UCSF chimera

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Revision as of 08:30, 11 July 2011 (view source) Igchoi (Talk | contribs) ← Older edit		Revision as of 16:11, 17 July 2011 (view source) Igchoi (Talk | contribs) (→Examples) Newer edit →
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	match #3:1001@O5,C1,C2,O5,C3,C4,O3 #2:375.A@O5,C5,C4,O5,C3,C2,O3		match #3:1001@O5,C1,C2,O5,C3,C4,O3 #2:375.A@O5,C5,C4,O5,C3,C2,O3
	</pre>		</pre>
		+	;Fig.3 in the BBRC draft
		+	<pre>
		+	arg51
		+	tyr335
		+	gln361b
		+	glu265
		+	his264
		+	asp207
		+	lys222
		+	arg235
		+	glu224
		+	ala356b
		+	ser358b
		+	tyr359b
		+	trp89
		+	phe87
		+	sel #0,1:.A
		+	color gold #0; color cyan #1
		+	sel :51,52,335,361,265,264,207,222,235,224,358,359,89,87
		+	sel #0:GLA.A;
		+	focus #0:GLA.A; col magenta #0:GLA.A
		+	colordef tgold 1 .843 0 .2;
		+	colordef tcyan 0 1 1 .15;
		+	color tgold,r #0;
		+	color tcyan,r #1;
		+	ribscale slim
-	*Movie [http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/movie.html commands]	+	colordef tblue 0 0 1 .15;
-	**[http://www.cgl.ucsf.edu/chimera/tutorials/movies09/moviemaking.html '09 tutorial]	+	color tblue,r #2;
		+	====
		+	ahgA
		+	sel #2:96,97,134,132,309,269,280,381,252,267,310
		+	color skyblue
		+	===
		+	sel #1:74,127,249
		+	</pre>
		+
		+	;Movie [http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/movie.html commands]
		+	;[http://www.cgl.ucsf.edu/chimera/tutorials/movies09/moviemaking.html '09 tutorial]

---

Revision as of 16:11, 17 July 2011

Popular command

focus

alias

Presets

for residues within 3.6 Å of a ligand residue or metal ion ( ligand zr<3.6)

Examples

NABH

alias active1 #0:52,207,265;
alias contact1 #0:222.B,224.B,235.B,264.B;
alias contact2 #0:358-359;
alias contact #0:222,224,235,264,359,361;
alias gal #0:gla;
alias active ligand z<3.5 & ~ligand & ~solvent;
alias active ligand z<3.5 & ~ligand & ~solvent & without CA/C1';
alias loop #:351-366;
select active & without CA/C1';
sel ligand zr<3.5 & solvent zr<3.5 & ~ligand & ~solvent

match #3:1001@O5,C1,C2,O5,C3,C4,O3 #2:375.A@O5,C5,C4,O5,C3,C2,O3

Fig.3 in the BBRC draft

arg51
tyr335
gln361b
glu265
his264
asp207
lys222
arg235
glu224
ala356b
ser358b
tyr359b
trp89
phe87

sel #0,1:.A
color gold #0; color cyan #1
sel :51,52,335,361,265,264,207,222,235,224,358,359,89,87
sel #0:GLA.A;
focus #0:GLA.A; col magenta #0:GLA.A
colordef tgold 1 .843 0 .2;
colordef tcyan 0 1 1 .15;
color tgold,r #0;
color tcyan,r #1;
ribscale slim

colordef tblue 0 0 1 .15;
color tblue,r #2;
====
ahgA
sel #2:96,97,134,132,309,269,280,381,252,267,310
color skyblue
===
sel #1:74,127,249

Movie commands

'09 tutorial