi-language:EN-US'><span
848
style='mso-spacerun:yes'>? </span><o:p></o:p></span></p>
849

    
850
<p class=MsoNormal><span class=GramE><span lang=EN-US style='mso-ansi-language:
851
EN-US'>ligands</span></span><span lang=EN-US style='mso-ansi-language:EN-US'> ?
852
action ? find ? polar contacts ? to any excluding solvent<o:p></o:p></span></p>
853

    
854
<p class=MsoNormal><span class=GramE><span lang=EN-US style='mso-ansi-language:
855
EN-US'>ligands</span></span><span lang=EN-US style='mso-ansi-language:EN-US'> ?
856
color ? by elements ? <span class=SpellE>purpele</span><o:p></o:p></span></p>
857

    
858
<p class=MsoNormal><span class=SpellE><span class=GramE><span lang=EN-US
859
style='mso-ansi-language:EN-US'>png</span></span></span><span lang=EN-US
860
style='mso-ansi-language:EN-US'> pic1.png<o:p></o:p></span></p>
861

    
862
<p class=MsoNormal><span style='mso-fareast-language:RU;mso-no-proof:yes'><!--[if gte vml 1]><v:shapetype
863
 id="_x0000_t75" coordsize="21600,21600" o:spt="75" o:preferrelative="t"
864
 path="m@4@5l@4@11@9@11@9@5xe" filled="f" stroked="f">
865
 <v:stroke joinstyle="miter"/>
866
 <v:formulas>
867
  <v:f eqn="if lineDrawn pixelLineWidth 0"/>
868
  <v:f eqn="sum @0 1 0"/>
869
  <v:f eqn="sum 0 0 @1"/>
870
  <v:f eqn="prod @2 1 2"/>
871
  <v:f eqn="prod @3 21600 pixelWidth"/>
872
  <v:f eqn="prod @3 21600 pixelHeight"/>
873
  <v:f eqn="sum @0 0 1"/>
874
  <v:f eqn="prod @6 1 2"/>
875
  <v:f eqn="prod @7 21600 pixelWidth"/>
876
  <v:f eqn="sum @8 21600 0"/>
877
  <v:f eqn="prod @7 21600 pixelHeight"/>
878
  <v:f eqn="sum @10 21600 0"/>
879
 </v:formulas>
880
 <v:path o:extrusionok="f" gradientshapeok="t" o:connecttype="rect"/>
881
 <o:lock v:ext="edit" aspectratio="t"/>
882
</v:shapetype><v:shape id="???????_x0020_1" o:spid="_x0000_i1028" type="#_x0000_t75"
883
 style='width:480pt;height:5in;visibility:visible;mso-wrap-style:square'>
884
 <v:imagedata src="str_bio_2.files/image001.png" o:title=""/>
885
</v:shape><![endif]--><![if !vml]><img width=640 height=480
886
src="str_bio_2.files/image001.png" v:shapes="???????_x0020_1"><![endif]></span><span
887
lang=EN-US style='mso-ansi-language:EN-US'><o:p></o:p></span></p>
888

    
889
<p class=MsoNormal><span lang=EN-US style='mso-ansi-language:EN-US'><o:p>&nbsp;</o:p></span></p>
890

    
891
<p class=MsoNormal>??????? ?3. ??????? ? ?????.</p>
892

    
893
<p class=MsoNormal><o:p>&nbsp;</o:p></p>
894

    
895
<p class=MsoNormal>Select 107Ala </p>
896

    
897
<p class=MsoNormal><span class=GramE><span lang=EN-US style='mso-ansi-language:
898
EN-US'>mutation</span></span><span lang=EN-US style='mso-ansi-language:EN-US'>
899
to THR<o:p></o:p></span></p>
900

    
901
<p class=MsoNormal><span class=GramE><span lang=EN-US style='mso-ansi-language:
902
EN-US'>apply</span></span><span lang=EN-US style='mso-ansi-language:EN-US'><o:p></o:p></span></p>
903

    
904
<p class=MsoNormal><span class=GramE><span lang=EN-US style='mso-ansi-language:
905
EN-US'>mutant</span></span><span lang=EN-US style='mso-ansi-language:EN-US'>
906
color green<o:p></o:p></span></p>
907

    
908
<p class=MsoNormal><span class=GramE><span lang=EN-US style='mso-ansi-language:
909
EN-US'>save</span></span><span lang=EN-US style='mso-ansi-language:EN-US'>
910
2lmp.pdb<o:p></o:p></span></p>
911

    
912
<p class=MsoNormal><span class=GramE><span lang=EN-US style='mso-ansi-language:
913
EN-US'>png</span></span><span lang=EN-US style='mso-ansi-language:EN-US'>
914
pic2.png<o:p></o:p></span></p>
915

