Opened 3 years ago

Closed 2 years ago

#8858 closed defect (fixed)

Saving shift_and_scale uses numpy array as boolean

Reported by: Tristan Croll Owned by: Tom Goddard
Priority: normal Milestone:
Component: Sessions Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description (last modified by Tom Goddard) 

The following bug report has been submitted:
Platform:        Windows-10-10.0.22621
ChimeraX Version: 1.6rc202304072249 (2023-04-07 22:49:08 UTC)
Description
Was trying to save a session to report another bug, and hit a failure in saving named views. Will report the bug I was originally trying to report in a separate ticket. :)

Log:
> isolde shorthand
    
    
    Initialising ISOLDE-specific command aliases:
    Alias	Equivalent full command
    -------------------------------------------------
    st	isolde step {arguments}
    aw	isolde add water {arguments}
    awsf	isolde add water {arguments} sim false
    al	isolde add ligand {arguments}
    aa	isolde add aa $1 sel {arguments}
    ht	isolde mod his sel {arguments}
    so	setattr sel atoms occupancy {arguments}
    ab	isolde adjust bfactors {arguments}
    ss	isolde sim start sel
    rt	isolde release torsions sel {arguments}
    rd	isolde release distances sel {arguments}
    ra	rd; rt
    pf	isolde pepflip sel
    cf	isolde cisflip sel
    cbb	color bfactor {arguments}
    cbo	color byattr occupancy {arguments}
    cbc	color {arguments} bychain; color {arguments} byhet
    cs	clipper set contourSensitivity {arguments}
    

  
UCSF ChimeraX version: 1.6rc202304072249 (2023-04-07)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 7y5e

Summary of feedback from opening 7y5e fetched from pdb  
---  
warnings | Atom C14 has no neighbors to form bonds with according to residue
template for CLA /AN:801  
Atom C14 has no neighbors to form bonds with according to residue template for
CLA /A2:802  
  
7y5e title:  
In situ single-PBS-PSII-PSI-LHCs megacomplex. [more info...]  
  
