'sym' command not finding mmCIF-format biomt symmetry info

[drorn@…]

The following bug report has been submitted:
Platform:        Darwin-19.6.0-x86_64-i386-64bit
ChimeraX Version: 1.1 (2020-09-09 22:22:27 UTC)
Description
The command sym with the biomt keyword does not find the biological info unit in the pdb file.
For example:
Loading pdb 5v8k into model #1 and executing
sym #1 biomt
returns an error message "Molecule 5v8k has no biological unit info"
Thgis is a bug since in chimera, the equivalent  command
sym #1 group biomt  
yields the symmetry clone

Log:
UCSF ChimeraX version: 1.1 (2020-09-09)  
© 2016-2020 Regents of the University of California. All rights reserved.  

> open "/Users/drornoy/Documents/Manuscripts/kaihong/Longest Arm 2020/ChimeraX
> sessions/Apc core purpureum 6KGX.cxs" format session

Log from Mon Sep 28 17:56:30 2020UCSF ChimeraX version: 1.1 (2020-09-09)  
© 2016-2020 Regents of the University of California. All rights reserved.  

> open "/Users/drornoy/Documents/Manuscripts/kaihong/Longest Arm 2020/ChimeraX
> sessions/Apc core purpureum 6KGX.cxs" format session

Log from Mon Sep 28 17:41:55 2020UCSF ChimeraX version: 1.0 (2020-06-04)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/drornoy/Documents/corePBM.pdb format pdb

Summary of feedback from opening /Users/drornoy/Documents/corePBM.pdb  
---  
warnings | Ignored bad PDB record found on line 80797  
TER ***** LEU k 361  
  
Ignored bad PDB record found on line 82948  
CONECT 1337***** 1336  
  
Ignored bad PDB record found on line 82996  
CONECT12731*****12730  
  
Ignored bad PDB record found on line 83006  
CONECT13950**********13949  
  
Ignored bad PDB record found on line 83016  
CONECT16397*****16396  
  
2157 messages similar to the above omitted  
  
Chain information for corePBM.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E F | No description available  
G I K N P R T X Z f i k o q s u w y | No description available  
H J L M O S U W Y h j l n p r t v x z | No description available  
Q g | No description available  
V m | No description available  
a | No description available  
b | No description available  
c | No description available  
d | No description available  
e | No description available  
  
Some installed bundles are out of date. Please update the following bundles:

  * UI to version 1.2.1 (currently 1.0)
  * UI to version 1.2 (currently 1.0)

  

> close session

> open 6kgx

Summary of feedback from opening 6kgx fetched from pdb  
---  
notes | Fetching compressed mmCIF 6kgx from
http://files.rcsb.org/download/6kgx.cif  
Fetching CCD PEB from http://ligand-expo.rcsb.org/reports/P/PEB/PEB.cif  
Fetching CCD PUB from http://ligand-expo.rcsb.org/reports/P/PUB/PUB.cif  
  
6kgx title:  
Structure of the phycobilisome from the red alga Porphyridium purpureum [more
info...]  
  
Chain information for 6kgx #1  
---  
Chain | Description  
11 14 A5 AC B1 B3 B4 B5 BC BD BE BG C5 C9 CC CJ D1 D3 D4 D8 DA DD DE DG E9 EJ
F1 F3 F4 F5 F8 FA FC FD FE FG G5 G9 GC GJ H1 H3 H4 H5 H8 HA HC HD HE HG I5 I9
IC IJ J1 J3 J4 J8 JA JD JE JG K5 K9 KC KJ L1 L3 L4 L5 L8 LA LC LD LE LG M9 MJ
N3 N8 NA ND NE NG O1 O4 O9 OJ P2 P3 P6 P7 P8 PA PB PD PE PF PG PI Q1 Q4 Q9 QJ
R2 R3 R6 R7 R8 RA RB RD RE RF RG RI S1 S4 S9 SJ T2 T3 T6 T7 T8 TA TB TD TE TF
TG TI U1 U4 U9 UJ V2 V3 V6 V7 V8 VA VB VD VE VF VG VI W1 W4 W9 WJ X3 X8 XA XD
XE XG Y1 Y2 Y4 Y6 Y7 Y9 YB YF YI YJ Z1 Z4 Z8 ZA ZE ZG a1 a2 a4 a6 a7 aB aF aI
bE bG c2 c6 c7 c8 cA cB cF cI d1 d4 dE dG e2 e6 e7 e8 eA eB eF eI f1 f4 fE fG
g2 g6 g7 g8 gA gB gF gI h1 h4 hE hG i2 i6 i7 i8 iA iB iF iI j1 j4 jE jG k2 k6
k7 k8 kA kB kF kI l1 l4 lE lG m2 m6 m7 m8 mA mB mF mI n1 n4 nE nG pE pG q1 q4
rE rG s1 s4 tE tG u1 u4 vE vG w1 w4 y1 y4 | B-phycoerythrin β chain  
1H YH | Phycobilisome linker polypeptide  
21 24 M1 M4 | LR7  
2H ZH | LRC4  
31 34 | LR9  
3H aH | LRC5  
4H bH | LRC6  
A1 A3 A4 AD AE AG B9 BJ C1 C3 C4 C8 CA CD CE CG D9 DJ E1 E3 E4 E8 EA ED EE EG
F9 FJ G1 G3 G4 G8 GA GD GE GG H9 HJ I1 I3 I4 I8 IA ID IE IG J5 J9 JC JJ K1 K3
K4 K8 KA KD KE KG L9 LJ M3 M8 MA MD ME MG N1 N4 N9 NJ O2 O3 O6 O7 O8 OA OB OD
OE OF OG OI P1 P4 P9 PJ Q2 Q3 Q6 Q7 Q8 QA QB QD QE QF QG QI R1 R4 R9 RJ S2 S3
S6 S7 S8 SA SB SD SE SF SG SI T1 T4 T9 TJ U2 U3 U6 U7 U8 UA UB UD UE UF UG UI
V1 V4 V9 VJ W2 W3 W6 W7 W8 WA WB WD WE WF WG WI X1 X4 X9 XJ Y8 YA YE YG Z2 Z6
Z7 ZB ZF ZI a8 aA aE aG b2 b6 b7 bB bF bI c1 c4 cE cG d2 d6 d7 d8 dA dB dF dI
e1 e4 eE eG f2 f6 f7 f8 fA fB fF fI g1 g4 gE gG h2 h6 h7 h8 hA hB hF hI i1 i4
iE iG j2 j6 j7 j8 jA jB jF jI k1 k4 kE kG l2 l6 l7 l8 lA lB lF lI m1 m4 mE mG
oE oG p1 p4 qE qG r1 r4 sE sG t1 t4 uE uG v1 v4 x1 x4 z1 z4 | Phycoerythrin α
subunit  
A2 A6 A7 A9 AB AF AI AJ Y3 YD | LR4  
A8 AA wE wG xE xG | LR5  
AH CH EH GH JH KH NH PH RH TH cH eH gH iH lH mH pH rH tH vH | Allophycocyanin
α subunit  
B2 B6 B7 BB BF BI | Phycobilisome rod-core linker polypeptide  
B8 BA yE yG | LR8  
BH DH FH HH IH LH MH OH QH SH UH dH fH hH jH kH nH oH qH sH uH wH |
Allophycocyanin β subunit  
C2 C6 C7 CB CF CI E2 E6 E7 EB EF EI G2 G6 G7 GB GF GI I2 I6 I7 IB IF II K2 K6
K7 KB KF KI M2 M6 M7 MB MF MI | C-phycocyanin α subunit  
D2 D6 D7 DB DF DI F2 F6 F7 FB FF FI H2 H6 H7 HB HF HI J2 J6 J7 JB JF JI L2 L6
L7 LB LF LI N2 N6 N7 NB NF NI | C-phycocyanin β subunit  
VH xH | Allophycocyanin γ subunit  
WH yH | Allophycocyanin β 18 subunit  
X2 X6 X7 XB XF XI | LR1  
XH zH | LC  
b1 b4 o1 o4 | LR2_Hb  
b8 bA | LRC2  
d9 dJ | LR3  
e3 eD | LR2  
zE zG | LRC3  
  