    
916
<p class=MsoNormal><span style='mso-fareast-language:RU;mso-no-proof:yes'><!--[if gte vml 1]><v:shape
917
 id="???????_x0020_3" o:spid="_x0000_i1027" type="#_x0000_t75" style='width:480pt;
918
 height:264pt;visibility:visible;mso-wrap-style:square'>
919
 <v:imagedata src="str_bio_2.files/image002.png" o:title=""/>
920
</v:shape><![endif]--><![if !vml]><img width=640 height=352
921
src="str_bio_2.files/image002.png" v:shapes="???????_x0020_3"><![endif]></span><span
922
lang=EN-US style='mso-ansi-language:EN-US'><o:p></o:p></span></p>
923

    
924
<p class=MsoNormal><span lang=EN-US style='mso-ansi-language:EN-US'><o:p>&nbsp;</o:p></span></p>
925

    
926
<p class=MsoNormal>???????<span lang=EN-US style='mso-ansi-language:EN-US'> 4. <o:p></o:p></span></p>
927

    
928
<p class=MsoNormal><span lang=EN-US style='mso-ansi-language:EN-US'><o:p>&nbsp;</o:p></span></p>
929

    
930
<p class=MsoNormal><span class=GramE><span lang=EN-US style='mso-ansi-language:
931
EN-US'>load</span></span><span lang=EN-US style='mso-ansi-language:EN-US'>
932
1lmp.pdb<o:p></o:p></span></p>
933

    
934
<p class=MsoNormal><span class=GramE><span lang=EN-US style='mso-ansi-language:
935
EN-US'>load</span></span><span lang=EN-US style='mso-ansi-language:EN-US'>
936
2lmp.pdb<o:p></o:p></span></p>
937

    
938
<p class=MsoNormal><span lang=EN-US style='mso-ansi-language:EN-US'><o:p>&nbsp;</o:p></span></p>
939

    
940
<p class=MsoNormal style='line-height:105%'><span class=GramE><span lang=EN-US
941
style='mso-ansi-language:EN-US'>set</span></span><span lang=EN-US
942
style='mso-ansi-language:EN-US'> <span class=SpellE>matrix_mode</span>, 1<o:p></o:p></span></p>
943

    
944
<p class=MsoNormal style='line-height:105%'><span class=GramE><span lang=EN-US
945
style='mso-ansi-language:EN-US'>set</span></span><span lang=EN-US
946
style='mso-ansi-language:EN-US'> <span class=SpellE>movie_panel</span>, 1<o:p></o:p></span></p>
947

    
948
<p class=MsoNormal style='line-height:105%'><span class=GramE><span lang=EN-US
949
style='mso-ansi-language:EN-US'>set</span></span><span lang=EN-US
950
style='mso-ansi-language:EN-US'> <span class=SpellE>scene_buttons</span>, 1<o:p></o:p></span></p>
951

    
952
<p class=MsoNormal style='line-height:105%'><span class=GramE><span lang=EN-US
953
style='mso-ansi-language:EN-US'>set</span></span><span lang=EN-US
954
style='mso-ansi-language:EN-US'> <span class=SpellE>cache_frames</span>, 1<o:p></o:p></span></p>
955

    
956
<p class=MsoNormal style='line-height:105%'><span lang=EN-US style='mso-ansi-language:
957
EN-US'><o:p>&nbsp;</o:p></span></p>
958

    
959
<p class=MsoNormal style='line-height:105%'><span class=GramE><span lang=EN-US
960
style='mso-ansi-language:EN-US'>hide</span></span><span lang=EN-US
961
style='mso-ansi-language:EN-US'> all<o:p></o:p></span></p>
962

    
963
<p class=MsoNormal style='line-height:105%'><span class=GramE><span lang=EN-US
964
style='mso-ansi-language:EN-US'>show</span></span><span lang=EN-US
965
style='mso-ansi-language:EN-US'> cartoon, all<o:p></o:p></span></p>
966

    
967
<p class=MsoNormal style='line-height:105%'><span class=GramE><span lang=EN-US
968
style='mso-ansi-language:EN-US'>show</span></span><span lang=EN-US
969
style='mso-ansi-language:EN-US'> sticks, <span class=SpellE>resi</span> 130-132<o:p></o:p></span></p>
970

    
971
<p class=MsoNormal style='line-height:105%'><span class=GramE><span lang=EN-US
972
style='mso-ansi-language:EN-US'>show</span></span><span lang=EN-US
973
style='mso-ansi-language:EN-US'> sticks, <span class=SpellE>resi</span> 107<o:p></o:p></span></p>
974

    
975
<p class=MsoNormal style='line-height:105%'><span class=GramE><span lang=EN-US
976
style='mso-ansi-language:EN-US'>set</span></span><span lang=EN-US
977
style='mso-ansi-language:EN-US'> <span class=SpellE>movie_auto_interpolate</span>,
978
off<o:p></o:p></span></p>
979