Chain information for 7y5e #1  
---  
Chain | Description | UniProt  
12 1N | Chlorophyll a-b binding protein, chloroplastic | A0A5J4Z6J3_PORPP
49-222  
16 1L 46 4L | CNT |  
18 1C B5 B7 B9 BA BB BF BI BK BP CB CD CQ D5 D7 D9 DA DB DF DI DJ DK DM DP ED
EQ F5 F7 F9 FA FB FF FI FJ FK FM FP GB GD GQ H5 H7 H9 HA HB HF HI HJ HK HM HP
IB ID IQ J5 J7 J9 JA JF JI JJ JK JM JP KD KQ L5 L7 L9 LA LB LF LI LJ LK LM LP
MB MD MQ N7 NA NB NF NJ NK NM NP O5 O9 OB OD OI OQ P1 P4 P7 PA PB PE PF PG PH
PJ PK PM PO PP Q5 Q9 QB QD QI QQ R1 R4 R7 RA RB RE RF RG RH RJ RK RM RO RP S5
S9 SB SD SI SQ T1 T4 T7 TA TE TF TG TH TJ TK TM TO TP U5 U9 UD UI UQ V1 V4 V7
VA VB VE VF VG VH VJ VK VM VO VP W5 W9 WD WI WQ X7 XA XB XF XJ XK XM XP Y1 Y4
Y5 Y9 YB YD YE YG YH YI YO YQ ZB ZF ZJ ZK ZM a1 a4 aB aE aG aH aO bB bF bK c1
c4 cE cG cH cJ cM cO dB dF dK e1 e4 eB eE eG eH eJ eM eO fF fK g1 g4 gB gE gG
gH gJ gM gO hF hK i1 i4 iE iG iH iJ iM iO jF jK k1 k4 kE kG kH kJ kM kO lF lK
m1 m4 mE mG mH mJ mM mO nF nK pF pK q8 qC rF rK s8 sC tF tK u8 uC vF vK w8 wC
y8 yC | B-phycoerythrin beta chain | PHEB_PORPP 1-177  
22 2N | Chlorophyll a-b binding protein of LHCII type III, chloroplastic |
P93450_PORPP 37-202  
23 Z3 | Lrc4 | A0A5J4YTV6_PORPP 20-178  
32 3N | Chlorophyll a-b binding protein, chloroplastic | A0A5J4YYC4_PORPP
42-210  
33 a3 | LRC5 | A0A5J4Z2M2_PORPP 10-297  
42 4N | Chlorophyll a-b binding protein 1B-21, chloroplastic |
A0A5J4ZAY0_PORPP 37-208  
43 b3 | FAS1 domain-containing protein | A0A5J4ZA95_PORPP 6-258  
52 5N | Chlorophyll a-b binding protein 1B-21, chloroplastic |
A0A5J4YSS5_PORPP 39-212  
53 Y3 | LPP2 | A0A5J4Z365_PORPP -104-57 -100-61  
62 6N | Chlorophyll a-b binding protein 1B-21, chloroplastic |
A0A5J4YN76_PORPP 47-215  
63 73 | Phycobiliprotein ApcE | A0A343KPB8_PORPP 1-879  
72 7N | Fucoxanthin-chlorophyll a-c binding protein, chloroplastic |
A0A5J4YKR2_PORPP 38-201  
82 8N | RedCAP | A0A5J4YP51_PORPP 34-213  
A1 A4 AD AE AG AH AO AQ Y7 YA | R-phycoerythrin gamma chain, chloroplastic |
A0A5J4YX19_PORPP 9-298  
A2 AN | PsaA | W0S1N1_PORPP 1-752  
A3 C3 E3 G3 J3 K3 N3 P3 R3 T3 c3 e3 g3 i3 l3 m3 p3 r3 t3 v3 | Allophycocyanin
alpha subunit | W0RYM0_PORPP 1-161  
A5 A7 A9 AA AF AI AK AP BD BQ C5 C7 C9 CA CF CI CJ CK CM CP DD DQ E5 E7 E9 EA
EF EI EJ EK EM EP FD FQ G5 G7 G9 GA GF GI GJ GK GM GP HD HQ I5 I7 I9 IA IF II
IJ IK IM IP JB JD JQ K5 K7 K9 KA KF KI KJ KK KM KP LD LQ M7 MA MF MJ MK MM MP
N5 N9 ND NI NQ O1 O4 O7 OA OE OF OG OH OJ OK OM OO OP P5 P9 PD PI PQ Q1 Q4 Q7
QA QE QF QG QH QJ QK QM QO QP R5 R9 RD RI RQ S1 S4 S7 SA SE SF SG SH SJ SK SM
SO SP T5 T9 TB TD TI TQ U1 U4 U7 UA UE UF UG UH UJ UK UM UO UP V5 V9 VD VI VQ
W1 W4 W7 WA WE WF WG WH WJ WK WM WO WP X5 X9 XD XI XQ YF YJ YK YM Z1 Z4 ZE ZG
ZH ZO aF aJ aK aM b1 b4 bE bG bH bO cF cK d1 d4 dE dG dH dJ dM dO eF eK f1 f4
fE fG fH fJ fM fO gF gK h1 h4 hE hG hH hJ hM hO iF iK j1 j4 jE jG jH jJ jM jO
kF kK l1 l4 lE lG lH lJ lM lO mF mK oF oK p8 pC qF qK r8 rC sF sK t8 tC uF uK
v8 vC x8 xC z8 zC | Phycoerythrin alpha subunit | E2IH77_PORPP 1-164  
A6 AL a6 aL | Photosystem II protein D1 | W0RZ08_PORPP 1-360  
A8 AC a8 aC | LRH |  
AB EB | Linker4 | A0A5J4YXP2_PORPP 287-424  
AJ AM wF wK xF xK | R-phycoerythrin gamma chain, chloroplastic |
A0A5J4YZM7_PORPP 11-283  
B1 B4 BE BG BH BO | Phycobilisome rod-core linker polypeptide | W0RZ90_PORPP
1-232  
B2 BN | Photosystem I P700 chlorophyll a apoprotein A2 | W0RYU6_PORPP 3-734  
B3 D3 F3 H3 I3 L3 M3 O3 Q3 S3 U3 d3 f3 h3 j3 k3 n3 o3 q3 s3 u3 w3 |
Allophycocyanin beta subunit | W0S279_PORPP 1-161  
B6 BL b6 bL | Photosystem II CP47 reaction center protein | W0RZ84_PORPP 1-509  
BJ BM yF yK | R-phycoerythrin gamma chain, chloroplastic | A0A5J4YZH3_PORPP
8-297  
C1 C4 CE CG CH CO E1 E4 EE EG EH EO G1 G4 GE GG GH GO I1 I4 IE IG IH IO K1 K4
KE KG KH KO M1 M4 ME MG MH MO | C-phycocyanin alpha subunit | W0RYI4_PORPP
1-162  
C2 CN | Photosystem I iron-sulfur center | W0S231_PORPP 1-81  
C6 CL c6 cL | Photosystem II CP43 reaction center protein | W0RYK4_PORPP 1-473  
D1 D4 DE DG DH DO F1 F4 FE FG FH FO H1 H4 HE HG HH HO J1 J4 JE JG JH JO L1 L4
LE LG LH LO N1 N4 NE NG NH NO | C-phycocyanin beta subunit | W0RZB2_PORPP
1-172  
D2 DN | Photosystem I reaction center subunit II | W0RZ23_PORPP -2-139  
D6 DL d6 dL | Photosystem II D2 protein | W0RYZ0_PORPP 2-352  
E2 EN | Photosystem I reaction center subunit IV | W0RYG1_PORPP 1-61  
E6 EL e6 eL | Cytochrome b559 subunit alpha | W0RYH5_PORPP 0-83  
F2 FN | Photosystem I reaction center subunit III | W0RZ71_PORPP 1-185  
F6 FL f6 fL | Cytochrome b559 subunit beta | W0S1X0_PORPP 2-45  
G2 GN | Cytochrome c6 | W0S1L8_PORPP 7-110  
G6 GL g6 gL | PSII_Pbs31 domain-containing protein | A0A5J4Z270_PORPP 1-213  
H6 HL h6 hL | Photosystem II reaction center protein H | W0RYU5_PORPP 1-67  
I2 IN | Photosystem I reaction center subunit VIII | W0RZ51_PORPP 1-37  
I6 IL i6 iL | Photosystem II reaction center protein I | W0RYJ5_PORPP 1-38  
J2 JN | Photosystem I reaction center subunit IX | W0RYG9_PORPP 1-42  
J6 JL j6 jL | Photosystem II reaction center protein J | W0RYQ6_PORPP 2-40  
K2 KN | Photosystem I reaction center subunit PsaK | W0RZ04_PORPP 1-70  
K6 KL k6 kL | Photosystem II reaction center protein K | W0RZ28_PORPP 1-45  
KB UB | CaRSPs1 | A0A5J4YJY8_PORPP 1-288  
L2 LN | Photosystem I reaction center subunit XI | W0S1Z0_PORPP 3-142  
L6 LL l6 lL | PsbL | W0RZ31_PORPP 0-37  
M2 MN | Photosystem I reaction center subunit XII | W0S1Z9_PORPP 1-30  
M5 M9 Z5 Z9 | R-phycoerythrin gamma chain, chloroplastic | A0A5J4YNU6_PORPP
-34-298 -33-299  
M6 ML m6 mL | PsbM | A0A5J4YYD7_PORPP -56-44  
MI ZI | Phycobilisome 27.9 kDa linker polypeptide, phycoerythrin-associated,
rod | A0A5J4Z323_PORPP 1-316  
N2 NN | Ferredoxin | W0RYF9_PORPP 1-99  
N6 NL n6 nL | Psb34 |  
O2 ON | Photosystem I subunit O | A0A5J4YUC8_PORPP 46-137  
O6 OL o6 oL | Oxygen-evolving enhancer protein | E5RPB3_PORPP -32-254  
Q6 QL q6 qL | PsbQ' | A0A5J4Z679_PORPP 1-205  
R2 RN | PsaR | A0A5J4YR43_PORPP 44-121  
R6 RL r6 rL | Photosystem II protein Y | W0S1X5_PORPP 2-34  
S6 SL | LPP1 |  
T6 TL t6 tL | Photosystem II reaction center protein T | W0RYV0_PORPP 1-31  
U6 UL u6 uL | PS II complex 12 kDa extrinsic protein | A0A5J4YLQ6_PORPP
-46-103 -46-105  
V3 x3 | Allophycocyanin gamma subunit | W0S1U6_PORPP 1-161  
V6 VL v6 vL | Cytochrome c550 | W0RYZ6_PORPP -24-137  
W3 y3 | Allophycocyanin beta 18 subunit | W0RZE2_PORPP 1-173  
W6 WL w6 wL | PsbW |  
WB cB | CaRSP2 | A0A5J4YX67_PORPP 1-327  
X1 X4 XE XG XH XO | Phycobilisome 31.8 kDa linker polypeptide, phycoerythrin-
associated, rod | A0A5J4YM59_PORPP 9-371  
X3 z3 | Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated,
core | A0A5J4YVZ2_PORPP 40-132  
X6 XL x6 xL | Photosystem II reaction center X protein | W0RZ76_PORPP 3-41  
Y6 YL y6 yL | Photosystem II reaction center protein Ycf12 | W0RZ91_PORPP 1-34  
YP bP | Phycobilisome 31.8 kDa linker polypeptide, phycoerythrin-associated,
rod | A0A5J4YMI8_PORPP -16-409  
Z2 ZN | LPS1 |  
Z6 ZL z6 zL | Photosystem II reaction center protein Z | W0RZ40_PORPP 1-62  
bJ bM | Phycobilisome 32.1 kDa linker polypeptide, phycocyanin-associated, rod
| A0A5J4YX63_PORPP -28-461  
dD dQ | Phycobilisome 27.9 kDa linker polypeptide, phycoerythrin-associated,
rod | A0A5J4Z162_PORPP 5-346  
e7 eA | Phycobilisome 31.8 kDa linker polypeptide, phycoerythrin-associated,
rod | A0A5J4Z7F4_PORPP -12-290  
fB hB | FAS1 domain-containing protein | A0A5J4Z027_PORPP 0-287  
zF zK | Phycobilisome 31.8 kDa linker polypeptide, phycoerythrin-associated,
rod | A0A5J4YI31_PORPP 1-498  
  
