[Chimera-users] Could chimera draw shapes faster?

Ferdinando Randisi ferdinando.randisi at gmail.com
Thu Feb 25 14:11:01 PST 2016


Hi!

I'm one of the developers of oxDNA (
https://dna.physics.ox.ac.uk/index.php/Main_Page), a code aimed at
simulation of large DNA structures for biology and nanotechnology.

We often use chimera because, frankly, it makes gorgeous pictures. Since we
simulate DNA as made by rigid nucleotides instead of atoms, we hijack it to
make it plot various shapes instead of using atoms directly, but it takes
forever to get it to load a configuration like the one attached.

Could you guys do something to make it faster/give as some advice on how to
make it plot these things faster? We currently use the input files
attached. (chimera.txt should be renamed chimera.com so that it can be
understood by chimera).



Best,

Ferdinando

-- 
Ferdinando Randisi
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bond #0:1106.A,1105.A
bond #0:1107.A,1106.A
bond #0:1108.A,1107.A
bond #0:1109.A,1108.A
bond #0:1110.A,1109.A
bond #0:1111.A,1110.A
bond #0:1112.A,1111.A
bond #0:1113.A,1112.A
bond #0:1114.A,1113.A
bond #0:1115.A,1114.A
bond #0:1116.A,1115.A
bond #0:1117.A,1116.A
bond #0:1118.A,1117.A
bond #0:1119.A,1118.A
bond #0:1120.A,1119.A
bond #0:1121.A,1120.A
bond #0:1122.A,1121.A
bond #0:1123.A,1122.A
bond #0:1124.A,1123.A
bond #0:1125.A,1124.A
bond #0:1126.A,1125.A
bond #0:1127.A,1126.A
bond #0:1128.A,1127.A
bond #0:1129.A,1128.A
bond #0:1130.A,1129.A
bond #0:1131.A,1130.A
bond #0:1132.A,1131.A
bond #0:1133.A,1132.A
bond #0:1134.A,1133.A
bond #0:1135.A,1134.A
bond #0:1136.A,1135.A
bond #0:1137.A,1136.A
bond #0:1138.A,1137.A
bond #0:1139.A,1138.A
bond #0:1140.A,1139.A
bond #0:1141.A,1140.A
bond #0:1142.A,1141.A
bond #0:1143.A,1142.A
bond #0:1144.A,1143.A
bond #0:1145.A,1144.A
bond #0:1146.A,1145.A
bond #0:1147.A,1146.A
bond #0:1148.A,1147.A
bond #0:1149.A,1148.A
bond #0:1150.A,1149.A
bond #0:1151.A,1150.A
bond #0:1152.A,1151.A
bond #0:1153.A,1152.A
bond #0:1154.A,1153.A
bond #0:1155.A,1154.A
bond #0:1156.A,1155.A
bond #0:1157.A,1156.A
bond #0:1158.A,1157.A
bond #0:1159.A,1158.A
bond #0:1160.A,1159.A
bond #0:1161.A,1160.A
bond #0:1162.A,1161.A
bond #0:1163.A,1162.A
bond #0:1164.A,1163.A
bond #0:1165.A,1164.A
bond #0:1166.A,1165.A
bond #0:1167.A,1166.A
bond #0:1168.A,1167.A
bond #0:1169.A,1168.A
bond #0:1170.A,1169.A
bond #0:1171.A,1170.A
bond #0:1172.A,1171.A
bond #0:1173.A,1172.A
bond #0:1174.A,1173.A
bond #0:1175.A,1174.A
bond #0:1176.A,1175.A
bond #0:1177.A,1176.A
bond #0:1178.A,1177.A
bond #0:1179.A,1178.A
bond #0:1180.A,1179.A
bond #0:1181.A,1180.A
bond #0:1182.A,1181.A
bond #0:1183.A,1182.A
bond #0:1184.A,1183.A
bond #0:1185.A,1184.A
bond #0:1186.A,1185.A
bond #0:1187.A,1186.A
bond #0:1188.A,1187.A
bond #0:1189.A,1188.A
bond #0:1190.A,1189.A
bond #0:1191.A,1190.A
bond #0:1192.A,1191.A
bond #0:1193.A,1192.A
bond #0:1194.A,1193.A
bond #0:1195.A,1194.A
bond #0:1196.A,1195.A
bond #0:1197.A,1196.A
bond #0:1198.A,1197.A
bond #0:1199.A,1198.A
bond #0:1200.A,1199.A
bond #0:1201.A,1200.A
bond #0:1202.A,1201.A
bond #0:1203.A,1202.A
bond #0:1204.A,1203.A
bond #0:1205.A,1204.A
bond #0:1206.A,1205.A
bond #0:1207.A,1206.A
bond #0:1208.A,1207.A
bond #0:1209.A,1208.A
bond #0:1210.A,1209.A
bond #0:1211.A,1210.A
bond #0:1212.A,1211.A
bond #0:1213.A,1212.A
bond #0:1214.A,1213.A
bond #0:1215.A,1214.A
bond #0:1216.A,1215.A
bond #0:1217.A,1216.A
bond #0:1218.A,1217.A
bond #0:1219.A,1218.A
bond #0:1220.A,1219.A
bond #0:1221.A,1220.A
bond #0:1222.A,1221.A