    
980
<p class=MsoNormal style='line-height:105%'><span class=GramE><span lang=EN-US
981
style='mso-ansi-language:EN-US'>set</span></span><span lang=EN-US
982
style='mso-ansi-language:EN-US'> <span class=SpellE>matrix_mode</span>, 1<o:p></o:p></span></p>
983

    
984
<p class=MsoNormal style='line-height:105%'><span class=GramE><span lang=EN-US
985
style='mso-ansi-language:EN-US'>set</span></span><span lang=EN-US
986
style='mso-ansi-language:EN-US'> <span class=SpellE>movie_panel</span>, 1<o:p></o:p></span></p>
987

    
988
<p class=MsoNormal style='line-height:105%'><span class=GramE><span lang=EN-US
989
style='mso-ansi-language:EN-US'>set</span></span><span lang=EN-US
990
style='mso-ansi-language:EN-US'> <span class=SpellE>scene_buttons</span>, 1<o:p></o:p></span></p>
991

    
992
<p class=MsoNormal style='line-height:105%'><span class=GramE><span lang=EN-US
993
style='mso-ansi-language:EN-US'>set</span></span><span lang=EN-US
994
style='mso-ansi-language:EN-US'> <span class=SpellE>cache_frames</span>, 1<o:p></o:p></span></p>
995

    
996
<p class=MsoNormal style='line-height:105%'><span lang=EN-US style='mso-ansi-language:
997
EN-US'><o:p>&nbsp;</o:p></span></p>
998

    
999
<p class=MsoNormal style='line-height:105%'><span class=GramE><span lang=EN-US
1000
style='mso-ansi-language:EN-US'>select</span></span><span lang=EN-US
1001
style='mso-ansi-language:EN-US'> target, <span class=SpellE>resi</span> 107<o:p></o:p></span></p>
1002

    
1003
<p class=MsoNormal style='line-height:105%'><span lang=EN-US style='mso-ansi-language:
1004
EN-US'><o:p>&nbsp;</o:p></span></p>
1005

    
1006
<p class=MsoNormal style='line-height:105%'><span class=GramE><span lang=EN-US
1007
style='mso-ansi-language:EN-US'>translate</span></span><span lang=EN-US
1008
style='mso-ansi-language:EN-US'> [150,0,0]<o:p></o:p></span></p>
1009

    
1010
<p class=MsoNormal style='line-height:105%'><span class=GramE><span lang=EN-US
1011
style='mso-ansi-language:EN-US'>rotate</span></span><span lang=EN-US
1012
style='mso-ansi-language:EN-US'> y, 15, object=1<o:p></o:p></span></p>
1013

    
1014
<p class=MsoNormal style='line-height:105%'><span lang=EN-US style='mso-ansi-language:
1015
EN-US'><o:p>&nbsp;</o:p></span></p>
1016

    
1017
<p class=MsoNormal style='line-height:105%'><span class=GramE><span lang=EN-US
1018
style='mso-ansi-language:EN-US'>orient</span></span><span lang=EN-US
1019
style='mso-ansi-language:EN-US'> 2lmp or 1lmp<o:p></o:p></span></p>
1020

    
1021
<p class=MsoNormal style='line-height:105%'><span lang=EN-US style='mso-ansi-language:
1022
EN-US'><o:p>&nbsp;</o:p></span></p>
1023

    
1024
<p class=MsoNormal style='line-height:105%'><span class=SpellE><span
1025
class=GramE><span lang=EN-US style='mso-ansi-language:EN-US'>mset</span></span></span><span
1026
lang=EN-US style='mso-ansi-language:EN-US'> 1 x150<o:p></o:p></span></p>
1027

    
1028
<p class=MsoNormal style='line-height:105%'><span class=GramE><span lang=EN-US
1029
style='mso-ansi-language:EN-US'>frame</span></span><span lang=EN-US
1030
style='mso-ansi-language:EN-US'> 1<o:p></o:p></span></p>
1031

    
1032
<p class=MsoNormal style='line-height:105%'><span class=SpellE><span
1033
class=GramE><span lang=EN-US style='mso-ansi-language:EN-US'>mview</span></span></span><span
1034
lang=EN-US style='mso-ansi-language:EN-US'> store<o:p></o:p></span></p>
1035

    
1036
<p class=MsoNormal style='line-height:105%'><span class=SpellE><span
1037
class=GramE><span lang=EN-US style='mso-ansi-language:EN-US'>mview</span></span></span><span
1038
lang=EN-US style='mso-ansi-language:EN-US'> store, object=1lmp<o:p></o:p></span></p>
1039

    
1040
<p class=MsoNormal style='line-height:105%'><span class=SpellE><span
1041
class=GramE><span lang=EN-US style='mso-ansi-language:EN-US'>mview</span></span></span><span
1042
lang=EN-US style='mso-ansi-language:EN-US'> store, object=2lmp<o:p></o:p></span></p>
1043