Non-standard residues in 7y5e #1  
---  
3XQ — (2S)-2,3-dihydroxypropyl octadecanoate  
BCR — β-carotene  
BCT — bicarbonate ion  
BGC — beta-D-glucopyranose (beta-D-glucose; D-glucose; glucose)  
CL — chloride ion  
CLA — chlorophyll A  
CYC — phycocyanobilin  
DGD — digalactosyl diacyl glycerol (DGDG)  
FE — Fe (III) ion  
FES — FE2/S2 (inorganic) cluster  
GOL — glycerol (glycerin; propane-1,2,3-triol)  
HEM — protoporphyrin IX containing Fe (HEME)  
LHG — 1,2-dipalmitoyl-phosphatidyl-glycerole  
LMG — 1,2-distearoyl-monogalactosyl-diglyceride  
OEX — Ca-MN4-O5 cluster  
PEB — phycoerythrobilin  
PHO — pheophytin A  
PL9 —
2,3-dimethyl-5-(3,7,11,15,19,23,27,31,35-nonamethyl-2,6,10,14,18,22,26,30,34-hexatriacontanonaenyl-2,5-cyclohexadiene-1,4-dione-2,3-dimethyl-5-solanesyl-1,4-benzoquinone
(plastoquinone 9)  
PQN — phylloquinone (vitamin K1; 2-methyl-3-phytyl-1,4-naphthoquinone)  
PUB — phycourobilin  
SF4 — iron/sulfur cluster  
ZEX —
(1R,2S)-4-{(1E,3E,5E,7E,9E,11E,13E,15E,17E)-18-[(4S)-4-hydroxy-2,6,6-trimethylcyclohex-1-en-1-yl]-3,7,12,16-tetramethyloctadeca-1,3,5,7,9,11,13,15,17-nonaen-1-yl}-2,5,5-trimethylcyclohex-3-en-1-ol  
  

> log metadata #1

Metadata for 7y5e #1  
---  
Title | In situ single-PBS-PSII-PSI-LHCs megacomplex.  
Citation | You, X., Zhang, X., Cheng, J., Xiao, Y.N., Sui, S.F. (?). Structure
of in situ single-PBS-PSII-PSI-LHCs megacomplex at 3.3 Angstroms resolution.
To Be Published  
Non-standard residues | 3XQ — (2S)-2,3-dihydroxypropyl octadecanoate  
BCR — β-carotene  
BCT — bicarbonate ion  
BGC — beta-D-glucopyranose (beta-D-glucose; D-glucose; glucose)  
CL — chloride ion  
CLA — chlorophyll A  
CYC — phycocyanobilin  
DGD — digalactosyl diacyl glycerol (DGDG)  
FE — Fe (III) ion  
FES — FE2/S2 (inorganic) cluster  
GOL — glycerol (glycerin; propane-1,2,3-triol)  
HEM — protoporphyrin IX containing Fe (HEME)  
LHG — 1,2-dipalmitoyl-phosphatidyl-glycerole  
LMG — 1,2-distearoyl-monogalactosyl-diglyceride  
OEX — Ca-MN4-O5 cluster  
PEB — phycoerythrobilin  
PHO — pheophytin A  
PL9 —
2,3-dimethyl-5-(3,7,11,15,19,23,27,31,35-nonamethyl-2,6,10,14,18,22,26,30,34-hexatriacontanonaenyl-2,5-cyclohexadiene-1,4-dione-2,3-dimethyl-5-solanesyl-1,4-benzoquinone
(plastoquinone 9)  
PQN — phylloquinone (vitamin K1; 2-methyl-3-phytyl-1,4-naphthoquinone)  
PUB — phycourobilin  
SF4 — iron/sulfur cluster  
ZEX —
(1R,2S)-4-{(1E,3E,5E,7E,9E,11E,13E,15E,17E)-18-[(4S)-4-hydroxy-2,6,6-trimethylcyclohex-1-en-1-yl]-3,7,12,16-tetramethyloctadeca-1,3,5,7,9,11,13,15,17-nonaen-1-yl}-2,5,5-trimethylcyclohex-3-en-1-ol  
Gene source | Porphyridium purpureum  
CryoEM Map | EMDB 33618 — open map  
Experimental method | Electron microscopy  
Resolution | 3.3Å  
  
> open 33618 fromDatabase emdb

Opened emdb 33618 as #2, grid size 384,384,384, pixel 1.63, shown at level
2.11, step 2, values float32  