bond #0:1223.A,1222.A
bond #0:1224.A,1223.A
bond #0:1225.A,1224.A
bond #0:1226.A,1225.A
bond #0:1227.A,1226.A
bond #0:1228.A,1227.A
bond #0:1229.A,1228.A
bond #0:1230.A,1229.A
bond #0:1231.A,1230.A
bond #0:1232.A,1231.A
bond #0:1233.A,1232.A
bond #0:1234.A,1233.A
bond #0:1235.A,1234.A
bond #0:1236.A,1235.A
bond #0:1237.A,1236.A
bond #0:1238.A,1237.A
bond #0:1239.A,1238.A
bond #0:1240.A,1239.A
bond #0:1241.A,1240.A
bond #0:1242.A,1241.A
bond #0:1243.A,1242.A
bond #0:1244.A,1243.A
bond #0:1245.A,1244.A
bond #0:1246.A,1245.A
bond #0:1247.A,1246.A
preset apply int ribbons
set bg_color white
color sandy brown #0:ALA
col deep sky blue #0:ALA at N
col deep sky blue #0:ALA at O
col deep sky blue #0:ALA at S
col deep sky blue #0:ALA at K
bondcolor sandy brown #0:ALA
color blue #0:GLY
col deep sky blue #0:GLY at N
col deep sky blue #0:GLY at O
col deep sky blue #0:GLY at S
col deep sky blue #0:GLY at K
bondcolor blue #0:GLY
color red #0:CYS
col deep sky blue #0:CYS at N
col deep sky blue #0:CYS at O
col deep sky blue #0:CYS at S
col deep sky blue #0:CYS at K
bondcolor red #0:CYS
color green #0:TYR
col deep sky blue #0:TYR at N
col deep sky blue #0:TYR at O
col deep sky blue #0:TYR at S
col deep sky blue #0:TYR at K
bondcolor green #0:TYR
color purple #0:ARG
col deep sky blue #0:ARG at N
col deep sky blue #0:ARG at O
col deep sky blue #0:ARG at S
col deep sky blue #0:ARG at K
bondcolor purple #0:ARG
color dark gray #0:PHE
col deep sky blue #0:PHE at N
col deep sky blue #0:PHE at O
col deep sky blue #0:PHE at S
col deep sky blue #0:PHE at K
bondcolor dark gray #0:PHE
color yellow #0:LYS
col deep sky blue #0:LYS at N
col deep sky blue #0:LYS at O
col deep sky blue #0:LYS at S
col deep sky blue #0:LYS at K
bondcolor yellow #0:LYS
color orange #0:SER
col deep sky blue #0:SER at N
col deep sky blue #0:SER at O
col deep sky blue #0:SER at S
col deep sky blue #0:SER at K
bondcolor orange #0:SER
color deep pink #0:PRO
col deep sky blue #0:PRO at N
col deep sky blue #0:PRO at O
col deep sky blue #0:PRO at S
col deep sky blue #0:PRO at K
bondcolor deep pink #0:PRO
color magenta #0:VAL
col deep sky blue #0:VAL at N
col deep sky blue #0:VAL at O
col deep sky blue #0:VAL at S
col deep sky blue #0:VAL at K
bondcolor magenta #0:VAL
color sienna #0:ASN
col deep sky blue #0:ASN at N
col deep sky blue #0:ASN at O
col deep sky blue #0:ASN at S
col deep sky blue #0:ASN at K
bondcolor sienna #0:ASN
color goldenrod #0:ASP
col deep sky blue #0:ASP at N
col deep sky blue #0:ASP at O
col deep sky blue #0:ASP at S
col deep sky blue #0:ASP at K
bondcolor goldenrod #0:ASP
color gray #0:CYX
col deep sky blue #0:CYX at N
col deep sky blue #0:CYX at O
col deep sky blue #0:CYX at S
col deep sky blue #0:CYX at K
bondcolor gray #0:CYX
color plum #0:HSP
col deep sky blue #0:HSP at N
col deep sky blue #0:HSP at O
col deep sky blue #0:HSP at S
col deep sky blue #0:HSP at K
bondcolor plum #0:HSP
color olive drab #0:HSD
col deep sky blue #0:HSD at N
col deep sky blue #0:HSD at O
col deep sky blue #0:HSD at S
col deep sky blue #0:HSD at K
bondcolor olive drab #0:HSD
color dark red #0:MET
col deep sky blue #0:MET at N
col deep sky blue #0:MET at O
col deep sky blue #0:MET at S
col deep sky blue #0:MET at K
bondcolor dark red #0:MET
color steel blue #0:LEU
col deep sky blue #0:LEU at N
col deep sky blue #0:LEU at O
col deep sky blue #0:LEU at S
col deep sky blue #0:LEU at K
bondcolor steel blue #0:LEU
aniso scale 0.75 smoothing 4
setattr m stickScale 0.6 #0
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