    
1044
<p class=MsoNormal style='line-height:105%'><span lang=EN-US style='mso-ansi-language:
1045
EN-US'><o:p>&nbsp;</o:p></span></p>
1046

    
1047
<p class=MsoNormal style='line-height:105%'><span class=GramE><span lang=EN-US
1048
style='mso-ansi-language:EN-US'>frame</span></span><span lang=EN-US
1049
style='mso-ansi-language:EN-US'> 80<o:p></o:p></span></p>
1050

    
1051
<p class=MsoNormal style='line-height:105%'><span class=GramE><span lang=EN-US
1052
style='mso-ansi-language:EN-US'>orient</span></span><span lang=EN-US
1053
style='mso-ansi-language:EN-US'> 1lmp and target<o:p></o:p></span></p>
1054

    
1055
<p class=MsoNormal style='line-height:105%'><span class=SpellE><span
1056
class=GramE><span lang=EN-US style='mso-ansi-language:EN-US'>mview</span></span></span><span
1057
lang=EN-US style='mso-ansi-language:EN-US'> store<o:p></o:p></span></p>
1058

    
1059
<p class=MsoNormal style='line-height:105%'><span class=SpellE><span
1060
class=GramE><span lang=EN-US style='mso-ansi-language:EN-US'>mview</span></span></span><span
1061
lang=EN-US style='mso-ansi-language:EN-US'> store, object=1lmp<o:p></o:p></span></p>
1062

    
1063
<p class=MsoNormal style='line-height:105%'><span class=SpellE><span
1064
class=GramE><span lang=EN-US style='mso-ansi-language:EN-US'>mview</span></span></span><span
1065
lang=EN-US style='mso-ansi-language:EN-US'> store, object=2lmp<o:p></o:p></span></p>
1066

    
1067
<p class=MsoNormal style='line-height:105%'><span lang=EN-US style='mso-ansi-language:
1068
EN-US'><o:p>&nbsp;</o:p></span></p>
1069

    
1070
<p class=MsoNormal style='line-height:105%'><span class=GramE><span lang=EN-US
1071
style='mso-ansi-language:EN-US'>frame</span></span><span lang=EN-US
1072
style='mso-ansi-language:EN-US'> 120<o:p></o:p></span></p>
1073

    
1074
<p class=MsoNormal style='line-height:105%'><span class=GramE><span lang=EN-US
1075
style='mso-ansi-language:EN-US'>orient</span></span><span lang=EN-US
1076
style='mso-ansi-language:EN-US'> 2lmp and target<o:p></o:p></span></p>
1077

    
1078
<p class=MsoNormal style='line-height:105%'><span class=SpellE><span
1079
class=GramE><span lang=EN-US style='mso-ansi-language:EN-US'>mview</span></span></span><span
1080
lang=EN-US style='mso-ansi-language:EN-US'> store<o:p></o:p></span></p>
1081

    
1082
<p class=MsoNormal style='line-height:105%'><span class=SpellE><span
1083
class=GramE><span lang=EN-US style='mso-ansi-language:EN-US'>mview</span></span></span><span
1084
lang=EN-US style='mso-ansi-language:EN-US'> store, object=1lmp<o:p></o:p></span></p>
1085

    
1086
<p class=MsoNormal style='line-height:105%'><span class=SpellE><span
1087
class=GramE><span lang=EN-US style='mso-ansi-language:EN-US'>mview</span></span></span><span
1088
lang=EN-US style='mso-ansi-language:EN-US'> store, object=2lmp<o:p></o:p></span></p>
1089

    
1090
<p class=MsoNormal style='line-height:105%'><span lang=EN-US style='mso-ansi-language:
1091
EN-US'><o:p>&nbsp;</o:p></span></p>
1092

    
1093
<p class=MsoNormal style='line-height:105%'><span class=GramE><span lang=EN-US
1094
style='mso-ansi-language:EN-US'>frame</span></span><span lang=EN-US
1095
style='mso-ansi-language:EN-US'> 150<o:p></o:p></span></p>
1096

    
1097
<p class=MsoNormal style='line-height:105%'><span class=GramE><span lang=EN-US
1098
style='mso-ansi-language:EN-US'>python</span></span><span lang=EN-US
1099
style='mso-ansi-language:EN-US'><o:p></o:p></span></p>
1100

    
1101
<p class=MsoNormal style='line-height:105%'><span class=SpellE><span
1102
class=GramE><span lang=EN-US style='mso-ansi-language:EN-US'>cmd.madd</span></span></span><span
1103
class=GramE><span lang=EN-US style='mso-ansi-language:EN-US'>(</span></span><span
1104
lang=EN-US style='mso-ansi-language:EN-US'>&quot;1 x5&quot;); <span
1105
class=SpellE>cmd.frame</span>(3000);<o:p></o:p></span></p>
1106