Non-standard residues in 6kgx #1  
---  
CYC — phycocyanobilin  
PEB — phycoerythrobilin  
PUB — phycourobilin  
  

> style sphere

Changed 1013398 atom styles  

> show cartoons

> hide target a

> color bychain

> interfaces ~solvent

1980 buried areas: YH HH 2956, 1H jH 2527, b4 Z4 1998, b8 F8 1991, bA FA 1980,
B6 J6 1979, BB JB 1979, b1 Z1 1955, YH WH 1816, 1H yH 1815, aH JB 1813, 3H J6
1794, zE LE 1774, zG LG 1763, D1 C1 1733, D4 C4 1709, DI CI 1679, lE kE 1677,
eI dI 1676, D2 C2 1672, L7 K7 1671, H2 G2 1667, HI GI 1665, H6 G6 1659, HB GB
1659, LF KF 1657, D7 C7 1650, NF MF 1648, BD AD 1647, q4 p4 1646, DF CF 1643,
XG WG 1640, ND MD 1638, e2 d2 1637, DE CE 1634, PD OD 1632, lG kG 1631, XD WD
1631, D6 C6 1629, N6 M6 1627, F4 E4 1627, mI lI 1627, N7 M7 1626, NI MI 1626,
KC JC 1626, TI SI 1626, NB MB 1625, N2 M2 1625, RI QI 1625, N3 M3 1625, HF GF
1624, X3 W3 1624, T2 S2 1624, Y9 X9 1624, c2 b2 1623, F2 E2 1621, R2 Q2 1620,
F1 E1 1620, P3 O3 1620, J2 I2 1620, JI II 1619, g2 f2 1619, DB CB 1619, FI EI
1619, J3 I3 1616, L6 K6 1614, jE iE 1614, k7 j7 1614, s4 r4 1613, FG EG 1613,
gI fI 1613, H1 G1 1610, PI OI 1609, DG CG 1608, H7 G7 1608, J1 I1 1607, F7 E7
1606, rH 2H 1606, YF WF 1605, L2 K2 1605, L4 K4 1605, H4 G4 1604, FF EF 1604,
TD SD 1604, Y2 W2 1603, P2 O2 1603, LB KB 1603, D3 C3 1602, LI KI 1602, d4 c4
1602, K5 J5 1601, R3 Q3 1599, T3 S3 1599, m2 l2 1598, H3 G3 1598, FE EE 1597,
zE HE 1597, zG HG 1597, FD ED 1597, fE eE 1596, jG iG 1595, PE OE 1595, u1 t1
1595, eF dF 1593, nG mG 1593, J4 I4 1593, YI WI 1592, BE AE 1591, JD ID 1591,
rG qG 1591, eA dA 1591, B3 A3 1590, aI ZI 1590, e8 d8 1590, XE WE 1590, Q4 P4
1588, M9 L9 1587, YJ XJ 1587, a2 Z2 1586, L3 K3 1586, LD KD 1585, RD QD 1585,
bE aE 1583, NG MG 1583, J7 I7 1583, PH ZH 1582, rE qE 1582, V3 U3 1581, kB jB
1581, RF QF 1581, WJ VJ 1580, BG AG 1579, HG GG 1579, bG aG 1579, KJ JJ 1579,
PG OG 1578, LG KG 1578, fG eG 1577, q1 p1 1577, C9 B9 1577, VD UD 1576, cI bI
1576, MJ LJ 1576, kF jF 1576, LE KE 1575, JF IF 1575, VI UI 1575, T6 S6 1573,
RB QB 1572, hG gG 1572, nE mE 1570, R7 Q7 1570, V2 U2 1570, F6 E6 1569, HE GE
1569, NE ME 1568, iI hI 1568, y1 x1 1568, DD CD 1568, 14 z4 1567, XA WA 1567,
CJ BJ 1567, Q1 P1 1566, JB IB 1566, FB EB 1566, mB lB 1566, P8 O8 1564, IJ HJ
1564, B1 A1 1564, Z8 Y8 1563, dE cE 1563, e6 d6 1563, ZA YA 1561, 11 z1 1561,
X8 W8 1561, pE oE 1561, h4 g4 1560, R6 Q6 1560, J6 I6 1560, y4 x4 1559, s1 r1
1559, yH iH 1559, a7 Z7 1558, PF OF 1558, PA OA 1557, e7 d7 1557, c6 b6 1556,
L1 K1 1556, P7 O7 1555, W9 V9 1554, i6 h6 1554, Y7 W7 1553, K9 J9 1552, TB SB
1551, j4 i4 1549, i2 h2 1549, hE gE 1549, U4 T4 1549, m6 l6 1548, W4 V4 1548,
Q9 P9 1548, UJ TJ 1547, eB dB 1547, g6 f6 1547, G9 F9 1547, kI jI 1546, d1 c1
1544, w4 v4 1544, ZG YG 1544, k2 j2 1544, RG QG 1544, WH GH 1542, RE QE 1542,
pG oG 1542, JE IE 1542, k6 j6 1541, LA KA 1541, YB WB 1541, U1 T1 1540, F8 E8
1539, S4 R4 1539, aF ZF 1538, QJ PJ 1538, W1 V1 1538, Y6 W6 1537, O1 N1 1536,
BI NI 1535, TE SE 1535, RH QH 1535, O4 N4 1535, L8 K8 1535, u4 t4 1534, JG IG
1534, cB bB 1534, FA EA 1534, HD GD 1532, N9 O9 1532, a6 Z6 1531, B4 A4 1531,
gB fB 1530, h1 g1 1529, aB ZB 1529, TA SA 1529, T8 S8 1528, S9 R9 1527, J8 I8
1526, TG SG 1526, B2 N2 1525, E9 D9 1524, g8 f8 1524, EJ DJ 1524, NA MA 1524,
GJ FJ 1524, m1 n1 1523, tH sH 1523, f1 e1 1523, VE UE 1523, U9 T9 1521, JA IA
1521, Y1 X1 1521, F3 E3 1520, eD TD 1520, cA aA 1519, ZE YE 1518, S1 R1 1518,
P6 O6 1518, e3 T3 1517, Y4 X4 1517, V6 U6 1517, NJ OJ 1516, PB OB 1516, gA fA
1514, I9 H9 1514, N8 M8 1513, VG UG 1512, VB UB 1512, m8 l8 1510, iB hB 1510,
mA lA 1508, mF lF 1507, dG cG 1507, V8 U8 1507, VA UA 1507, cF bF 1507, EH FH
1504, DA CA 1504, j1 i1 1503, D8 C8 1502, gH fH 1502, m7 l7 1501, dJ IJ 1498,
i8 h8 1496, kA jA 1494, f4 e4 1493, YH BH 1493, c7 b7 1488, iF hF 1487, H8 G8
1484, iA hA 1479, CH DH 1476, w1 v1 1475, HA GA 1473, VH LH 1472, tE sE 1472,
nH xH 1471, 3H vH 1469, VF UF 1467, k8 j8 1467, l4 k4 1466, cH hH 1464, l1 k1
1464, aH TH 1460, Q8 R8 1459, YH DH 1458, QA RA 1454, TF SF 1453, rH wH 1452,
SJ RJ 1451, PH UH 1451, tG sG 1448, n4 m4 1445, 4H I5 1444, d9 I9 1444, AH BH
1443, lH kH 1442, pH oH 1441, NH MH 1438, vG uG 1436, vE uE 1436, a8 c8 1432,
eH dH 1428, b4 S4 1428, V7 U7 1421, JH IH 1415, vH uH 1415, T7 S7 1414, B7 L7
1412, i7 h7 1403, g7 f7 1400, qH mH 1391, TH SH 1391, bH IC 1390, KH OH 1386,
BF LF 1386, gF fF 1376, 3H LI 1361, b8 N8 1348, b1 S1 1347, NJ PJ 1342, YH XH
1339, 1H zH 1334, XB TB 1329, aH L2 1310, X6 T6 1309, N9 P9 1300, 1H kH 1292,
