Chimera的基本操作

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UCSF Chimera���������ݴ�ѧʥ���Ǹ��УCGLʵ���ң�UCSF Computer Graphics Laboratory��CGL)������һ������ѧ�����UCSF Chimera��һ��߶ȿ����ġ�����ʽ�ķ��ӽṹ��ʾ������ϵͳ��Chimera���Զ�ȡ���ָ�ʽ�ķ��ӽṹ�������ݣ����ò�ͬ�ķ�ʽ��ʾ��������ܹ���ɸ������ͼ�񡢶����Ա���ӡˢ��չʾ��Chimera�����ԣ���ʾ������羵�ܶ�ͼ�����öԳ������ʾ�߶�����Ľṹ����ʾ�����бȶԣ���������Ӷ������ê����docking������ Chimera��ѧ����������ӯ���Ժ͸��˵�ʹ������ѵģ����кܶ��ĵ���ָ���ָ����ѧ��ʹ�á�Chimera�����ڸ���ƽ̨��ʹ�ã����Windows,MacOS X,Linux,SGI,Unix��ƽ̨�� ���ص�ַ [[1]]

��װChimera��˫���Chimera����ʾ���½��棺

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Ȼ�󵥻�File��������Open������Ŀ���ļ�ѡ����棬����ͼ:

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Chimera����֧�ֺܶ��ָ�ʽ�������и�ʽ�������,���all (guess type)���� ��ʾ֧�ֵ��ļ���ʽ���籾���е�MRC��ʽ�� Image:Types.JPG

��MRC�ļ��󣬳������������ʾ�ṹ�⣬ͬʱ����һ��Volume Viewer���ڡ� Image:VolumeViewer1.JPG

��Volume View���кܶ����Թ��ߣ������ڲ˵���Features���˵���ѡ��Ҳ���Զ���Ĭ�Ͻ��档 Ĭ�Ͻ����в��ֲ������������ͼ�� Image:VolumeViewer2.JPG

��MRC��ݺ���Chimera��ڴ򿪲˵���Tools��������Volume data��������Volume Eraser���� Image:Eraser.JPG

������г���һ��ۺ�ɫС�򣬲�����һ��Volume Eraser���ڡ���Volume Eraser�����У� Color���Ըı�С�����ɫ��radius���Ըı�С��İ뾶��С������á�Ctrl+����Ҽ�Ĭ�Ϸ�ʽ���ƶ�. Image:Eraser2.JPG

�������ͼ���ֱ���Eraseǰ�����ͼ�񣬿ɼ�ۺ�С�����ݱ�����erase)�ˡ� Image:Eraser3.JPG Image:Eraser4.JPG

Ϊ�˷��������֮����໥��֣����ǿ����á�Surface Color���������ݽ���Ⱦɫ�� Image:SurfaceColor1.JPG

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UCSF Chimera��Tutorials

һ��ǿ���ͼ�δ�����������ǽṹ����ѧ��Ҫ�ij������֮һ�� ��ϸ���û��ֲ�˵��

��Ҫ����棺 1��ָ��---�������� 2������Chinmera �ĺ������� 3�����ߡ�רҵ���ߺ�Ӧ�� ���ذ�װ����һЩ�޷�ʵ�ֵĹ��ܣ�����e-mail�� the UCSF Computer Graphics Laboratory (CGL) web site ��ȡ���µ�˵��ͷ���

���棺 The Chimera ����


���ڰ����˵IJ˵�ѡ�ͼ����ʾ�Ĺ�����������к�״̬� �˵���Menu Bar�� File, Select, Actions, Tools, Favorites, and Help. �ļ���File�� ѡ�� (Select) ��Ϊ (Actions) ���� (Tools) ƫ�� (Favorites) ���� (Help)