    
1107
<p class=MsoNormal style='line-height:105%'><span class=SpellE><span
1108
class=GramE><span lang=EN-US style='mso-ansi-language:EN-US'>cmd.rotate</span></span></span><span
1109
class=GramE><span lang=EN-US style='mso-ansi-language:EN-US'>(</span></span><span
1110
lang=EN-US style='mso-ansi-language:EN-US'>&quot;y&quot;, -15.5,
1111
object=&quot;1lmp&quot;)<o:p></o:p></span></p>
1112

    
1113
<p class=MsoNormal style='line-height:105%'><span class=SpellE><span
1114
class=GramE><span lang=EN-US style='mso-ansi-language:EN-US'>cmd.mview</span></span></span><span
1115
class=GramE><span lang=EN-US style='mso-ansi-language:EN-US'>(</span></span><span
1116
lang=EN-US style='mso-ansi-language:EN-US'>&quot;store&quot;, object=&quot;1lmp&quot;)<o:p></o:p></span></p>
1117

    
1118
<p class=MsoNormal style='line-height:105%'><span class=SpellE><span
1119
class=GramE><span lang=EN-US style='mso-ansi-language:EN-US'>cmd.mview</span></span></span><span
1120
class=GramE><span lang=EN-US style='mso-ansi-language:EN-US'>(</span></span><span
1121
lang=EN-US style='mso-ansi-language:EN-US'>&quot;store&quot;,
1122
object=&quot;2lmp&quot;)<o:p></o:p></span></p>
1123

    
1124
<p class=MsoNormal style='line-height:105%'><span class=SpellE><span
1125
class=GramE><span lang=EN-US style='mso-ansi-language:EN-US'>cmd.mview</span></span></span><span
1126
class=GramE><span lang=EN-US style='mso-ansi-language:EN-US'>(</span></span><span
1127
lang=EN-US style='mso-ansi-language:EN-US'>&quot;interpolate&quot;,
1128
object=&quot;1lmp&quot;)<o:p></o:p></span></p>
1129

    
1130
<p class=MsoNormal style='line-height:105%'><span class=SpellE><span
1131
class=GramE><span lang=EN-US style='mso-ansi-language:EN-US'>cmd.mview</span></span></span><span
1132
class=GramE><span lang=EN-US style='mso-ansi-language:EN-US'>(</span></span><span
1133
lang=EN-US style='mso-ansi-language:EN-US'>&quot;<span class=SpellE>reinterpolate</span>&quot;)<o:p></o:p></span></p>
1134

    
1135
<p class=MsoNormal style='line-height:105%'><span class=GramE><span lang=EN-US
1136
style='mso-ansi-language:EN-US'>python</span></span><span lang=EN-US
1137
style='mso-ansi-language:EN-US'> end<o:p></o:p></span></p>
1138

    
1139
<p class=MsoNormal style='line-height:105%'><span lang=EN-US style='mso-ansi-language:
1140
EN-US'><o:p>&nbsp;</o:p></span></p>
1141

    
1142
<p class=MsoNormal style='line-height:105%'><span class=GramE><span lang=EN-US
1143
style='mso-ansi-language:EN-US'>super</span></span><span lang=EN-US
1144
style='mso-ansi-language:EN-US'> 2lmp, 1lmp<o:p></o:p></span></p>
1145

    
1146
<p class=MsoNormal style='line-height:105%'><span lang=EN-US style='mso-ansi-language:
1147
EN-US'><span style='mso-spacerun:yes'>?</span><o:p></o:p></span></p>
1148

    
1149
<p class=MsoNormal style='line-height:105%'><span class=GramE><span lang=EN-US
1150
style='mso-ansi-language:EN-US'>orient</span></span><span lang=EN-US
1151
style='mso-ansi-language:EN-US'> target<o:p></o:p></span></p>
1152

    
1153
<p class=MsoNormal style='line-height:105%'><span class=SpellE><span
1154
class=GramE><span lang=EN-US style='mso-ansi-language:EN-US'>mview</span></span></span><span
1155
lang=EN-US style='mso-ansi-language:EN-US'> store<o:p></o:p></span></p>
1156

    
1157
<p class=MsoNormal style='line-height:105%'><span lang=EN-US style='mso-ansi-language:
1158
EN-US'><o:p>&nbsp;</o:p></span></p>
1159

    
1160
<p class=MsoNormal style='line-height:105%'><span class=SpellE><span
1161
class=GramE><span lang=EN-US style='mso-ansi-language:EN-US'>madd</span></span></span><span
1162
lang=EN-US style='mso-ansi-language:EN-US'> 1 x30<o:p></o:p></span></p>
1163

    
1164
<p class=MsoNormal style='line-height:105%'><span lang=EN-US style='mso-ansi-language:
1165
EN-US'><o:p>&nbsp;</o:p></span></p>
1166