XI VI 1282, X2 V2 1281, iE gE 1274, bA NA 1273, YH IH 1267, QA OA 1258, 34 H2
1251, T9 R9 1250, Q8 O8 1248, X7 Y7 1247, uG sG 1238, QE SE 1237, kE mE 1233,
k1 m1 1229, 31 HI 1228, L9 J9 1225, gG iG 1225, XF YF 1223, j7 l7 1220, X2 B2
1218, QG SG 1215, l8 j8 1212, uE sE 1209, IE KE 1206, B6 N6 1202, d7 b7 1202,
h7 f7 1199, XI BI 1199, lF jF 1196, IG KG 1195, p1 r1 1190, W8 Y8 1189, KD ID
1188, BB aH 1186, jA lA 1185, g1 i1 1184, B6 3H 1183, YA WA 1182, U6 S6 1182,
JJ LJ 1182, mG kG 1181, f8 h8 1181, SB UB 1179, UE WE 1178, RJ TJ 1173, I8 G8
1171, hF fF 1169, XF BF 1169, GE EE 1168, UA SA 1165, hA fA 1162, OE ME 1161,
X6 B6 1159, XJ VJ 1158, U7 S7 1157, U8 S8 1157, GA IA 1157, N4 P4 1155, Q6 O6
1155, X1 V1 1154, T4 R4 1153, bF dF 1153, D9 B9 1152, eE cE 1152, EA CA 1150,
X4 V4 1149, BJ DJ 1148, ZF WF 1147, F9 H9 1146, g4 i4 1143, K3 I3 1142, 1H hH
1141, GG EG 1140, o1 n1 1140, LH XH 1139, X7 B7 1139, Z6 W6 1139, E3 G3 1139,
nH zH 1139, XB BB 1137, N1 P1 1136, b4 O4 1134, o1 f1 1133, zG GG 1131, eG cG
1131, OG MG 1131, YH FH 1131, QB OB 1129, aE YE 1129, T1 R1 1127, M8 K8 1127,
WB ZB 1127, MA KA 1126, oE qE 1126, UF SF 1126, oG qG 1125, zE GE 1123, X7 T7
1122, xE wE 1121, E8 C8 1121, XF TF 1120, WG UG 1119, X9 V9 1118, 1H fH 1115,
h6 f6 1115, A4 C4 1112, b1 O1 1111, K4 I4 1111, Z7 W7 1111, YH UH 1107, lB jB
1106, l6 j6 1106, m4 k4 1102, c1 e1 1101, p4 r4 1096, YG aG 1095, QF OF 1093,
CG AG 1093, bA MA 1090, K1 I1 1090, CE AE 1089, 1H wH 1089, Q7 O7 1089, x1 z1
1088, HJ FJ 1087, b8 M8 1084, fB hB 1082, a8 d8 1079, A3 C3 1077, d6 b6 1077,
34 LC 1076, xG wG 1076, DF GF 1075, ED GD 1075, c4 e4 1075, 31 L5 1073, zE pH
1072, G6 I6 1070, A1 C1 1068, dJ MJ 1068, 1H dH 1068, b1 W1 1066, GB IB 1066,
JF MF 1063, KB EB 1061, X6 P6 1061, zG NH 1059, U2 S2 1057, J7 M7 1057, UI SI
1056, o4 f4 1054, XB PB 1049, d9 M9 1049, dB bB 1047, Q2 O2 1045, K6 E6 1040,
l2 j2 1036, UD WD 1035, z4 x4 1035, aA dA 1034, Z2 W2 1032, t4 v4 1031, SD QD
1030, ZI WI 1028, Q3 S3 1026, W3 U3 1024, h2 f2 1023, I2 G2 1022, jI lI 1021,
II GI 1020, dI bI 1019, XF FF 1015, hI fI 1011, b2 d2 1010, b4 W4 1010, d9 E9
1007, BF JF 1005, CD AD 1003, CI MI 1002, E4 G4 1001, XI aI 1000, X2 a2 1000,
b8 KH 999, v1 t1 997, C2 M2 997, X7 F7 997, QI OI 996, MD OD 996, dJ EJ 996,
XF DF 995, O3 M3 994, C7 M7 992, X6 H6 991, CF MF 990, E1 G1 989, XB HB 989,
E7 K7 978, eD W2 974, KF EF 973, bA mH 969, XF PF 968, e3 WI 966, B7 J7 958,
IF GF 957, XB FB 957, C6 M6 957, X2 D2 955, BI LI 952, I7 G7 951, XI HI 951,
3H uH 951, aH SH 951, X2 H2 950, X6 F6 949, XI DI 948, X2 R2 948, EI KI 947,
X7 D7 946, E2 K2 939, B2 L2 935, bA 4H 934, XI RI 932, YH QH 931, J2 2H 930,
CB MB 929, qH xH 929, 1H 2H 929, 1H sH 925, JI ZH 919, YH ZH 908, B2 2H 898,
b8 bH 898, BI ZH 890, 34 OD 889, AJ OJ 888, X7 P7 887, 31 O3 886, nE kE 883,
o4 n4 881, XB YB 878, o4 j4 876, 1H mH 876, YH KH 874, YH SH 873, 1H uH 871,
nG kG 865, X6 Y6 861, BB NB 849, o1 j1 846, bA JA 843, WH DH 843, eD PD 842,
lE mE 840, yH dH 840, tE uE 838, b8 J8 836, yG wG 834, vE sE 833, e3 P3 831,
B8 A8 831, 24 u4 830, tG uG 826, vG sG 824, gB hB 818, 21 u1 818, rE oE 817,
yE wE 817, 4H NA 815, l1 m1 814, j1 g1 813, zG yG 811, hG iG 811, bH N8 809,
ZE aE 805, zE yE 805, BA AA 803, hE iE 802, 34 V2 798, zE DE 797, j4 g4 796,
Y9 V9 796, g6 h6 796, 31 VI 793, ZG aG 792, l4 m4 792, Q8 P8 791, 31 UI 789,
lG mG 789, M4 F4 789, 34 U2 788, zG DG 786, rG oG 785, QA PA 784, dE eE 781,
jE gE 779, iB fB 777, pE qE 777, M1 K1 774, jG gG 773, g7 h7 772, M1 F1 772,
A2 Y2 771, AI YI 771, M4 K4 771, RF OF 770, NE OE 770, AF VF 769, YJ VJ 769,
k7 l7 768, mF jF 767, G9 H9 767, RB OB 767, LE IE 765, R6 O6 765, R7 O7 764,
c8 d8 764, 24 s4 764, CJ DJ 764, dG eG 763, 21 s1 762, bE YE 762, GJ HJ 762,
lG oG 761, PJ OJ 761, gF hF 760, AB RB 760, O9 P9 759, bG YG 759, gA hA 759,
A6 R6 757, BE CE 756, SJ TJ 756, n4 k4 754, A9 N9 753, g8 h8 753, XA YA 753,
PE ME 753, pG qG 752, C9 D9 751, h1 i1 751, XE UE 751, V7 S7 751, kF lF 750,
NG OG 750, A7 V7 749, d6 c6 749, i6 f6 748, VH OH 747, X8 Y8 747, NH JH 747,
BB LB 747, AI eI 746, S9 T9 744, lH pH 744, PG MG 743, xG rG 743, EJ BJ 743,
E9 B9 742, VE WE 742, a8 e8 742, f4 c4 740, LG IG 740, P6 Q6 739, kA lA 738,
kB lB 738, PB QB 737, YB ZB 737, U9 R9 737, V6 S6 736, aA eA 735, AJ YJ 735,
VG WG 735, K5 Y4 735, TA UA 732, B6 L6 732, A9 Y9 732, Y6 Z6 732, RE SE 731,
m7 j7 731, Q1 N1 730, k1 n1 730, M1 A1 729, UJ RJ 728, fE cE 728, BG CG 728,
T8 U8 728, O4 P4 727, LA MA 727, W9 X9 727, dB cB 727, k8 l8 726, AJ NJ 726,