������(Toolbar) ��ͼ��Ĺ����� ��ͨ��General preferencesѡ�������Լ�ͨ��Tools preferencesѡ���Ƿ���ʾ����Favorites��preferences�� ͼ�δ��ڣ�Graphics Window�� ���ӽṹ��3D��ݶ���ͨ��ͼ�δ�����ʾ��Ĭ�ϵı���Ϊ��ɫ������ͨ��(Actions... Color) ���� set bg_color����, Background preferences��ı䱳����ɫ�� �����У�The Command Line ��


������� ���ִ򿪷�ʽ��������General Controls���С���Favorites��preferences�� There are several ways to start the Command Line, a tool in the category. Ctrl-u % ������������� up arrow and down arrow or Ctrl-p and Ctrl-n % �����ƶ������� ���������ĵ����ͼ�꣬���Կ�����ʷ��¼ ��Command Line���һ���ʾ�����������е�ģ�͡��򿪵�ģ�ͻ��ú�������ʾ���������ǰ��ķ���ͼ�����ѡ���Ƿ񼤻�ģ�͡�ʧ���ģ�Ͳ�����Ӧ�ƶ�����ƽ�Ƶ�������All ���Լ���ȫ����ģ�͡� ������ͨ��Model Panel ��������selectʵ�� Selection��ѡ�� ��Chimera�У�ѡ�������Ԫ��Ӧ�ã�ԭ�ӣ��л�ȣ���ִ�ж�����߲���Ԫ������ͨ��the Actions menu, the Selection Inspector, or commands�ȵ��á��������У�����ͨ��selected, sel, or picked�ȵ��á���ǰ��ѡ��������Ա�����͵��á����磺sel=selection_name ���� selection_name. Ĭ������£�ѡ������ɫ���������status line��ʾ������ѡ��ť���Դ�Selection Inspector�� ��ѡ��ķ����� ? ��ͼ���ڡ�picking ? ѡ��˵� ? Ӧ��select���� ? ijЩ���ߵ�Ӧ�� ����ͨ��Select... Selection Mode (current_mode)��ӣ����٣����룬���������Ѵ��ѡ��current_mode����ʾ��ǰ���á�

Summary of Arrow Key Shortcuts����ͷ�����ܽᣩ �����̾۽�����Chimera����ʱ����ͷ����Լ���ѡ�� ? up arrow - broaden the selection ѡ����� ? down arrow - narrow the selection ѡ����С ? right arrow - invert the selection within selected models ѡ��ת ? Shift-right arrow - invert the selection within all models ģ��ȫ����ת ? left arrow - undo the most recent selection operation ���� ? Shift-left arrow - clear the selection ���ѡ��

״̬���Status Line��


����ͨ��Messages preferences ��the Accelerators dialog�����״̬���ʾ��������The selection ��ť������ʾ��ѡĿ�ꡣ�����the Selection Inspector.

The Selection Inspector��ѡ������� ���ã��ı�ijЩ��ǰѡ������ԡ� �򿪷����� ? �˵� Actions... Inspect ? the status line ����İ�ť ? by choosing Inspect from the context menu obtained by double-picking an atom, bond, or pseudobond (that is, doubleclicking with the button assigned to picking) ����ѡ������ݣ� ? Atom ԭ�� ? Bond �� ? Residue �л� ? Molecule model ����ģ�� ? Pseudobond �ټ� ? MSMS surface MSMS ���� Write List... ���Դ�ר�ŵĴ��ڣ�������ר�Ź���˵������ʽ����ѡ�� Write PDB... ���Դ�ר�ŵĴ��ڣ�������ר�ŵ�PDB��ʽ����ѡ�� Close �ر�the Selection Inspector�� Help �����ļ��� ���ѡ���Ŀ���ж������ԣ�����"-- multiple --" or ">1"��ʾ