> addh

Summary of feedback from adding hydrogens to 7y5e #1  
---  
warnings | Not adding hydrogens to /AB MET 375 CB because it is missing heavy-
atom bond partners  
Not adding hydrogens to /AB ARG 392 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /AB ASP 416 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /AB LEU 418 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /CB ASP 13 CB because it is missing heavy-atom bond
partners  
2300 messages similar to the above omitted  
Unknown hybridization for atoms (O1, O2, O3, O5) of residue type OEX; not
adding hydrogens to them  
Unknown hybridization for atom (C14) of residue type CLA; not adding hydrogens
to it  
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /bM PRO 399 N; /zF PRO 418 N; /53 PRO 15 N; /zF PRO 419 N; /bM
PRO 404 N; /bJ PRO 399 N; /bJ PRO 404 N; /BL ARG 476 NE; /B6 ARG 476 NE; /b6
ARG 476 NE; /bL ARG 476 NE  
notes | Termini for 7y5e (#1) chain AA determined from SEQRES records  
Termini for 7y5e (#1) chain BA determined from SEQRES records  
Termini for 7y5e (#1) chain CA determined from SEQRES records  
Termini for 7y5e (#1) chain DA determined from SEQRES records  
Termini for 7y5e (#1) chain EA determined from SEQRES records  
889 messages similar to the above omitted  
Chain-initial residues that are actual N termini: /AA MET 1, /BA MET 1, /CA
MET 1, /DA MET 1, /EA MET 1, /FA MET 1, /GA MET 1, /HA MET 1, /IA MET 1, /JA
MET 1, /KA MET 1, /LA MET 1, /MA MET 1, /NA MET 1, /OA MET 1, /PA MET 1, /QA
MET 1, /RA MET 1, /SA MET 1, /TA MET 1, /UA MET 1, /VA MET 1, /WA MET 1, /XA
MET 1, /BB MET 1, /CB MET 1, /FB MET 1, /GB MET 1, /IB MET 1, /JB MET 1, /LB
MET 1, /MB MET 1, /OB MET 1, /PB MET 1, /RB MET 1, /SB MET 1, /TB MET 1, /VB
MET 1, /XB MET 1, /YB MET 1, /AC UNK 1, /BD MET 1, /CD MET 1, /DD MET 1, /ED
MET 1, /FD MET 1, /GD MET 1, /HD MET 1, /ID MET 1, /JD MET 1, /KD MET 1, /LD
MET 1, /MD MET 1, /ND MET 1, /OD MET 1, /PD MET 1, /QD MET 1, /RD MET 1, /SD
MET 1, /TD MET 1, /UD MET 1, /VD MET 1, /WD MET 1, /XD MET 1, /YD MET 1, /CE
MET 1, /DE MET 1, /EE MET 1, /FE MET 1, /GE MET 1, /HE MET 1, /IE MET 1, /JE
MET 1, /KE MET 1, /LE MET 1, /ME MET 1, /NE MET 1, /OE MET 1, /PE MET 1, /QE
MET 1, /RE MET 1, /SE MET 1, /TE MET 1, /UE MET 1, /VE MET 1, /WE MET 1, /YE
MET 1, /ZE MET 1, /AF MET 1, /BF MET 1, /CF MET 1, /DF MET 1, /EF MET 1, /FF
MET 1, /GF MET 1, /HF MET 1, /IF MET 1, /JF MET 1, /KF MET 1, /LF MET 1, /MF
MET 1, /NF MET 1, /OF MET 1, /PF MET 1, /QF MET 1, /RF MET 1, /SF MET 1, /TF
MET 1, /UF MET 1, /VF MET 1, /WF MET 1, /XF MET 1, /YF MET 1, /ZF MET 1, /CG
MET 1, /DG MET 1, /EG MET 1, /FG MET 1, /GG MET 1, /HG MET 1, /IG MET 1, /JG
MET 1, /KG MET 1, /LG MET 1, /MG MET 1, /NG MET 1, /OG MET 1, /PG MET 1, /QG
MET 1, /RG MET 1, /SG MET 1, /TG MET 1, /UG MET 1, /VG MET 1, /WG MET 1, /YG
MET 1, /ZG MET 1, /CH MET 1, /DH MET 1, /EH MET 1, /FH MET 1, /GH MET 1, /HH
MET 1, /IH MET 1, /JH MET 1, /KH MET 1, /LH MET 1, /MH MET 1, /NH MET 1, /OH
MET 1, /PH MET 1, /QH MET 1, /RH MET 1, /SH MET 1, /TH MET 1, /UH MET 1, /VH
MET 1, /WH MET 1, /YH MET 1, /ZH MET 1, /AI MET 1, /BI MET 1, /CI MET 1, /DI
MET 1, /EI MET 1, /FI MET 1, /GI MET 1, /HI MET 1, /II MET 1, /JI MET 1, /KI
MET 1, /LI MET 1, /NI MET 1, /OI MET 1, /PI MET 1, /QI MET 1, /RI MET 1, /SI
MET 1, /TI MET 1, /UI MET 1, /VI MET 1, /WI MET 1, /XI MET 1, /YI MET 1, /CJ
MET 1, /DJ MET 1, /EJ MET 1, /FJ MET 1, /GJ MET 1, /HJ MET 1, /IJ MET 1, /JJ
MET 1, /KJ MET 1, /LJ MET 1, /MJ MET 1, /NJ MET 1, /OJ MET 1, /PJ MET 1, /QJ
MET 1, /RJ MET 1, /SJ MET 1, /TJ MET 1, /UJ MET 1, /VJ MET 1, /WJ MET 1, /XJ
MET 1, /YJ MET 1, /ZJ MET 1, /AK MET 1, /BK MET 1, /CK MET 1, /DK MET 1, /EK
MET 1, /FK MET 1, /GK MET 1, /HK MET 1, /IK MET 1, /JK MET 1, /KK MET 1, /LK
MET 1, /MK MET 1, /NK MET 1, /OK MET 1, /PK MET 1, /QK MET 1, /RK MET 1, /SK
MET 1, /TK MET 1, /UK MET 1, /VK MET 1, /WK MET 1, /XK MET 1, /YK MET 1, /ZK
MET 1, /IL MET 1, /NL UNK 1, /RL ASP 2, /SL UNK 1, /TL MET 1, /WL UNK 1, /XL
MET 3, /YL MET 1, /CM MET 1, /DM MET 1, /EM MET 1, /FM MET 1, /GM MET 1, /HM
MET 1, /IM MET 1, /JM MET 1, /KM MET 1, /LM MET 1, /MM MET 1, /NM MET 1, /OM
MET 1, /PM MET 1, /QM MET 1, /RM MET 1, /SM MET 1, /TM MET 1, /UM MET 1, /VM
MET 1, /WM MET 1, /XM MET 1, /YM MET 1, /ZM MET 1, /BN THR 3, /KN MET 1, /LN