JE KE 726, RG SG 725, Q4 N4 725, 21 11 725, Y1 V1 725, X2 F2 725, XI FI 725,
AF cF 724, WJ XJ 724, BF NF 723, T6 U6 723, W1 X1 723, L8 M8 722, B2 J2 721,
CH BH 721, W4 X4 721, YD KD 720, A7 c7 720, ZA WA 720, TE QE 719, fG cG 719,
Y4 V4 718, k6 l6 717, BI JI 717, VA SA 717, BF JH 716, VB SB 716, B7 N7 716,
I9 F9 715, RA OA 715, R8 O8 715, PF QF 714, J8 G8 714, B7 lH 714, JA GA 714,
Y3 K3 713, TB UB 712, B8 Q8 712, e7 b7 712, BA QA 712, S1 T1 712, H8 I8 711,
c7 d7 711, 21 q1 711, TG QG 711, HA IA 709, O1 P1 709, NJ WJ 709, JG KG 708,
Z8 W8 708, KJ LJ 707, FE GE 706, P7 Q7 706, i8 f8 705, FA CA 705, Y3 D3 704,
V8 S8 704, bA oH 704, YD DD 703, 24 14 703, m8 j8 703, M4 A4 703, d9 W6 702,
S4 T4 700, MJ JJ 700, F8 C8 700, M9 J9 700, K9 L9 699, tH wH 697, AA mA 697,
FB KB 697, NA KA 697, A8 m8 696, KC Y1 696, F6 K6 696, C5 A5 696, EH DH 695,
i7 f7 695, N8 K8 695, xE rE 695, eF bF 695, iA fA 694, cF dF 693, AB kB 693,
B7 K7 692, A2 e2 692, U1 R1 692, dJ WB 692, A6 k6 691, RH UH 690, a6 W6 690,
aB WB 690, s1 z1 690, U4 R4 690, gH dH 690, f1 c1 689, YH RH 689, d4 g4 689,
N9 W9 688, N9 Q9 688, M4 D4 688, FG GG 687, mA jA 687, eH hH 686, lH jH 685,
GB JB 684, M4 B4 684, G6 J6 683, YF ZF 683, M1 D1 683, M1 B1 681, PH SH 680,
YD JD 680, lE oE 679, iH kH 679, QA VA 679, JH HH 679, iF fF 678, aF WF 678,
GH IH 678, rH uH 677, s4 z4 675, NJ QJ 674, cG aG 673, A2 c2 673, Y3 J3 673,
wE bE 673, 1H tH 673, wG bG 672, H1 C1 672, J3 A3 672, a7 W7 671, M4 L4 671,
AI cI 670, D7 G7 669, y4 p4 669, wG jG 668, wE jE 667, t4 r4 667, 24 y4 667,
y1 p1 667, VG MG 667, VH GH 666, Q8 V8 666, ZF OF 666, JD AD 665, mH oH 665,
3H QH 665, iH xH 664, cH fH 664, b8 MH 664, DD KD 663, BF KF 663, B6 I6 661,
BI MI 660, AH FH 660, F2 C2 660, BB IB 659, pG sG 659, FI CI 658, l1 c1 657,
aH sH 656, a8 k8 656, aA kA 656, I1 G1 656, I3 G3 655, AJ QJ 654, M1 J1 654,
XF HF 654, 24 q4 654, DB GB 653, eD XD 653, H4 C4 653, 3H K5 652, D6 G6 652,
M1 L1 651, KH MH 651, 21 y1 651, XB DB 651, f8 d8 650, Y7 Z7 650, B2 M2 649,
tG kG 649, X6 D6 648, l4 c4 648, VE ME 648, X7 H7 647, T7 U7 647, e3 X3 647,
p1 z1 646, yG VG 646, p4 z4 646, nE uE 644, tE kE 644, D8 E8 643, d1 g1 641,
D8 G8 640, YD BD 640, mF hF 640, aH KC 639, ZG cG 638, aE cE 638, YD LD 638,
Y3 B3 637, yE VE 637, M4 J4 637, G4 I4 637, HB EB 637, ZE cE 636, DA GA 636,
FD ID 636, DA EA 635, pE sE 635, H6 E6 635, FF CF 635, A9 W9 635, d6 i6 634,
S9 V9 634, AA gA 633, gA jA 633, L1 G1 633, B3 E3 632, BA PA 632, f1 m1 632,
TF UF 631, xE nE 630, f4 m4 630, H2 E2 629, P8 S8 629, FB CB 629, HI EI 628,
J1 A1 628, KF CF 628, xG uG 628, A9 Q9 628, Y3 L3 627, H7 E7 627, L4 G4 627,
J4 A4 627, iE YE 626, CA MA 626, fG aG 625, g8 j8 624, NH LH 624, vH sH 624,
F6 C6 623, fE aE 623, A8 i8 623, A8 g8 622, h4 k4 622, AF gF 622, F7 C7 622,
JE AE 621, E9 L9 621, cB fB 621, m8 h8 621, N6 K6 621, N7 K7 621, NF KF 620,
YG iG 619, O1 R1 619, C8 M8 618, AI iI 618, kE uE 618, A2 i2 618, xE uE 617,
s1 p1 617, F3 I3 617, h1 k1 617, Q9 X9 617, AJ WJ 617, IJ DJ 617, EJ LJ 617,
B8 P8 616, i8 d8 616, U9 P9 616, BA VA 616, JB MB 616, xG lG 615, O4 R4 615,
wG ZG 615, dJ DJ 614, HF EF 614, AA iA 614, fA dA 614, D2 G2 614, pH nH 613,
TH QH 613, A7 g7 613, nG uG 613, DI GI 613, eF lF 613, PA SA 612, xG nG 612,
iA dA 611, LD GD 611, NI ZH 611, wE ZE 611, J6 M6 611, N2 2H 611, JG AG 610,
hE YE 610, m7 h7 609, B1 E1 609, L3 G3 608, dB iB 608, BD ED 608, NB KB 607,
D4 K4 607, VF QF 607, yE XE 607, xE vE 607, B8 V8 607, bG iG 607, ID GD 607,
mA hA 607, c6 f6 606, V7 Q7 606, g2 j2 606, QE OE 605, M4 H4 605, LI II 605,
D1 K1 605, AB mB 605, I9 D9 605, dE gE 604, a6 U6 604, dG gG 604, L2 I2 604,
N8 I8 604, QG OG 603, aB UB 602, J8 E8 602, YJ TJ 602, LB IB 602, JA EA 602,
Y9 T9 601, k7 b7 601, F4 I4 600, L7 I7 600, vG qG 600, L6 I6 599, A6 g6 599,
i1 n1 599, T4 V4 599, bA IA 599, gF jF 599, R9 P9 599, AB gB 598, UJ PJ 598,
Y3 H3 597, t1 r1 597, D3 K3 597, T7 W7 597, WH BH 597, gG eG 596, d6 f6 596,
MG WG 596, LF IF 595, aF UF 595, QJ XJ 595, F1 I1 595, LE GE 595, PF SF 595,
e7 l7 595, A9 O9 594, b8 I8 594, P7 S7 594, N2 K2 594, bE iE 594, 11 v1 594,
kG uG 593, BB vH 593, j4 e4 593, LG GG 593, jG eG 592, AJ UJ 591, vE qE 591,
A6 h6 591, x1 v1 590, 24 w4 590, M1 H1 590, 21 w1 590, NI KI 589, ME WE 588,
eE gE 588, JI MI 588, AF kF 588, J2 M2 588, H3 C3 588, c4 m4 587, WF UF 586,
VB QB 585, q4 t4 584, 21 x1 584, NA IA 584, R6 Z6 584, j1 e1 584, A7 k7 584,
HA KA 584, i2 d2 584, AB dB 584, P6 S6 584, YD HD 583, bH LG 583, HG CG 583,
hG YG 583, VJ TJ 583, TG OG 583, w4 r4 583, FA MA 583, B4 E4 583, Y4 T4 583,