ԭ�����ԣ� ��ʾ��ʽ�� o dot ���� o ball ���� o endcap ����״ o sphere ������ ? color (a color well) �Cԭ��ˮƽȾɫ ? displayed -�Ƿ���ԭ��ˮƽ����ʾ o false o true ? IDATM type -ԭ������ ����ǰ���ɸ�ģ� ? label �C ��ӱ�ǩ��Ϣ ? label color ��ǩ��ɫ ? radius �C ��ʾ����ԭ�ӵİ뾶 ? surface color (a color well) �C ԭ��ˮƽ�ı�����ɫ ? surface displayed -�Ƿ���ԭ��ˮƽ��ʾ������ɫ o false o true ? surface opacity - ����͸���ԣ�0����ȫ͸��1����ȫ��͸������ʾӦ�ò�͸���� �����ԣ� ? ����ʽ����ͼ��ģʽ�� o wire ��״ o stick ��״ ? color (a color well)Ⱦɫ �C ��ĵ���Ⱦɫ������ͨ��bondcolor������á�ע�⣺Ⱦɫ�ķ���ֻ���ڰ��ģʽ��halfbond mode���رյ�����¿ɼ����ֻ����ԭ�Ӳ���ɼ� ? displayed ����ʾ��-����ѡ�����ͨ�� bonddisplay������Ƶ����ˮƽ����ʾ�� o true o false o if atoms shown��ֻ�����ԭ�Ӷ���ʾʱ�ɼ� ? halfbond mode �����ģʽ��- �Ƿ��������Ϊ�����ʵ�塣��halfbond mode ����ʱ��ÿ��������Ӧ��ԭ�� (Ҳ����bondcolor�������). o on o off ? label����ǩ��- ����ı�ǩ ? label color (a color well) ��ǩ��ɫ- ? radius���뾶��-��״��ʾ�İ뾶

�л����ԣ�: ? in helix �Ƿ����� o false o true ? in strand �Ƿ����״ o false o true ? label �C��ǩ ? label color (a color well) �C ��ǩ��ɫ ? ribbon color��״Ⱦɫ(a color well) - ? ribbon cross section - �����ṹ�Ĵ�״��ʾģʽ o edged o flat o rounded ������ͨ��Ribbon Style Editor��Ӻ�������ģʽ�� ? ribbon display ����ʾ��- �Ƿ�����ṹ�Դ�״��ʽ��ʾ����ֻ����ʾ���׺ͺ��ᣩ���׵Ķ����ṹ�Ĺ滮�������Ľṹ�ļ�����ͨ��ksdssp���� o off o on ? ribbon scaling ����ű�������ṹ�Ĵ�״��ʾ��ָ���ĸߺͿ���� o Chimera default Ĭ��ֵ

������ͨ��Ribbon Style Editor�����������µı���

����ģ�����ԣ�: ? Active������ - �Ƿ�ģ�Ͷ���� o false o true ? auto-chaining���Զ������ -�Ƿ��ϵǰ���ԭ�� o off o on ? ball scale -��״ģʽ�ı������� ? color (a color well) �C Ⱦɫ ? displayed -�Ƿ���ģ��ˮƽ����ʾ o false o true ? line width -������ȵ����� ? ribbon hides backbone atoms -�Ƿ���ʾ�߶����ṹ�IJл��е����ԭ�� o false o true ? stick scale -��״��ı������á���ͨ����ȫ��Ӧ�ã� ? surface color (a color well) -������ɫ ? surface opacity �C ����͸���0 (��ȫ͸��) to 1 (��ȫ��͸��); ? vdw density - relative density of dots used in any VDW surfaces (as with the command vdwdensity) VDW����ĵ��ܶ� ? vdw dot size - pixel size of dots in any VDW surfaces VDW����ĵ����� �ټ������ ��ͬ�����ã�


MSMS��������� ? active - whether the model is activated for motion o false o true ? color source - whether the surface color reflects the color at the model or atom level (see coloring hierarchy). When surface color is set independent of these levels, unknown is reported. This occurs when the surface is custom-colored, for example, when it is colored by electrostatic potential using DelPhiViewer. o model o atoms o unknown ? displayed - whether surface display is enabled at the model level (see display hierarchy) o false o true ? dot size - pixel size of dots used in the dot surface representation ? line width - pixel width of lines used in the mesh surface representation ? probe radius - radius in angstroms of the probe sphere used to compute the surface. A larger probe decreases surface bumpiness because it fits into fewer crevices. A probe radius of 1.4 angstroms is commonly used to approximate the size of a water molecule. ? representation - which type of surface representation is being used o solid o mesh o dots ? vertex density - number of vertices per square angstrom used to compute the surface. Greater density results in a smoother surface but increases computational demands for calculating and moving the surface.