ASP 3, /MN MET 1, /NN MET 1, /ON TYR 46, /RN ASP 44, /ZN UNK 6, /CO MET 1, /DO
MET 1, /EO MET 1, /FO MET 1, /GO MET 1, /HO MET 1, /IO MET 1, /JO MET 1, /KO
MET 1, /LO MET 1, /MO MET 1, /NO MET 1, /OO MET 1, /PO MET 1, /QO MET 1, /RO
MET 1, /SO MET 1, /TO MET 1, /UO MET 1, /VO MET 1, /WO MET 1, /YO MET 1, /ZO
MET 1, /AP MET 1, /BP MET 1, /CP MET 1, /DP MET 1, /EP MET 1, /FP MET 1, /GP
MET 1, /HP MET 1, /IP MET 1, /JP MET 1, /KP MET 1, /LP MET 1, /MP MET 1, /NP
MET 1, /OP MET 1, /PP MET 1, /QP MET 1, /RP MET 1, /SP MET 1, /TP MET 1, /UP
MET 1, /VP MET 1, /WP MET 1, /XP MET 1, /BQ MET 1, /CQ MET 1, /DQ MET 1, /EQ
MET 1, /FQ MET 1, /GQ MET 1, /HQ MET 1, /IQ MET 1, /JQ MET 1, /KQ MET 1, /LQ
MET 1, /MQ MET 1, /NQ MET 1, /OQ MET 1, /PQ MET 1, /QQ MET 1, /RQ MET 1, /SQ
MET 1, /TQ MET 1, /UQ MET 1, /VQ MET 1, /WQ MET 1, /XQ MET 1, /YQ MET 1, /L1
MET 1, /M1 MET 1, /N1 MET 1, /O1 MET 1, /P1 MET 1, /Q1 MET 1, /R1 MET 1, /S1
MET 1, /T1 MET 1, /U1 MET 1, /C1 MET 1, /D1 MET 1, /E1 MET 1, /F1 MET 1, /G1
MET 1, /H1 MET 1, /I1 MET 1, /J1 MET 1, /K1 MET 1, /V1 MET 1, /W1 MET 1, /Y1
MET 1, /Z1 MET 1, /f1 MET 1, /g1 MET 1, /h1 MET 1, /i1 MET 1, /j1 MET 1, /k1
MET 1, /l1 MET 1, /m1 MET 1, /a1 MET 1, /b1 MET 1, /c1 MET 1, /d1 MET 1, /e1
MET 1, /12 PRO 49, /22 PRO 37, /32 PRO 42, /42 SER 37, /52 PRO 39, /62 PHE 47,
/72 PHE 38, /82 ALA 34, /B2 THR 3, /K2 MET 1, /L2 ASP 3, /M2 MET 1, /N2 MET 1,
/O2 TYR 46, /R2 ASP 44, /Z2 UNK 6, /B3 MET 1, /D3 MET 1, /F3 MET 1, /H3 MET 1,
/I3 MET 1, /L3 MET 1, /M3 MET 1, /O3 MET 1, /Q3 MET 1, /S3 MET 1, /U3 MET 1,
/W3 MET 1, /d3 MET 1, /f3 MET 1, /h3 MET 1, /j3 MET 1, /k3 MET 1, /n3 MET 1,
/o3 MET 1, /q3 MET 1, /s3 MET 1, /u3 MET 1, /w3 MET 1, /y3 MET 1, /F4 MET 1,
/G4 MET 1, /H4 MET 1, /I4 MET 1, /J4 MET 1, /K4 MET 1, /L4 MET 1, /M4 MET 1,
/N4 MET 1, /O4 MET 1, /C4 MET 1, /D4 MET 1, /E4 MET 1, /P4 MET 1, /Q4 MET 1,
/R4 MET 1, /S4 MET 1, /T4 MET 1, /U4 MET 1, /V4 MET 1, /W4 MET 1, /Y4 MET 1,
/Z4 MET 1, /i4 MET 1, /j4 MET 1, /k4 MET 1, /l4 MET 1, /m4 MET 1, /a4 MET 1,
/b4 MET 1, /c4 MET 1, /d4 MET 1, /e4 MET 1, /f4 MET 1, /g4 MET 1, /h4 MET 1,
/A5 MET 1, /B5 MET 1, /C5 MET 1, /D5 MET 1, /E5 MET 1, /F5 MET 1, /G5 MET 1,
/H5 MET 1, /I5 MET 1, /J5 MET 1, /K5 MET 1, /L5 MET 1, /N5 MET 1, /O5 MET 1,
/P5 MET 1, /Q5 MET 1, /R5 MET 1, /S5 MET 1, /T5 MET 1, /U5 MET 1, /V5 MET 1,
/W5 MET 1, /X5 MET 1, /Y5 MET 1, /I6 MET 1, /N6 UNK 1, /R6 ASP 2, /S6 UNK 1,
/T6 MET 1, /W6 UNK 1, /X6 MET 3, /Y6 MET 1, /Z6 MET 1, /i6 MET 1, /n6 UNK 1,
/r6 ASP 2, /t6 MET 1, /w6 UNK 1, /x6 MET 3, /y6 MET 1, /z6 MET 1, /A7 MET 1,
/B7 MET 1, /C7 MET 1, /D7 MET 1, /E7 MET 1, /F7 MET 1, /G7 MET 1, /H7 MET 1,
/I7 MET 1, /J7 MET 1, /K7 MET 1, /L7 MET 1, /M7 MET 1, /N7 MET 1, /O7 MET 1,
/P7 MET 1, /Q7 MET 1, /R7 MET 1, /S7 MET 1, /T7 MET 1, /U7 MET 1, /V7 MET 1,
/W7 MET 1, /X7 MET 1, /A8 UNK 1, /a8 UNK 1, /y8 MET 1, /z8 MET 1, /18 MET 1,
/p8 MET 1, /q8 MET 1, /r8 MET 1, /s8 MET 1, /t8 MET 1, /u8 MET 1, /v8 MET 1,
/w8 MET 1, /x8 MET 1, /A9 MET 1, /B9 MET 1, /C9 MET 1, /D9 MET 1, /E9 MET 1,
/F9 MET 1, /G9 MET 1, /H9 MET 1, /I9 MET 1, /J9 MET 1, /K9 MET 1, /L9 MET 1,
/N9 MET 1, /O9 MET 1, /P9 MET 1, /Q9 MET 1, /R9 MET 1, /S9 MET 1, /T9 MET 1,
/U9 MET 1, /V9 MET 1, /W9 MET 1, /X9 MET 1, /Y9 MET 1, /aB MET 1, /bB MET 1,
/dB MET 1, /eB MET 1, /aC UNK 1, /yC MET 1, /zC MET 1, /1C MET 1, /pC MET 1,
/qC MET 1, /rC MET 1, /sC MET 1, /tC MET 1, /uC MET 1, /vC MET 1, /wC MET 1,
/xC MET 1, /aE MET 1, /bE MET 1, /cE MET 1, /dE MET 1, /eE MET 1, /fE MET 1,
/gE MET 1, /hE MET 1, /iE MET 1, /jE MET 1, /kE MET 1, /lE MET 1, /mE MET 1,
/aF MET 1, /bF MET 1, /cF MET 1, /dF MET 1, /eF MET 1, /fF MET 1, /gF MET 1,
/hF MET 1, /iF MET 1, /jF MET 1, /kF MET 1, /lF MET 1, /mF MET 1, /nF MET 1,
/oF MET 1, /pF MET 1, /qF MET 1, /rF MET 1, /sF MET 1, /tF MET 1, /uF MET 1,
/vF MET 1, /aG MET 1, /bG MET 1, /cG MET 1, /dG MET 1, /eG MET 1, /fG MET 1,
/gG MET 1, /hG MET 1, /iG MET 1, /jG MET 1, /kG MET 1, /lG MET 1, /mG MET 1,
/fH MET 1, /gH MET 1, /hH MET 1, /iH MET 1, /jH MET 1, /kH MET 1, /lH MET 1,
/mH MET 1, /aH MET 1, /bH MET 1, /cH MET 1, /dH MET 1, /eH MET 1, /aJ MET 1,
/cJ MET 1, /dJ MET 1, /eJ MET 1, /fJ MET 1, /gJ MET 1, /hJ MET 1, /iJ MET 1,
/jJ MET 1, /kJ MET 1, /lJ MET 1, /mJ MET 1, /aK MET 1, /bK MET 1, /cK MET 1,
/dK MET 1, /eK MET 1, /fK MET 1, /gK MET 1, /hK MET 1, /iK MET 1, /jK MET 1,