A6 m6 582, yG XG 582, l2 b2 582, TB WB 582, O7 Z7 582, RB ZB 582, dJ AJ 582,
d9 D9 581, H8 K8 581, q1 t1 581, PB SB 581, S4 V4 581, dB fB 581, xG vG 580,
HE CE 580, B2 rH 580, v4 x4 580, YB OB 580, U7 W7 580, A6 d6 579, jI hI 579,
4H LE 579, K3 A3 579, pH zH 579, MJ HJ 579, gI jI 579, C7 K7 579, F8 M8 579,
A2 g2 578, W4 N4 578, Y6 O6 578, T1 V1 578, TD OD 578, yH hH 577, Y1 T1 577,
V6 Q6 577, kF bF 577, 34 Y8 576, AA eA 576, W1 N1 576, S1 V1 575, XA OA 575,
iI dI 575, BA RA 574, m6 h6 574, HD CD 574, c8 f8 574, B8 R8 573, MF GF 573,
j2 h2 573, BI PH 573, TE OE 573, cA fA 573, m2 h2 572, w4 t4 572, T3 O3 572,
fF dF 572, n4 i4 572, aI UI 572, RA YA 572, R7 Z7 572, yE RE 572, SJ VJ 572,
c1 m1 572, jE eE 572, NH XH 572, G9 J9 571, T6 W6 571, C9 F9 571, a2 U2 571,
CJ FJ 571, X8 O8 571, O8 Y8 570, R8 Y8 570, KB CB 569, M9 H9 569, cF fF 569,
XG SG 569, rG mG 569, mI hI 569, K6 C6 568, gB jB 568, i7 d7 568, AI mI 568,
kB bB 568, yG RG 568, xE lE 567, RG UG 567, aA lA 567, k6 b6 566, B6 TH 566,
AB hB 566, 31 YA 566, KJ BJ 566, KD AD 565, AF lF 565, 14 v4 565, KG AG 564,
PG WG 564, NE QE 564, YF OF 564, U4 P4 564, IF EF 564, 24 x4 563, K9 B9 563,
R2 Z2 563, U1 P1 563, TI WI 563, XE SE 563, VI QI 563, TF WF 563, bF lF 562,
G7 M7 562, c7 f7 562, wE hE 562, AF bF 562, DG KG 561, Y7 O7 560, AJ XJ 560,
B8 U8 560, eA lA 560, GJ JJ 560, RJ PJ 559, yE OE 559, dI fI 559, A9 X9 559,
BG EG 559, RE UE 559, AB cB 558, BA UA 558, A2 m2 558, xG kG 558, A2 d2 558,
e8 l8 557, V2 Q2 557, eI lI 557, R3 U3 557, AI gI 557, T2 W2 557, qH zH 556,
A6 i6 556, wG iG 556, a8 l8 556, B9 L9 556, T8 W8 556, a7 U7 555, b7 l7 555,
DE KE 555, yE UE 555, k2 b2 555, TA WA 554, PE WE 554, g7 j7 554, OH XH 554,
bI lI 554, FE IE 554, g1 e1 554, PD WD 554, P3 W3 554, M2 G2 554, rE mE 553,
XD SD 553, yE ME 553, w1 r1 553, wE iE 553, yE PE 553, g6 j6 553, X3 S3 553,
h6 j6 552, Q4 X4 552, yG PG 552, A6 c6 552, RD UD 552, mB hB 551, T9 V9 551,
xG tG 551, xE mE 551, UD SD 551, GI MI 550, AI fI 549, yG OG 549, FG IG 549,
f2 d2 549, e2 l2 549, S3 U3 549, u4 x4 549, RI ZI 549, I7 E7 548, A7 j7 548,
BJ LJ 548, Q1 X1 548, B7 cH 548, AB jB 547, RF ZF 547, A9 U9 547, kI bI 547,
A8 e8 547, BE EE 547, A7 b7 546, yG UG 546, CD ED 545, 14 x4 545, P2 S2 545,
E3 C3 545, A2 f2 545, OA YA 545, AA cA 544, iF dF 544, oG mG 544, XF AF 544,
A8 a8 543, NG QG 543, BA ZA 543, AI dI 543, I6 E6 542, VD MD 541, Y2 O2 541,
IB EB 541, ND QD 541, BI sH 540, yG JG 540, wG hG 539, A7 m7 539, B8 Z8 539,
PI SI 539, O9 R9 539, yE JE 539, DJ FJ 538, A6 l6 538, N3 Q3 537, LA CA 537,
c2 f2 537, e6 l6 537, y1 z1 537, yG MG 537, V3 M3 536, xG mG 536, oE mE 535,
hB jB 535, XB EB 534, YD FD 534, GB MB 534, u1 x1 533, AB iB 533, X6 E6 533,
AI kI 533, T7 H7 533, AB lB 532, A8 k8 532, B6 G6 532, eB lB 532, g4 e4 532,
AF eF 532, cI fI 532, xE kE 532, ZA UA 531, AF jF 531, X7 A7 531, A8 l8 531,
Z8 U8 530, B2 QH 530, B7 E7 530, sG qG 530, hF jF 530, Y3 F3 529, o1 i1 528,
YI OI 528, d9 A9 527, AA lA 527, RJ OJ 527, AF mF 527, AI bI 527, xE tE 526,
B8 X8 526, BA DA 526, sE qE 525, L8 C8 525, G6 M6 525, AA aA 524, AA kA 524,
XI GI 524, w1 t1 524, 11 x1 524, BA XA 523, IE GE 523, F9 D9 522, AJ VJ 522,
CG EG 522, 4H qH 522, M3 W3 521, Q6 S6 521, YD AD 521, W8 U8 520, A9 V9 520,
C2 K2 520, j7 h7 520, TF HF 519, BF AH 519, 21 p1 519, wE fE 519, yE NE 518,
E2 I2 518, II EI 518, BF EF 518, UI WI 517, wG fG 517, U2 W2 517, UA WA 517,
O6 Z6 516, bH MH 516, Y3 A3 516, bH OH 516, yE WE 516, BB GB 515, AF iF 515,
s4 p4 515, OB ZB 514, B8 T8 514, aH X1 513, BA TA 513, 24 z4 513, A6 j6 512,
KE AE 512, W6 U6 512, A2 k2 512, X6 A6 511, 1H FG 511, 4H oH 511, SB QB 511,
A7 e7 511, d7 f7 510, o4 i4 510, XB AB 509, L3 I3 509, B8 D8 508, 3H X4 508,
R1 P1 508, A2 b2 508, S2 Q2 508, OI ZI 507, WB UB 507, X2 G2 507, MD WD 506,
A4 K4 505, IG GG 505, bA I5 505, d4 e4 504, K1 A1 504, A6 e6 504, a2 F2 503,
A8 c8 503, YH FE 502, yG NG 502, A7 l7 501, M4 UA 501, R4 P4 501, AF dF 501,
O2 Z2 500, o1 SB 500, b8 IC 500, SI QI 500, yG WG 498, M4 I4 498, CI KI 497,
aI FI 497, b4 U4 497, y4 z4 496, 31 EI 496, 34 E2 495, AB eB 495, M1 I1 494,
d1 e1 494, aH vH 494, 4H zH 493, GA EA 493, JJ HJ 491, 21 z1 491, yE FE 491,
N9 X9 490, jA hA 490, A7 d7 490, l6 b6 490, J9 H9 489, F3 G3 488, CE EE 488,
AJ SJ 488, wE gE 488, 24 r4 487, B8 O8 487, yG FG 487, bH XH 487, FD GD 486,
YD eD 486, 3H TH 485, yE TE 485, wE dE 485, BA OA 484, b8 L8 484, 1H vH 484,
1H cH 484, wE YE 483, lB bB 483, cA dA 483, bA LA 482, xG pG 482, yG TG 482,