Draw Mode����ʾģʽ�� ԭ�ӵ���ʾģʽ�� ? ball (as in the ball-and-stick representation) - radii equal the VDW radii multiplied by the ball scale factor ���� ? dot (as in the wire representation) �� ? endcap (as in the stick representation) ��״ ? sphere (as in the sphere representation) - radii equal the VDW radii ���� ��ͼټ����ʾģʽ�� ? stick (as in the stick and ball-and-stick representations) ��״ ? wire (as in the wire representation) ��״ �����ʾʱ�� ? ball and stick includes ball atoms and stick bonds ��� ? sphere (or CPK) includes sphere atoms and wire bonds ������״ ? stick includes endcap atoms and stick bonds ��״ ? wire (or wireframe) includes dot atoms and wire bonds ����ʽ

Molecular Display Styles��������ʾ���ͣ�

ԭ�ӻ��߼���Chimera�е���ʾ��ʽ ? wire - a simple line drawing with dot atoms and wire bonds ��ʽ ? stick - "endcap" atoms and stick bonds ��״ ? ball-and-stick - ball atoms (scaled VDW radius) and stick bonds ��� ? sphere - sphere atoms (full VDW radius) and wire bonds; also called Corey-Pauling-Koltun (CPK) ����


һ����������

���ƥ��ͷ��������Ƶĵ����ʽṹ ͼ����� ����ʵ�ֽṹ���ã�����λ�úʹ���רҵ�ij����ͼ��ȹ��ܡ� ��Glycoside hydrolases (GH)���ǻ�ˮ��ø������Ϊ��ʵ�ִ���GH families 32, 43, and 68�����ͼ������Ƚ����Ǽ�ṹ�������ԡ�

1����� Windows/Mac, ��� chimera ͼ��. On UNIX, ϵͳ��� unix: chimera 2����Command Line ( Tools... General Controls... Command Line). 3) �ṹͼ�ο���ֱ��ͨ���������أ�from the Protein Data Bank��: ѡFile... Fetch by ID ���´򿪵ĶԻ�����ѡ��the PDB ID option ��the option to Keep dialog up after Fetch. ��˳������1uyp, 1gyd, �� 1oyg, �رնԻ��� 4��ͨ�����ʵ��ͼ�ε���ת��ƽ�ƣ����XY- �᷽���Z-�᷽�򣩺ͷŴ���С��

��ת��������ͨ������ ʵ�� �����ͼ�����ij��� ͼ�꣬ XY- �᷽��ƽ�ƣ� Z-�᷽��ƽ�ƣ� �Ŵ���С��

������ã�Favorites... Preferences��Preferences Tool

Some salient features of the structures: GH family ��һЩ�������� PDB ID enzyme family chains conserved residues 1uyp invertase, T. maritima GH32 A-F Asp17 Asp138 Glu190 1gyd arabinanase A, C. japonicus GH43 B Asp38 Asp158 Glu221 1oyg levansucrase, B. subtilis GH68 A Asp86 Asp247 Glu342