/kK MET 1, /lK MET 1, /mK MET 1, /nK MET 1, /oK MET 1, /pK MET 1, /qK MET 1,
/rK MET 1, /sK MET 1, /tK MET 1, /uK MET 1, /vK MET 1, /iL MET 1, /nL UNK 1,
/rL ASP 2, /tL MET 1, /wL UNK 1, /xL MET 3, /yL MET 1, /aM MET 1, /cM MET 1,
/dM MET 1, /eM MET 1, /fM MET 1, /gM MET 1, /hM MET 1, /iM MET 1, /jM MET 1,
/kM MET 1, /lM MET 1, /mM MET 1, /1N PRO 49, /2N PRO 37, /3N PRO 42, /4N SER
37, /5N PRO 39, /6N PHE 47, /7N PHE 38, /8N ALA 34, /iO MET 1, /jO MET 1, /kO
MET 1, /lO MET 1, /mO MET 1, /aO MET 1, /bO MET 1, /cO MET 1, /dO MET 1, /eO
MET 1, /fO MET 1, /gO MET 1, /hO MET 1, /46 UNK 1, /16 UNK 1, /4L UNK 1, /1L
UNK 1  
Chain-initial residues that are not actual N termini: /YA ARG 62, /AB ASP 322,
/DB ALA 32, /EB ASP 322, /HB ALA 4, /KB VAL 36, /NB ALA 32, /QB ALA 4, /UB VAL
36, /WB THR 184, /ZB ALA 26, /AD THR 43, /AE LEU 42, /BE SER 2, /XE ARG 48,
/AG LEU 42, /BG SER 2, /XG ARG 48, /AH LEU 42, /BH SER 2, /XH ARG 48, /MI SER
46, /ZI SER 46, /AJ GLN 46, /BJ VAL 48, /AL ALA 11, /BL GLY 2, /CL SER 22, /DL
ARG 12, /EL SER 4, /FL GLY 5, /GL GLY 62, /HL ALA 2, /JL THR 5, /KL ALA 9, /LL
SER 1, /ML GLY 1, /OL PHE 1, /QL ALA 64, /UL GLU 11, /VL ASP 4, /ZL VAL 2, /AM
GLN 46, /BM VAL 48, /AN GLN 8, /CN ALA 2, /DN MET 6, /EN LYS 3, /FN VAL 26,
/GN ASP 27, /IN THR 2, /JN ASN 3, /AO LEU 42, /BO SER 2, /XO ARG 48, /YP LEU
32, /AQ THR 43, /A1 LEU 42, /B1 SER 2, /X1 ARG 48, /A2 GLN 8, /C2 ALA 2, /D2
MET 6, /E2 LYS 3, /F2 VAL 26, /G2 ASP 27, /I2 THR 2, /J2 ASN 3, /23 GLN 47,
/33 SER 36, /43 ARG 45, /A3 SER 2, /C3 SER 2, /E3 SER 2, /G3 SER 2, /J3 SER 2,
/K3 SER 2, /N3 SER 2, /P3 SER 2, /R3 SER 2, /T3 SER 2, /V3 SER 2, /X3 ALA 41,
/Z3 GLN 47, /a3 SER 36, /b3 ARG 45, /c3 SER 2, /e3 SER 2, /g3 SER 2, /i3 SER
2, /l3 SER 2, /m3 SER 2, /p3 SER 2, /r3 SER 2, /t3 SER 2, /v3 SER 2, /x3 SER
2, /z3 ALA 41, /63 VAL 2, /63 ALA 127, /73 VAL 2, /73 THR 119, /A4 LEU 42, /B4
SER 2, /X4 ARG 48, /M5 LYS 61, /Z5 LYS 61, /A6 ALA 11, /B6 GLY 2, /C6 SER 22,
/D6 ARG 12, /E6 SER 4, /F6 GLY 5, /G6 GLY 62, /H6 ALA 2, /J6 THR 5, /K6 ALA 9,
/L6 SER 1, /M6 GLY 1, /O6 PHE 1, /Q6 ALA 64, /S6 UNK 97, /U6 GLU 11, /V6 ASP
4, /a6 ALA 11, /b6 GLY 2, /c6 SER 22, /d6 GLY 11, /e6 GLY 3, /f6 GLY 5, /g6
GLY 62, /h6 ALA 2, /j6 THR 5, /k6 ALA 9, /l6 SER 1, /m6 GLY 1, /o6 PHE 1, /q6
ALA 64, /u6 GLU 11, /v6 ASP 4, /Y7 ARG 62, /e7 ALA 43, /eA ALA 43, /fB ALA 1,
/cB GLY 179, /gB ALA 26, /hB ALA 1, /dD ILE 49, /wF GLN 46, /xF GLN 46, /yF
VAL 48, /zF LEU 28, /bJ LYS 1, /wK GLN 46, /xK GLN 46, /yK VAL 48, /zK LEU 28,
/aL ALA 11, /bL GLY 2, /cL SER 22, /dL GLY 11, /eL GLY 3, /fL GLY 5, /gL GLY
62, /hL ALA 2, /jL THR 5, /kL ALA 9, /lL SER 1, /mL GLY 1, /oL PHE 1, /qL ALA
64, /uL GLU 11, /vL ASP 4, /zL VAL 2, /bM LYS 1, /bP LEU 32, /dQ ILE 49, /Z9
TRP 25, /M9 TRP 25, /Y3 SER 1, /53 LYS 1  
Chain-final residues that are actual C termini: /AA SER 164, /BA SER 177, /CA
SER 164, /DA SER 177, /EA SER 164, /FA SER 177, /GA SER 164, /HA SER 177, /IA
SER 164, /JA SER 177, /KA SER 164, /LA SER 177, /MA SER 164, /NA SER 177, /OA
SER 164, /PA SER 177, /QA SER 164, /RA SER 177, /SA SER 164, /TA SER 177, /UA
SER 164, /VA SER 177, /WA SER 164, /XA SER 177, /YA TYR 298, /AB LEU 424, /BB
SER 177, /CB SER 177, /DB SER 177, /EB LEU 424, /FB SER 177, /GB SER 177, /HB
SER 177, /IB SER 177, /JB SER 164, /LB SER 177, /MB SER 177, /NB SER 177, /OB
SER 177, /PB SER 177, /QB SER 177, /RB SER 177, /SB SER 177, /TB SER 164, /VB
SER 177, /XB SER 177, /YB SER 177, /ZB SER 177, /AD TYR 298, /BD SER 164, /CD
SER 177, /DD SER 164, /ED SER 177, /FD SER 164, /GD SER 177, /HD SER 164, /ID
SER 177, /JD SER 164, /KD SER 177, /LD SER 164, /MD SER 177, /ND SER 164, /OD
SER 177, /PD SER 164, /QD SER 177, /RD SER 164, /SD SER 177, /TD SER 164, /UD
SER 177, /VD SER 164, /WD SER 177, /XD SER 164, /YD SER 177, /AE TYR 298, /BE
LEU 232, /CE SER 162, /DE VAL 172, /EE SER 162, /FE VAL 172, /GE SER 162, /HE
VAL 172, /IE SER 162, /JE VAL 172, /KE SER 162, /LE VAL 172, /ME SER 162, /NE
VAL 172, /OE SER 164, /PE SER 177, /QE SER 164, /RE SER 177, /SE SER 164, /TE
SER 177, /UE SER 164, /VE SER 177, /WE SER 164, /XE LEU 371, /YE SER 177, /ZE
SER 164, /AF SER 164, /BF SER 177, /CF SER 164, /DF SER 177, /EF SER 164, /FF
SER 177, /GF SER 164, /HF SER 177, /IF SER 164, /JF SER 177, /KF SER 164, /LF
SER 177, /MF SER 164, /NF SER 177, /OF SER 164, /PF SER 177, /QF SER 164, /RF