YH TH 481, B8 S8 480, LD ID 480, xE sE 479, A8 f8 479, YH AH 479, QD OD 478,
BA SA 477, A6 f6 477, b1 U1 476, A9 S9 475, AF fF 475, XB aB 475, zG CG 473,
wG dG 473, o4 S6 472, 1H 3H 472, xG sG 472, X7 C7 472, xE pE 472, wG gG 472,
LI ZH 471, wG YG 470, zE CE 469, Q3 O3 469, w4 dA 469, H1 E1 469, N4 X4 468,
j8 h8 468, X6 a6 468, YH aH 467, XF CF 466, L2 2H 466, N1 X1 466, C1 E1 465,
AA fA 465, Y3 e3 464, E4 C4 463, eD ND 463, b1 KB 462, NJ XJ 462, 21 r1 462,
QF SF 462, X2 P2 462, b8 JF 461, e3 N3 460, bA J7 460, 24 p4 460, G8 E8 459,
3H L6 458, A7 i7 458, Y3 G3 457, q1 r1 457, aH LB 456, XF OF 454, h4 i4 453,
M4 C4 453, I8 K8 453, KA IA 452, u1 v1 452, u4 v4 451, PF FF 450, JC 2H 450,
J5 ZH 450, X7 O7 449, YD CD 449, A8 h8 449, XI PI 448, Y3 C3 448, b4 K6 447,
YD GD 447, A9 P9 446, S7 Q7 446, UE SE 446, SG UG 445, HD ED 445, A8 j8 444,
P6 D6 443, PB DB 443, M1 U8 443, q4 r4 442, mB jB 442, e6 b6 442, BI CI 440,
XI AI 440, X2 A2 440, M1 C1 440, AJ PJ 439, eB bB 439, J3 K3 439, 21 v1 438,
BA LA 438, AA hA 438, B8 L8 437, F1 G1 437, bA BA 436, m6 j6 436, mI jI 435,
B2 C2 434, H3 E3 433, D1 A1 433, o4 m4 432, m2 j2 432, A2 h2 431, b8 B8 431,
A7 f7 430, VF SF 430, D4 A4 429, 3H BI 428, M1 E1 425, AI hI 424, Q8 S8 423,
i2 f2 423, 24 g7 423, V3 W3 422, AA jA 420, X7 R7 419, B2 K2 418, cI dI 418,
XF RF 418, JD KD 418, AF aF 417, BI KI 417, AB fB 417, iI fI 417, BD CD 416,
G9 Y9 416, R2 O2 416, ND OD 416, RI OI 415, YJ GJ 415, zG KG 415, AJ RJ 414,
c2 d2 413, QA SA 413, 1H gH 413, 34 S2 413, aH QH 412, DF TF 412, L4 I4 412,
N3 O3 412, C9 U9 412, 31 SI 411, VD WD 411, eI bI 411, e3 V3 411, B1 C1 410,
gI hI 410, YH EH 409, a2 W2 409, eD VD 408, AJ TJ 408, F4 G4 408, aI WI 407,
eD WD 407, M4 E4 406, aH B2 406, YD ID 406, Y3 I3 406, XI QI 405, iH DH 405,
24 v4 405, dJ EB 404, zE KE 404, L1 I1 404, 3H sH 404, VF cF 404, X2 Q2 404,
P7 F7 404, d9 E6 404, XB WB 403, A7 a7 403, e3 W3 403, B6 rH 403, YI ZI 402,
GH dH 402, k1 i1 402, dJ HJ 402, e2 b2 402, 21 t1 401, CJ UJ 401, k4 i4 401,
BB PH 401, V2 S2 401, BE TE 400, wG aG 400, b4 R4 399, oH zH 399, zE FE 399,
MH XH 399, zG FG 399, 21 gF 398, g2 h2 398, d9 H9 397, T3 Q3 397, xG qG 396,
wE aE 396, Y2 Z2 396, TD QD 396, BG TG 396, T2 U2 395, TI UI 395, P2 Q2 394,
c7 V7 394, PD MD 393, P3 M3 393, VI SI 392, aH BI 392, b1 R1 392, hG nG 391,
YF FF 391, Y6 H6 391, k2 l2 391, PI QI 391, T7 D7 391, A9 R9 390, d9 T6 390,
M4 G4 390, 3H B2 389, YB HB 388, Y7 F7 388, TA eA 388, T8 e8 387, A9 K9 387,
q4 h7 387, N8 MH 386, 24 t4 386, DE AE 385, X6 W6 385, XG UG 385, D3 A3 385,
XA iA 384, dJ TB 384, BB DB 384, DD AD 384, ZG rG 384, H4 E4 383, L7 E7 383,
RD SD 382, e3 aI 382, R3 S3 382, M1 G1 382, B6 D6 381, eD a2 381, bA HA 381,
q1 hF 380, B4 C4 380, AJ KJ 380, B3 C3 380, BI FI 380, AI lI 379, B2 F2 379,
i8 X8 378, dG vG 378, b8 H8 377, l8 OD 377, A2 l2 377, kI lI 376, A2 T2 376,
HE EE 375, LF EF 375, AI TI 375, BF HF 374, V2 D2 372, VI DI 372, zE I5 372,
VG bG 372, vE dE 372, lA O3 371, A9 T9 371, 1H lH 371, DG AG 371, 1H UH 371,
P2 i2 371, YH wH 371, iI PI 371, YH JH 370, AI jI 370, J1 K1 369, IJ FJ 369,
A6 V6 368, NA oH 367, AB VB 367, zG IC 367, hE nE 366, rE ZE 366, N6 C6 365,
BF IF 365, TB HB 365, XD UD 365, B7 I7 364, X3 U3 364, T6 H6 363, J4 K4 363,
HF IF 363, LB EB 362, kB RB 362, GJ UJ 361, R6 k6 359, VE bE 359, D6 M6 358,
A9 G9 358, 24 V7 358, H2 I2 358, J7 G7 358, xE qE 358, HI II 357, H7 I7 357,
HG EG 357, L6 E6 355, JF GF 355, NB CB 352, DB MB 351, xG oG 351, a2 H2 351,
o1 m1 351, DF MF 351, gH UH 351, aI HI 350, JI GI 350, RF kF 350, F2 K2 349,
AJ GJ 349, TD U2 349, LD RD 349, J2 G2 349, B7 H7 349, FI KI 348, N7 C7 348,
3H SH 347, wG cG 346, aH uH 346, zE nH 345, L2 E2 344, LI EI 344, zG LH 344,
21 VF 343, I5 nH 343, A2 j2 343, I5 NA 343, EH wH 343, Y3 E3 342, NI CI 342,
L3 R3 342, wE cE 341, N2 C2 340, 3H J5 339, D7 M7 339, G9 U9 336, DD VD 336,
d9 C9 336, D2 M2 335, D3 V3 335, NF CF 335, IC N8 334, DI MI 334, Q2 EF 334,
R7 k7 334, XF ZF 333, aH JC 333, T3 UI 333, fE NE 333, SG ZH 330, FF KF 330,
NG fG 329, b1 Y1 329, H6 I6 328, wE eE 328, HB IB 327, A6 b6 327, SE 2H 325,
F7 K7 325, 1H oH 324, YD ED 324, b4 Y4 324, 31 E7 324, YH MH 324, wG eG 323,
AB bB 322, IC LH 322, B6 M6 321, XE FE 320, dJ CJ 320, QI E7 320, BB MB 320,
PA mA 319, XG FG 318, 34 EF 317, JE PE 314, xE oE 314, 1H 4H 313, JG PG 313,
C3 G4 313, e3 O3 311, P8 m8 310, 1H xH 310, 31 T3 310, zG EG 309, 34 TD 309,
dJ FB 309, YH bH 309, dH kH 309, IC J8 308, W1 NB 307, I5 JA 307, eD OD 306,
A8 d8 306, X7 Z7 306, IH DH 305, zG BG 305, W4 N6 304, zE BE 302, PB FB 301  