    
1167
<p class=MsoNormal style='line-height:105%'><span class=SpellE><span
1168
class=GramE><span lang=EN-US style='mso-ansi-language:EN-US'>mview</span></span></span><span
1169
lang=EN-US style='mso-ansi-language:EN-US'> interpolate, object=1mp<o:p></o:p></span></p>
1170

    
1171
<p class=MsoNormal style='line-height:105%'><span class=SpellE><span
1172
class=GramE><span lang=EN-US style='mso-ansi-language:EN-US'>mview</span></span></span><span
1173
lang=EN-US style='mso-ansi-language:EN-US'> interpolate, object=2lmp<o:p></o:p></span></p>
1174

    
1175
<p class=MsoNormal style='line-height:105%'><span class=SpellE><span
1176
class=GramE><span lang=EN-US style='mso-ansi-language:EN-US'>mview</span></span></span><span
1177
lang=EN-US style='mso-ansi-language:EN-US'> <span class=SpellE>reinterpolate</span><o:p></o:p></span></p>
1178

    
1179
<p class=MsoNormal style='line-height:105%'><span lang=EN-US style='mso-ansi-language:
1180
EN-US'><span style='mso-spacerun:yes'>?</span><o:p></o:p></span></p>
1181

    
1182
<p class=MsoNormal style='line-height:105%'><span class=SpellE><span
1183
class=GramE><span lang=EN-US style='mso-ansi-language:EN-US'>mplay</span></span></span><span
1184
lang=EN-US style='mso-ansi-language:EN-US'><o:p></o:p></span></p>
1185

    
1186
<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
1187
normal;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span
1188
class=SpellE><span class=GramE><span lang=EN-US style='font-size:10.0pt;
1189
font-family:"Courier New";mso-fareast-font-family:"Times New Roman";color:black;
1190
mso-ansi-language:EN-US;mso-fareast-language:RU'>mpng</span></span></span><span
1191
lang=EN-US style='font-size:10.0pt;font-family:"Courier New";mso-fareast-font-family:
1192
"Times New Roman";color:black;mso-ansi-language:EN-US;mso-fareast-language:
1193
RU'> <span class=SpellE>mov</span><o:p></o:p></span></p>
1194

    
1195
<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
1196
normal;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span
1197
lang=EN-US style='font-size:10.0pt;font-family:"Courier New";mso-fareast-font-family:
1198
"Times New Roman";color:black;mso-ansi-language:EN-US;mso-fareast-language:
1199
RU'><o:p>&nbsp;</o:p></span></p>
1200

    
1201
<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
1202
normal;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span
1203
lang=EN-US style='font-size:10.0pt;font-family:"Courier New";mso-fareast-font-family:
1204
"Times New Roman";color:black;mso-ansi-language:EN-US;mso-fareast-language:
1205
RU'>(</span><span class=GramE><span style='font-size:10.0pt;font-family:"Courier New";
1206
mso-fareast-font-family:"Times New Roman";color:black;mso-fareast-language:
1207
RU'>??????</span></span><span style='font-size:10.0pt;font-family:"Courier New";
1208
mso-fareast-font-family:"Times New Roman";color:black;mso-ansi-language:EN-US;
1209
mso-fareast-language:RU'> </span><span style='font-size:10.0pt;font-family:
1210
"Courier New";mso-fareast-font-family:"Times New Roman";color:black;mso-fareast-language:
1211
RU'>??</span><span style='font-size:10.0pt;font-family:"Courier New";
1212
mso-fareast-font-family:"Times New Roman";color:black;mso-ansi-language:EN-US;
1213
mso-fareast-language:RU'> </span><span style='font-size:10.0pt;font-family:
1214
"Courier New";mso-fareast-font-family:"Times New Roman";color:black;mso-fareast-language:
1215
RU'>?????</span><span lang=EN-US style='font-size:10.0pt;font-family:"Courier New";
1216
mso-fareast-font-family:"Times New Roman";color:black;mso-ansi-language:EN-US;
1217
mso-fareast-language:RU'>)<o:p></o:p></span></p>
1218

    
1219
<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
1220
normal;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span
1221
lang=EN-US style='font-size:10.0pt;font-family:"Courier New";mso-fareast-font-family:
1222
"Times New Roman";color:black;mso-ansi-language:EN-US;mso-fareast-language:
1223
RU'><a href="https://drive.google.com/file/d/0B43yozs610EXR2ZndV9SSnBGZXM/view">https://drive.google.com/file/d/0B43yozs610EXR2ZndV9SSnBGZXM/view</a><o:p></o:p></span></p>
1224

    
1225
<p class=MsoNormal>??????? ?5. ????????????? ?????????????? ?????.</p>
1226

    
1227
<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1228

    
1229
<p class=MsoNormal><span class=SpellE>Load</span> <span class=SpellE>Tamra.sdf</span></p>
1230

    
1231
<p class=MsoNormal><span class=GramE><span lang=EN-US style='mso-ansi-language:
1232
EN-US'>load</span></span><span lang=EN-US style='mso-ansi-language:EN-US'>
1233
1lmp.pdb<o:p></o:p></span></p>
1234