SER 177, /SF SER 164, /TF SER 177, /UF SER 164, /VF SER 177, /WF SER 164, /XF
SER 177, /YF SER 164, /ZF SER 177, /AG TYR 298, /BG LEU 232, /CG SER 162, /DG
VAL 172, /EG SER 162, /FG VAL 172, /GG SER 162, /HG VAL 172, /IG SER 162, /JG
VAL 172, /KG SER 162, /LG VAL 172, /MG SER 162, /NG VAL 172, /OG SER 164, /PG
SER 177, /QG SER 164, /RG SER 177, /SG SER 164, /TG SER 177, /UG SER 164, /VG
SER 177, /WG SER 164, /XG LEU 371, /YG SER 177, /ZG SER 164, /AH TYR 298, /CH
SER 162, /DH VAL 172, /EH SER 162, /FH VAL 172, /GH SER 162, /HH VAL 172, /IH
SER 162, /JH VAL 172, /KH SER 162, /LH VAL 172, /MH SER 162, /NH VAL 172, /OH
SER 164, /PH SER 177, /QH SER 164, /RH SER 177, /SH SER 164, /TH SER 177, /UH
SER 164, /VH SER 177, /WH SER 164, /XH LEU 371, /YH SER 177, /ZH SER 164, /AI
SER 164, /BI SER 177, /CI SER 164, /DI SER 177, /EI SER 164, /FI SER 177, /GI
SER 164, /HI SER 177, /II SER 164, /JI SER 177, /KI SER 164, /LI SER 177, /NI
SER 164, /OI SER 177, /PI SER 164, /QI SER 177, /RI SER 164, /SI SER 177, /TI
SER 164, /UI SER 177, /VI SER 164, /WI SER 177, /XI SER 164, /YI SER 177, /AJ
TYR 283, /BJ TYR 297, /CJ SER 164, /DJ SER 177, /EJ SER 164, /FJ SER 177, /GJ
SER 164, /HJ SER 177, /IJ SER 164, /JJ SER 177, /KJ SER 164, /LJ SER 177, /MJ
SER 164, /NJ SER 177, /OJ SER 164, /PJ SER 177, /QJ SER 164, /RJ SER 177, /SJ
SER 164, /TJ SER 177, /UJ SER 164, /VJ SER 177, /WJ SER 164, /XJ SER 177, /YJ
SER 164, /ZJ SER 177, /AK SER 164, /BK SER 177, /CK SER 164, /DK SER 177, /EK
SER 164, /FK SER 177, /GK SER 164, /HK SER 177, /IK SER 164, /JK SER 177, /KK
SER 164, /LK SER 177, /MK SER 164, /NK SER 177, /OK SER 164, /PK SER 177, /QK
SER 164, /RK SER 177, /SK SER 164, /TK SER 177, /UK SER 164, /VK SER 177, /WK
SER 164, /XK SER 177, /YK SER 164, /ZK SER 177, /CL ASP 473, /DL LEU 352, /FL
ARG 45, /GL GLU 213, /HL ASN 67, /JL LEU 40, /KL ARG 45, /LL ASN 37, /NL UNK
29, /OL GLU 254, /RL LEU 34, /SL UNK 119, /TL LYS 31, /UL ARG 103, /VL TYR
137, /WL UNK 46, /XL SER 41, /AM TYR 283, /BM TYR 297, /CM SER 164, /DM SER
177, /EM SER 164, /FM SER 177, /GM SER 164, /HM SER 177, /IM SER 164, /JM SER
177, /KM SER 164, /LM SER 177, /MM SER 164, /NM SER 177, /OM SER 164, /PM SER
177, /QM SER 164, /RM SER 177, /SM SER 164, /TM SER 177, /UM SER 164, /VM SER
177, /WM SER 164, /XM SER 177, /YM SER 164, /ZM SER 177, /AN GLY 752, /BN GLY
734, /CN TYR 81, /GN TRP 110, /KN ILE 70, /LN PRO 142, /MN THR 30, /NN TYR 99,
/ON LYS 137, /RN LYS 121, /ZN UNK 71, /AO TYR 298, /CO SER 162, /DO VAL 172,
/EO SER 162, /FO VAL 172, /GO SER 162, /HO VAL 172, /IO SER 162, /JO VAL 172,
/KO SER 162, /LO VAL 172, /MO SER 162, /NO VAL 172, /OO SER 164, /PO SER 177,
/QO SER 164, /RO SER 177, /SO SER 164, /TO SER 177, /UO SER 164, /VO SER 177,
/WO SER 164, /XO LEU 371, /YO SER 177, /ZO SER 164, /AP SER 164, /BP SER 177,
/CP SER 164, /DP SER 177, /EP SER 164, /FP SER 177, /GP SER 164, /HP SER 177,
/IP SER 164, /JP SER 177, /KP SER 164, /LP SER 177, /MP SER 164, /NP SER 177,
/OP SER 164, /PP SER 177, /QP SER 164, /RP SER 177, /SP SER 164, /TP SER 177,
/UP SER 164, /VP SER 177, /WP SER 164, /XP SER 177, /AQ TYR 298, /BQ SER 164,
/CQ SER 177, /DQ SER 164, /EQ SER 177, /FQ SER 164, /GQ SER 177, /HQ SER 164,
/IQ SER 177, /JQ SER 164, /KQ SER 177, /LQ SER 164, /MQ SER 177, /NQ SER 164,
/OQ SER 177, /PQ SER 164, /QQ SER 177, /RQ SER 164, /SQ SER 177, /TQ SER 164,
/UQ SER 177, /VQ SER 164, /WQ SER 177, /XQ SER 164, /YQ SER 177, /L1 VAL 172,
/M1 SER 162, /N1 VAL 172, /O1 SER 164, /P1 SER 177, /Q1 SER 164, /R1 SER 177,
/S1 SER 164, /T1 SER 177, /U1 SER 164, /A1 TYR 298, /C1 SER 162, /D1 VAL 172,
/E1 SER 162, /F1 VAL 172, /G1 SER 162, /H1 VAL 172, /I1 SER 162, /J1 VAL 172,
/K1 SER 162, /V1 SER 177, /W1 SER 164, /X1 LEU 371, /Y1 SER 177, /Z1 SER 164,
/f1 SER 164, /g1 SER 177, /h1 SER 164, /i1 SER 177, /j1 SER 164, /k1 SER 177,
/l1 SER 164, /m1 SER 177, /a1 SER 177, /b1 SER 164, /c1 SER 177, /d1 SER 164,
/e1 SER 177, /12 ILE 222, /22 LEU 202, /32 GLY 210, /42 SER 208, /52 LEU 212,
/62 LYS 215, /72 PRO 201, /82 ALA 213, /A2 GLY 752, /B2 GLY 734, /C2 TYR 81,
/G2 TRP 110, /K2 ILE 70, /L2 PRO 142, /M2 THR 30, /N2 TYR 99, /O2 LYS 137, /R2
LYS 121, /Z2 UNK 71, /23 LYS 178, /A3 GLN 161, /B3 SER 161, /C3 GLN 161, /D3
SER 161, /E3 GLN 161, /F3 SER 161, /G3 GLN 161, /H3 SER 161, /I3 SER 161, /J3