> select /1H

6837 atoms, 6976 bonds, 1 pseudobond, 2 models selected  

> select /1H,YH

13917 atoms, 14208 bonds, 2 pseudobonds, 2 models selected  

> select ~sel

999481 atoms, 1022413 bonds, 1 model selected  

> hide sel cartoons

> ui tool show "Show Sequence Viewer"

> sequence chain /YH /1H

Alignment identifier is 1  

> select /1H,YH,AH,BH,CH,DH,EH,FH

21573 atoms, 21977 bonds, 2 pseudobonds, 2 models selected  

> show sel cartoons

> select /1H,YH,AH,BH,CH,DH,EH,FH,GH,HH

24098 atoms, 24538 bonds, 2 pseudobonds, 2 models selected  

> show sel cartoons

> select /1H,YH,AH,BH,CH,DH,EH,FH,GH,HH,IH,JH,KH,LH,MH

30610 atoms, 31149 bonds, 2 pseudobonds, 2 models selected  

> show sel cartoons

> select /1H,YH,AH,BH,CH,DH,EH,FH,GH,HH,IH,JH,KH,LH,MH,NH

31916 atoms, 32475 bonds, 2 pseudobonds, 2 models selected  

> show sel cartoons

> select /OH

1300 atoms, 1319 bonds, 1 model selected  

> show sel cartoons

> select /PH

1306 atoms, 1326 bonds, 1 model selected  

> show sel cartoons

> hide sel cartoons

> select /QH

1301 atoms, 1321 bonds, 1 model selected  

> show sel cartoons

> hide sel cartoons

> select /VH

1341 atoms, 1365 bonds, 1 model selected  

> show sel cartoons

> select /WH

1457 atoms, 1480 bonds, 1 model selected  

> show sel cartoons

> select /1H

6837 atoms, 6976 bonds, 1 pseudobond, 2 models selected  

> select /YH

7080 atoms, 7232 bonds, 1 pseudobond, 2 models selected  

> save "/Users/drornoy/Documents/Manuscripts/kaihong/BDFP YaNan/New
> Folder/Core PBM purpureum 6KGX.cxs"

[Errno 20] Not a directory: '/Users/drornoy/Documents/Manuscripts/kaihong/BDFP
YaNan/New Folder'  

> save "/Users/drornoy/Documents/Manuscripts/kaihong/Longest Arm 2020/ChimeraX
> sessions/Apc core purpureum 6KGX.cxs"

opened ChimeraX session  

> ui tool show "Model Panel"

> ui tool show "Basic Actions"

> select /YH

7080 atoms, 7232 bonds, 1 pseudobond, 848 residues, 2 models selected  

> select /XH

720 atoms, 732 bonds, 92 residues, 1 model selected  

> select /YH

7080 atoms, 7232 bonds, 1 pseudobond, 848 residues, 2 models selected  

> select /YH

7080 atoms, 7232 bonds, 1 pseudobond, 848 residues, 2 models selected  

> select /WH

1457 atoms, 1480 bonds, 174 residues, 1 model selected  

> select /YH

7080 atoms, 7232 bonds, 1 pseudobond, 848 residues, 2 models selected  

> show /XH target abp

> hide /XH target abp

> show /XH target abp

> hide /XH target abp

> color /XH #b3b3b3 target c

> show /YH target c

> select /YH

7080 atoms, 7232 bonds, 1 pseudobond, 848 residues, 2 models selected  

> color /YH #999999 target abp

> ui tool show Toolbar

> ui tool show "Side View"

> ui tool show Updates

> select /AH,BH,CH,DH,EH,FH,GH,HH,IH,JH,KH,LH,MH,NH,OH,WH

20756 atoms, 21066 bonds, 2594 residues, 1 model selected  

> hide sel cartoons

> select /AH,BH,CH,DH,EH,FH,GH,HH,IH,JH,KH,LH,MH,NH,OH,vH,WH

22062 atoms, 22392 bonds, 2755 residues, 1 model selected  

> show sel cartoons

> select /AH,BH,CH,DH,EH,FH,GH,HH,IH,JH,KH,LH,MH,NH,OH,VH,WH

22097 atoms, 22431 bonds, 2755 residues, 1 model selected  

> save "/Users/drornoy/Documents/Manuscripts/kaihong/Longest Arm 2020/ChimeraX
> sessions/Apc core purpureum 6KGX.cxs"

opened ChimeraX session  

> ui tool show "Show Sequence Viewer"

> sequence chain /YH /1H

Alignment identifier is 1  

> ui tool show "Color Actions"

> color sel sky blue

> ui tool show "Side View"

> ui tool show "Color Actions"

> color sel forest green

> color sel yellow

> select /YH::CYC

Nothing selected  

> select /YH:90

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select /YH::CYC

Nothing selected  

> select /YH::HIS

Nothing selected  

> select /YH:HIS

40 atoms, 40 bonds, 4 residues, 1 model selected  

> select /YH:CYC

324 atoms, 336 bonds, 4 residues, 1 model selected  

> show sel target ab

> style sel sphere

Changed 324 atom styles  

> color sel byhetero

> select /1H:CYC

81 atoms, 84 bonds, 1 residue, 1 model selected  

> show sel target ab

> color sel byhetero

> select /1H:CYC

81 atoms, 84 bonds, 1 residue, 1 model selected  

> select /YH:CYC

324 atoms, 336 bonds, 4 residues, 1 model selected  

> color sel magenta

> color sel byhetero

> ui tool show "Basic Actions"

> select /XH

720 atoms, 732 bonds, 92 residues, 1 model selected  

> show sel cartoons

> color sel medium violet red

> select /YH

7080 atoms, 7232 bonds, 1 pseudobond, 848 residues, 2 models selected  

> color sel crimson

> select /VH

1341 atoms, 1365 bonds, 161 residues, 1 model selected  

> color sel tomato

> select /WH

1457 atoms, 1480 bonds, 174 residues, 1 model selected  

> color sel indian red

> color sel gold

> select /VH

1341 atoms, 1365 bonds, 161 residues, 1 model selected  

> color sel orange

> select /AH

1306 atoms, 1326 bonds, 161 residues, 1 model selected  

> select /AH,CH,EH

3918 atoms, 3978 bonds, 483 residues, 1 model selected  

> color sel medium orchid

> select /BH,DH,FH

3738 atoms, 3790 bonds, 484 residues, 1 model selected  

> color sel light pink

> select /GH,JH

2612 atoms, 2652 bonds, 322 residues, 1 model selected  

> color sel orchid

> color sel medium purple

> color sel pale violet red

> color sel medium purple

> color sel sky blue

> color sel deep sky blue

> select /HH,IH

2519 atoms, 2554 bonds, 323 residues, 1 model selected  

> color sel powder blue

> color sel light blue

> color sel light sky blue

> select /KH,MH

2606 atoms, 2646 bonds, 323 residues, 1 model selected  

> select /KH,NH

2612 atoms, 2652 bonds, 322 residues, 1 model selected  

> select /KH,NH,PH

3918 atoms, 3978 bonds, 483 residues, 1 model selected  

> select /KH,NH

2612 atoms, 2652 bonds, 322 residues, 1 model selected  

> color sel medium aquamarine

> select /LH,MH,OH

3900 atoms, 3958 bonds, 486 residues, 1 model selected  

> color sel pale turquoise

> color sel pale green

> save "/Users/drornoy/Documents/Manuscripts/kaihong/Longest Arm 2020/ChimeraX
> sessions/Apc core purpureum 6KGX.cxs"