    
1235
<p class=MsoNormal><span class=GramE><span lang=EN-US style='mso-ansi-language:
1236
EN-US'>select</span></span><span lang=EN-US style='mso-ansi-language:EN-US'> m,
1237
/<span class=SpellE>Tamra</span>///UNK`0/C<o:p></o:p></span></p>
1238

    
1239
<p class=MsoNormal><span class=GramE><span lang=EN-US style='mso-ansi-language:
1240
EN-US'>select</span></span><span lang=EN-US style='mso-ansi-language:EN-US'> s,
1241
/1lmp//A/SER*37/CB<o:p></o:p></span></p>
1242

    
1243
<p class=MsoNormal><span class=GramE><span lang=EN-US style='mso-ansi-language:
1244
EN-US'>fuse</span></span><span lang=EN-US style='mso-ansi-language:EN-US'> s, m<o:p></o:p></span></p>
1245

    
1246
<p class=MsoNormal><span class=GramE><span lang=EN-US style='mso-ansi-language:
1247
EN-US'>torsion</span></span><span lang=EN-US style='mso-ansi-language:EN-US'>
1248
15<o:p></o:p></span></p>
1249

    
1250
<p class=MsoNormal><span class=SpellE><span class=GramE><span lang=EN-US
1251
style='mso-ansi-language:EN-US'>png</span></span></span><span lang=EN-US
1252
style='mso-ansi-language:EN-US'> pic4.png<o:p></o:p></span></p>
1253

    
1254
<p class=MsoNormal><span style='mso-fareast-language:RU;mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1255
 id="???????_x0020_2" o:spid="_x0000_i1026" type="#_x0000_t75" style='width:333.75pt;
1256
 height:333.75pt;visibility:visible;mso-wrap-style:square'>
1257
 <v:imagedata src="str_bio_2.files/image003.png" o:title=""/>
1258
</v:shape><![endif]--><![if !vml]><img border=0 width=445 height=445
1259
src="str_bio_2.files/image003.png" v:shapes="???????_x0020_2"><![endif]></span><span
1260
lang=EN-US style='mso-ansi-language:EN-US'><o:p></o:p></span></p>
1261

    
1262
<p class=MsoNormal><span lang=EN-US style='mso-ansi-language:EN-US'><o:p>&nbsp;</o:p></span></p>
1263

    
1264
<p class=MsoNormal>??????? ?6.</p>
1265

    
1266
<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1267

    
1268
<p class=MsoNormal>?????? ??? ?????????? <span class=SpellE>?????????????????</span>
1269
????.</p>
1270

    
1271
<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1272

    
1273
<p class=MsoNormal><span class=GramE><span lang=EN-US style='mso-ansi-language:
1274
EN-US'>frag</span></span><span lang=EN-US style='mso-ansi-language:EN-US'> <span
1275
class=SpellE>thr</span><o:p></o:p></span></p>
1276

    
1277
<p class=MsoNormal><span class=GramE><span lang=EN-US style='mso-ansi-language:
1278
EN-US'>python</span></span><span lang=EN-US style='mso-ansi-language:EN-US'> <o:p></o:p></span></p>
1279

    
1280
<p class=MsoNormal><span class=GramE><span lang=EN-US style='mso-ansi-language:
1281
EN-US'>for</span></span><span lang=EN-US style='mso-ansi-language:EN-US'> x in
1282
range(3,101):<o:p></o:p></span></p>
1283

    
1284
<p class=MsoNormal><span lang=EN-US style='mso-ansi-language:EN-US'><span
1285
style='mso-spacerun:yes'>??? </span><span class=SpellE><span class=GramE>cmd.edit</span></span><span
1286
class=GramE>(</span>&quot;/<span class=SpellE>thr</span>///&quot; + <span
1287
class=SpellE>str</span>(x-1) + &quot;/C&quot;)<o:p></o:p></span></p>
1288

    
1289
<p class=MsoNormal><span lang=EN-US style='mso-ansi-language:EN-US'><span
1290
style='mso-spacerun:yes'>??? </span><span class=SpellE>editor.attach_amino_<span
1291
class=GramE>acid</span></span><span class=GramE>(</span>&quot;pk1&quot;,&quot;thr&quot;)<o:p></o:p></span></p>
1292

    
1293
<p class=MsoNormal><span class=GramE><span lang=EN-US style='mso-ansi-language:
1294
EN-US'>for</span></span><span lang=EN-US style='mso-ansi-language:EN-US'> x in
1295
range(2,99):<o:p></o:p></span></p>
1296

    
1297
<p class=MsoNormal><span lang=EN-US style='mso-ansi-language:EN-US'><span
1298
style='mso-spacerun:yes'>??? </span><span class=SpellE>cmd.set_<span
1299
class=GramE>dihedral</span></span><span class=GramE>(</span><o:p></o:p></span></p>
1300