�ṹ�Ƚϣ� 1�� ��ͼ�Σ�ֻ����������Ҫ����������ɾ������������ܼ�ȣ���Ȼ����a-̼����ʽ��ʾ�ṹ�� Command: delete #0:.b-f % ���invertase��b-f� Command: delete solvent Command: chain @ca Command: linewidth 3 Since a set of structurally equivalent residues is known, an efficient way to superimpose the structures is by specifying atoms to use in a least-squares fit: Command: match #1:38.b,158.b,221.b@n@ca@c@o #0:17.a,138.a,190.a@n@ca@c@o Command: match #2:86.a,247.a,342.a@n@ca@c@o #0:17.a,138.a,190.a@n@ca@c@o 2�� In fact, the chain specifications .a and .b could be omitted from these match commands because the residues would still be specified uniquely without them (other chains containing the same residue numbers in the same model have been deleted). In the general case, chain ID codes are needed to specify residues uniquely because a given residue number may occur in more than one chain.


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UCSF Chimera��Tools

Tools Index(��������) 1. 2D Labels -����ǩ�����������ƶ��ı�ǩ���������� * 2. Accelerators -����� 3. Add Charge -��ӵ�ɣ� ָ����ɸ���Ӧ��ԭ�� 4. AddH - ������ԭ�� 5. Adjust Torsions -��ת����ı����� 6. Angles/Torsions - ����ǻ��߶���ǵ���ֵ 7. Area/Volume from Web �C �������ͨ���ͷ������嵽StrucTools server��ȡ�����ԭ����Ϣ���ԣ� 8. Attribute Calculator - generate new numerical attributes from existing ones; calculate totals or averages of a given numerical attribute�� �����֪����趨���ֻ����� ���������ƽ����ֵ���� 9. Benchmark - ��׼�����Ӳ��ִ��Ч���Ա�׼��Chimera rendering tasks Ϊ��׼ 10. Browser Configuration -��������ã�������������ڴ������ϻ��Chimera ��� 11. Build Structure - ����ṹ * 12. Camera - �������ƹۿ����� * 13. Collaboratory: Start Session and Join Session -��ԪΪ������ 14. Color Editor -ɫ�ʱ༭����������ʽɫ�� 15. Color Secondary Structure - �����ṹȾɫ 16. Color Zone - Ⱦɫ���򣺸�ijЩ�������Ⱦɫ���ƥ����ѡ���ԭ�ӡ� 17. Command Line - ������ * 18. Constrained Move -ǿ���ƶ��������ض�����ת��ƽ�� * 19. Define Attribute - ���Զ��壺��������ֵ����Ӧ��ԭ�ӣ��л��ģ�� 20. DelPhiController - DelPhi���ƣ�ͨ��DelPhi������㾲������ͼ�� 21. Demos and Demo Editor -��ʾ����ʾ�༭����������ʾ 22. Distances - ���룺���һ��ԭ�Ӽ�ľ��� 23. Dock Prep - Dock׼���������ԭ�Ӻ͵�ɵȣ�ΪDock�������������׼�� 24. Effects -��̬�����ƿ��ӻ�����Ч������ ��Ȼ��߲���Ӱ���Ե�� * 25. EnsembleMatch - match conformations from two ensembles ����ƥ�� * 26. EnsembleTile �C ƽ�����ƹ����� display ensemble members in a tiled arrangement 27. Find Clashes/Contacts - �����ͻ���߽Ӵ� 28. FindHBond -Ѱ�ҿ��ܵ���� * 29. Fit Models in Maps - locally optimize the fit of a structure within a density map Ӧ���ܶ�ͼ�׽��б������Ż�Ѱ�Һ��ʵĽṹ * 30. Icosahedron Surface -��ʮ������棺 ������ϵĶ�ʮ��������εı��� * 31. IDLE (Python Interactive DeveLopment Environment) - Python����ƽ̨�� ����Python���� 32. Intersurf -��������ʾ�������� 33. Lens Inspector - ��ͷ��ʾ���ڻ�ͼ�����д������δ�����ʾ 34. Lighting - ��ڹ�Ȳ��� 35. Match -> Align - �ɽṹ����������е��� * 36. MatchMaker -ͨ���һ�ι��������е����ж����ṹ�з����⹹������ӽṹ��Ȼ�����õ���л�� * 37. MD Movie �C ������ʾ�ͷ�����Ӷ�̬�켣 * 38. Measure Volume and Area -������ͱ���� 39. Minimize Structure - �����С���ṹ 40. Minrms Plot - �����MinRMS��������ĵ��׵Ľṹ���� 41. Model Loops -��MODELLER�Ľӿڣ����ڲ���ѡ���Ե��ɽṹ�ִ���ļ�Ƭ���γɵĹ��� * 42. Model Panel -ģ��ģ�棺ģ�͵��б�Ͷ��� 43. Morph Conformations -���幹�ͣ�����ͬһ�ṹ�IJ�ͬ���幹�͵Ĺ켣 * 44. Movie Recorder - ��׽ͼ��ṹ�����������γɵ�Ӱ�ļ� 45. Multalign Viewer -��ʾ�����е��� 46. Multiscale Models -�༶ģ�ͣ��ڵͻ��߸߷ֱ��ʵ��������ʾ�������װ����������Ͷ�λ�ṹ�IJ�� * 47. Nucleotides -�����᣺�����ض�����������������ʵı��� 48. Per-Model Clipping -ģ�ͼ�� �����ģ�� * 49. Phantom Force Feedback - use a Phantom force feedback device to trace paths in volume displays ��ʾ�����ʾ�켣 50. PipesAndPlanks -�Թ�״��"pipes"����ʾ���Ļ򵰰��������Դ�����"planks"����ʾ�ɵ��۵��ṹ 51. PseudoBond Panel - �������б�Ͷ��� 52. PseudoBond Reader - ǿ�ƽ����� 53. Rainbow - ���Ⱦɫ������ÿ��л������ģ�͸ı���ɫ�� 54. ReadStdin -��׼������� 55. Render by Attribute -ͨ������ֵ����ԭ�ӣ��л��ģ�ͣ�����ɫ����ʽ�� 56. Reply Log -�ظ����棺��ʾ��Ϣ������ʹ�����Ϣ 57. ResProp - ������Ⱦɫ�����᣻�����µ����� 58. Ribbon Style Editor - change ribbon heights/widths (scalings) and cross-sections (styles) �ı��ĸ߶�/��Ⱥͺ������ʽ 59. Rotation - ������ת���� 60. Scale Bar - ���Ʊ���ߣ�scale bar����ͼ�� 61. Sequence - ��ʾ����ģ�͵����� 62. Set Bond Length - �ı�� 63. Shininess Control - �����Ⱥ���� 64. Side View - scale the view and move clipping planes interactively ������ͼ�ͼ�λ��Ľ��� * 65. Surface Capping - cap surfaces where they intersect a clipping plane �����������ĺ���� 66. Surface Color -������ɫ��������ݻ��߼���ѧ�����磺�ӵ㣬���ƽ��ľ��룩 67. Surface Zone -������ij�ֱ�����ʽ��ʾһ����ѡԭ�ӵ���Χ���� 68. Surfnet - ���ն��ͱ��氼�� 69. Undo Move and Redo Move - ������ת��ƽ�Ƶ���ʷ��¼ 70. Unit Cell - generate crystallographic unit cell contents from coordinates and transformation matrices ���Э�����ת�����������ṹϸ��Ԫ 71. Values at Atom Positions - ���ԭ��λ�ú���������ֵ���������� * 72. ViewDock and HearDock - view and prioritize docked molecules output by DOCK % ���� 73. Volume Eraser - interactively zero out parts of volume data ���0��� 74. Volume Path Tracer �C·�������trace paths within volume displays 75. Volume Viewer - 3D��ݼ��Ŀ��ӻ� ������ �����ܶ�ͼ�ף� ? MinRMS ��һ��׿Խ�ģ��ǻ�ͼʽ��������Բ�����ʵĽṹ�滮��ڡ�ͨ��Chimera�����������У�������Chimera���ڲ��ֲ�ʽ�ṹ�����Ե������ء�


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