> select /PH,RH,TH

3918 atoms, 3978 bonds, 483 residues, 1 model selected  

> show sel cartoons

> color sel pale violet red

> color sel hot pink

> color sel orchid

> color sel deep pink

> color sel pale violet red

> select /QH,SH,UH

3903 atoms, 3963 bonds, 486 residues, 1 model selected  

> show sel cartoons

> color sel light pink

> select /:CYC

Expected an objects specifier or a keyword  

> select :CYC

6984 atoms, 7344 bonds, 120 residues, 1 model selected  

> color sel medium violet red

> color sel purple

> color sel deep pink

> color sel byhetero

> select clear

> lighting flat

> graphics silhouettes false

> graphics silhouettes true

> lighting shadows true intensity 0.5

> lighting shadows false

> lighting shadows true

> lighting shadows false

> select /vH

1306 atoms, 1326 bonds, 161 residues, 1 model selected  

> hide sel cartoons

> select /*H

84302 atoms, 85749 bonds, 2 pseudobonds, 10510 residues, 2 models selected  

> select clear

> lighting shadows true

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting soft

> graphics silhouettes false

> graphics silhouettes true

> lighting full

> lighting shadows false

> lighting simple

> lighting soft

> lighting full

> lighting shadows false

> lighting soft

> lighting shadows true intensity 0.5

> lighting shadows false

> lighting full

> lighting shadows false

> lighting simple

> lighting simple

> save "/Users/drornoy/Documents/Manuscripts/kaihong/Longest Arm 2020/ChimeraX
> sessions/Apc core purpureum 6KGX.cxs"

> close session

> open 5v8k format mmcif fromDatabase pdb

5v8k title:  
Homodimeric reaction center of H. modesticaldum [more info...]  
  
Chain information for 5v8k #1  
---  
Chain | Description  
A | p800 reaction center core protein  
B | proteinsubunit pshX  
  
Non-standard residues in 5v8k #1  
---  
AOH — 8(1)-OH-Chlorophyll aF  
C4D — 4,4'-Diaponeurosporene
((4E,6E,8E,10E,12E,14E,16E,18E)-2,6,10,15,19,23-hexamethyltetracosa-2,4,6,8,10,12,14,16,18,22-decaene)  
CA — calcium ion  
DGG — 1-[glycerolylphosphonyl]-2-[8-(2-hexyl-
cyclopropyl)-octanal-1-yl]-3-[hexadecanal-1-yl]-glycerol  
GB0 — Bacteriochlorophyll g'  
GBF — Bacteriochlorophyll g  
LMT — dodecyl-β-D-maltoside  
SF4 — iron/sulfur cluster  
  
5v8k mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
  

> help help:user

> ui tool show "Basic Actions"

> select #1

13193 atoms, 13244 bonds, 139 pseudobonds, 902 residues, 2 models selected  

> sym #1 biomt

Molecule 5v8k has no biological unit info  

> sym #1 biomt

Molecule 5v8k has no biological unit info  

> sym

Missing or invalid "structures" argument: empty atom specifier  

> sym #1

5v8k mmCIF Assemblies  
---  
1| author_and_software_defined_assembly| 2 copies of chains A,B  
  

> sym #1 group biomt

Expected a keyword  

> sym #1 biomt

Molecule 5v8k has no biological unit info  




OpenGL version: 4.1 ATI-3.10.16
OpenGL renderer: AMD Radeon Pro 560X OpenGL Engine
OpenGL vendor: ATI Technologies Inc.Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro15,1
      Processor Name: 6-Core Intel Core i7
      Processor Speed: 2.2 GHz
      Number of Processors: 1
      Total Number of Cores: 6
      L2 Cache (per Core): 256 KB
      L3 Cache: 9 MB
      Hyper-Threading Technology: Enabled
      Memory: 16 GB
      Boot ROM Version: 1037.147.4.0.0 (iBridge: 17.16.16610.0.0,0)

Software:

    System Software Overview:

      System Version: macOS 10.15.6 (19G2021)
      Kernel Version: Darwin 19.6.0
      Time since boot: 10 days 2:49

Graphics/Displays:

    Intel UHD Graphics 630:

      Chipset Model: Intel UHD Graphics 630
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x3e9b
      Revision ID: 0x0000
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal: Supported, feature set macOS GPUFamily2 v1

    Radeon Pro 560X:

      Chipset Model: Radeon Pro 560X
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x8
      VRAM (Total): 4 GB
      Vendor: AMD (0x1002)
      Device ID: 0x67ef
      Revision ID: 0x00c2
      ROM Revision: 113-C980AL-075
      VBIOS Version: 113-C97501U-005
      EFI Driver Version: 01.A1.075
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal: Supported, feature set macOS GPUFamily2 v1
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2880 x 1800 Retina
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal

PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.9
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.0
    Babel: 2.8.0
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.6.20
    chardet: 3.0.4
    ChimeraX-AddH: 2.1.1
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.6.1
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.0.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.0
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.0
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-CommandLine: 1.1.3
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.1
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.0.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-DataFormats: 1.0
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.0
    ChimeraX-Hbonds: 2.0
    ChimeraX-Help: 1.0
    ChimeraX-HKCage: 1.0
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.0
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0
    ChimeraX-Label: 1.0
    ChimeraX-ListInfo: 1.0
    ChimeraX-Log: 1.1.1
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Map: 1.0.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.0
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 1.1
    ChimeraX-MDcrds: 2.0
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.0
    ChimeraX-mmCIF: 2.2
    ChimeraX-MMTF: 2.0
    ChimeraX-Modeller: 1.0
    ChimeraX-ModelPanel: 1.0
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.0
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0
    ChimeraX-OpenCommand: 1.2.1
    ChimeraX-PDB: 2.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0
    ChimeraX-PubChem: 2.0
    ChimeraX-Read-Pbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.0
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.2
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.0
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.0
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.0.4
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.0
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.0
    ChimeraX-ToolshedUtils: 1.0
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.2.3
    ChimeraX-uniprot: 2.0
    ChimeraX-ViewDockX: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.3
    comtypes: 1.1.7
    cxservices: 1.0
    cycler: 0.10.0
    Cython: 0.29.20
    decorator: 4.4.2
    distlib: 0.3.1
    docutils: 0.16
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 2.10.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.16
    imagecodecs: 2020.5.30
    imagecodecs-lite: 2020.1.31
    imagesize: 1.2.0
    ipykernel: 5.3.0
    ipython: 7.15.0
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.3
    jupyter-core: 4.6.3
    kiwisolver: 1.2.0
    line-profiler: 2.1.2
    lxml: 4.5.1
    MarkupSafe: 1.1.1
    matplotlib: 3.2.1
    msgpack: 1.0.0
    netifaces: 0.10.9
    networkx: 2.4
    numexpr: 2.7.1
    numpy: 1.18.5
    numpydoc: 1.0.0
    openvr: 1.12.501
    packaging: 20.4
    parso: 0.7.1
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 7.1.2
    pip: 20.2.2
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.7
    psutil: 5.7.0
    ptyprocess: 0.6.0
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.6.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.12.3
    PyQt5-sip: 4.19.19
    PyQtWebEngine-commercial: 5.12.1
    python-dateutil: 2.8.1
    pytz: 2020.1
    pyzmq: 19.0.2
    qtconsole: 4.7.4
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.4.1
    setuptools: 49.4.0
    sfftk-rw: 0.6.6.dev0
    six: 1.15.0
    snowballstemmer: 2.0.0
    sortedcontainers: 2.2.2
    Sphinx: 3.1.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 1.0.3
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.4
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2020.6.3
    tinyarray: 1.2.2
    tornado: 6.0.4
    traitlets: 5.0.4
    urllib3: 1.25.10
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.34.2

[pett]

Reported by Dror Noy

[Tom Goddard]

Only files in the old PDB format have BIOMT matrices. You used "open 5v8k" which fetches the mmCIF file, not the old PDB format file. The symmetry in mmCIF format files is given as assemblies. When you use "open 5v8k" you will see in the Log panel a table of assemblies, in this case one assembly named "1" and clicking on that link would show the assembly, or you could use the command sym #1 assembly 1. If you want to load the old PDB format use "open 5vk8 format pdb" then "sym #1 biomt" works.