    
1301
<p class=MsoNormal><span lang=EN-US style='mso-ansi-language:EN-US'><span
1302
style='mso-spacerun:yes'>??????? </span>&quot;/<span class=SpellE>thr</span>///&quot;
1303
+ <span class=SpellE><span class=GramE>str</span></span><span class=GramE>(</span>x)
1304
+ &quot;/N&quot;, &quot;/<span class=SpellE>thr</span>///&quot; + <span
1305
class=SpellE>str</span>(x) + &quot;/CA&quot;,<o:p></o:p></span></p>
1306

    
1307
<p class=MsoNormal><span lang=EN-US style='mso-ansi-language:EN-US'><span
1308
style='mso-spacerun:yes'>??????? </span>&quot;/<span class=SpellE>thr</span>///&quot;
1309
+ <span class=SpellE><span class=GramE>str</span></span><span class=GramE>(</span>x)
1310
+ &quot;/C&quot;, &quot;/<span class=SpellE>thr</span>///&quot; + <span
1311
class=SpellE>str</span>(x+1) + &quot;/N&quot;, -47)<o:p></o:p></span></p>
1312

    
1313
<p class=MsoNormal><span lang=EN-US style='mso-ansi-language:EN-US'><span
1314
style='mso-spacerun:yes'>??? </span><span class=SpellE>cmd.set_<span
1315
class=GramE>dihedral</span></span><span class=GramE>(</span><o:p></o:p></span></p>
1316

    
1317
<p class=MsoNormal><span lang=EN-US style='mso-ansi-language:EN-US'><span
1318
style='mso-spacerun:yes'>??????? </span>&quot;/<span class=SpellE>thr</span>///&quot;
1319
+ <span class=SpellE><span class=GramE>str</span></span><span class=GramE>(</span>x)
1320
+ &quot;/CA&quot;, &quot;/<span class=SpellE>thr</span>///&quot; + <span
1321
class=SpellE>str</span>(x) + &quot;/C&quot;,<o:p></o:p></span></p>
1322

    
1323
<p class=MsoNormal><span lang=EN-US style='mso-ansi-language:EN-US'><span
1324
style='mso-spacerun:yes'>??????? </span>&quot;/<span class=SpellE>thr</span>///&quot;
1325
+ <span class=SpellE><span class=GramE>str</span></span><span class=GramE>(</span>x+1)
1326
+ &quot;/N&quot;, &quot;/<span class=SpellE>thr</span>///&quot; + <span
1327
class=SpellE>str</span>(x+1) + &quot;/CA&quot;, 180)<o:p></o:p></span></p>
1328

    
1329
<p class=MsoNormal><span lang=EN-US style='mso-ansi-language:EN-US'><span
1330
style='mso-spacerun:yes'>??? </span><span class=SpellE>cmd.set_<span
1331
class=GramE>dihedral</span></span><span class=GramE>(</span><o:p></o:p></span></p>
1332

    
1333
<p class=MsoNormal><span lang=EN-US style='mso-ansi-language:EN-US'><span
1334
style='mso-spacerun:yes'>??????? </span>&quot;/<span class=SpellE>thr</span>///&quot;
1335
+ <span class=SpellE><span class=GramE>str</span></span><span class=GramE>(</span>x)
1336
+ &quot;/C&quot;, &quot;/<span class=SpellE>thr</span>///&quot; + <span
1337
class=SpellE>str</span>(x+1) + &quot;/N&quot;,<o:p></o:p></span></p>
1338

    
1339
<p class=MsoNormal><span lang=EN-US style='mso-ansi-language:EN-US'><span
1340
style='mso-spacerun:yes'>??????? </span>&quot;/<span class=SpellE>thr</span>///&quot;
1341
+ <span class=SpellE><span class=GramE>str</span></span><span class=GramE>(</span>x+1)
1342
+ &quot;/CA&quot;, &quot;/<span class=SpellE>thr</span>///&quot; + <span
1343
class=SpellE>str</span>(x+1) + &quot;/C&quot;, -57)<o:p></o:p></span></p>
1344

    
1345
<p class=MsoNormal>python end</p>
1346

    
1347
<p class=MsoNormal><span style='mso-fareast-language:RU;mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1348
 id="???????_x0020_5" o:spid="_x0000_i1025" type="#_x0000_t75" style='width:859.5pt;
1349
 height:345.75pt;visibility:visible;mso-wrap-style:square'>
1350
 <v:imagedata src="str_bio_2.files/image004.png" o:title=""/>
1351
</v:shape><![endif]--><![if !vml]><img border=0 width=1146 height=461
1352
src="str_bio_2.files/image004.png" v:shapes="???????_x0020_5"><![endif]></span></p>
1353

    
1354
</div>
1355

    
1356
</body>
1357

    
1358
</html>