GLN 161, /K3 GLN 161, /L3 SER 161, /M3 SER 161, /N3 GLN 161, /O3 SER 161, /P3
GLN 161, /Q3 SER 161, /R3 GLN 161, /S3 SER 161, /T3 GLN 161, /U3 SER 161, /V3
SER 161, /W3 LEU 173, /X3 GLN 132, /Z3 LYS 178, /c3 GLN 161, /d3 SER 161, /e3
GLN 161, /f3 SER 161, /g3 GLN 161, /h3 SER 161, /i3 GLN 161, /j3 SER 161, /k3
SER 161, /l3 GLN 161, /m3 GLN 161, /n3 SER 161, /o3 SER 161, /p3 GLN 161, /q3
SER 161, /r3 GLN 161, /s3 SER 161, /t3 GLN 161, /u3 SER 161, /v3 GLN 161, /w3
SER 161, /x3 SER 161, /y3 LEU 173, /z3 GLN 132, /F4 VAL 172, /G4 SER 162, /H4
VAL 172, /I4 SER 162, /J4 VAL 172, /K4 SER 162, /L4 VAL 172, /M4 SER 162, /N4
VAL 172, /O4 SER 164, /A4 TYR 298, /C4 SER 162, /D4 VAL 172, /E4 SER 162, /P4
SER 177, /Q4 SER 164, /R4 SER 177, /S4 SER 164, /T4 SER 177, /U4 SER 164, /V4
SER 177, /W4 SER 164, /X4 LEU 371, /Y4 SER 177, /Z4 SER 164, /i4 SER 177, /j4
SER 164, /k4 SER 177, /l4 SER 164, /m4 SER 177, /a4 SER 177, /b4 SER 164, /c4
SER 177, /d4 SER 164, /e4 SER 177, /f4 SER 164, /g4 SER 177, /h4 SER 164, /A5
SER 164, /B5 SER 177, /C5 SER 164, /D5 SER 177, /E5 SER 164, /F5 SER 177, /G5
SER 164, /H5 SER 177, /I5 SER 164, /J5 SER 177, /K5 SER 164, /L5 SER 177, /M5
TYR 298, /N5 SER 164, /O5 SER 177, /P5 SER 164, /Q5 SER 177, /R5 SER 164, /S5
SER 177, /T5 SER 164, /U5 SER 177, /V5 SER 164, /W5 SER 177, /X5 SER 164, /Y5
SER 177, /Z5 TYR 298, /C6 ASP 473, /D6 LEU 352, /F6 ARG 45, /G6 GLU 213, /H6
ASN 67, /J6 LEU 40, /K6 ARG 45, /L6 ASN 37, /N6 UNK 29, /O6 GLU 254, /R6 LEU
34, /S6 UNK 119, /T6 LYS 31, /U6 ARG 105, /V6 TYR 137, /W6 UNK 46, /X6 SER 41,
/c6 ASP 473, /d6 LEU 352, /f6 ARG 45, /j6 LEU 40, /k6 ARG 45, /l6 ASN 37, /o6
GLU 254, /r6 LEU 34, /t6 LYS 31, /u6 ARG 105, /v6 TYR 137, /w6 UNK 46, /x6 SER
41, /A7 SER 164, /B7 SER 177, /C7 SER 164, /D7 SER 177, /E7 SER 164, /F7 SER
177, /G7 SER 164, /H7 SER 177, /I7 SER 164, /J7 SER 177, /K7 SER 164, /L7 SER
177, /M7 SER 164, /N7 SER 177, /O7 SER 164, /P7 SER 177, /Q7 SER 164, /R7 SER
177, /S7 SER 164, /T7 SER 177, /U7 SER 164, /V7 SER 177, /W7 SER 164, /X7 SER
177, /Y7 TYR 298, /e7 SER 290, /y8 SER 177, /z8 SER 164, /18 SER 177, /p8 SER
164, /q8 SER 177, /r8 SER 164, /s8 SER 177, /t8 SER 164, /u8 SER 177, /v8 SER
164, /w8 SER 177, /x8 SER 164, /A9 SER 164, /B9 SER 177, /C9 SER 164, /D9 SER
177, /E9 SER 164, /F9 SER 177, /G9 SER 164, /H9 SER 177, /I9 SER 164, /J9 SER
177, /K9 SER 164, /L9 SER 177, /N9 SER 164, /O9 SER 177, /P9 SER 164, /Q9 SER
177, /R9 SER 164, /S9 SER 177, /T9 SER 164, /U9 SER 177, /V9 SER 164, /W9 SER
177, /X9 SER 164, /Y9 SER 177, /eA SER 290, /aB SER 177, /bB SER 177, /dB SER
177, /eB SER 177, /gB SER 177, /yC SER 177, /zC SER 164, /1C SER 177, /pC SER
164, /qC SER 177, /rC SER 164, /sC SER 177, /tC SER 164, /uC SER 177, /vC SER
164, /wC SER 177, /xC SER 164, /aE SER 177, /bE SER 164, /cE SER 177, /dE SER
164, /eE SER 177, /fE SER 164, /gE SER 177, /hE SER 164, /iE SER 177, /jE SER
164, /kE SER 177, /lE SER 164, /mE SER 177, /aF SER 164, /bF SER 177, /cF SER
164, /dF SER 177, /eF SER 164, /fF SER 177, /gF SER 164, /hF SER 177, /iF SER
164, /jF SER 177, /kF SER 164, /lF SER 177, /mF SER 164, /nF SER 177, /oF SER
164, /pF SER 177, /qF SER 164, /rF SER 177, /sF SER 164, /tF SER 177, /uF SER
164, /vF SER 177, /wF TYR 283, /xF TYR 283, /yF TYR 297, /aG SER 177, /bG SER
164, /cG SER 177, /dG SER 164, /eG SER 177, /fG SER 164, /gG SER 177, /hG SER
164, /iG SER 177, /jG SER 164, /kG SER 177, /lG SER 164, /mG SER 177, /fH SER
164, /gH SER 177, /hH SER 164, /iH SER 177, /jH SER 164, /kH SER 177, /lH SER
164, /mH SER 177, /aH SER 177, /bH SER 164, /cH SER 177, /dH SER 164, /eH SER
177, /aJ SER 164, /cJ SER 177, /dJ SER 164, /eJ SER 177, /fJ SER 164, /gJ SER
177, /hJ SER 164, /iJ SER 177, /jJ SER 164, /kJ SER 177, /lJ SER 164, /mJ SER
177, /aK SER 164, /bK SER 177, /cK SER 164, /dK SER 177, /eK SER 164, /fK SER
177, /gK SER 164, /hK SER 177, /iK SER 164, /jK SER 177, /kK SER 164, /lK SER
177, /mK SER 164, /nK SER 177, /oK SER 164, /pK SER 177, /qK SER 164, /rK SER
177, /sK SER 164, /tK SER 177, /uK SER 164, /vK SER 177, /wK TYR 283, /xK TYR
283, /yK TYR 297, /cL ASP 473, /dL LEU 352, /fL ARG 45, /jL LEU 40, /kL ARG
45, /lL ASN 37, /oL GLU 254, /rL LEU 34, /tL LYS 31, /uL ARG 103, /vL TYR 137,
/wL UNK 46, /xL SER 41, /aM SER 164, /cM SER 177, /dM SER 164, /eM SER 177,
/fM SER 164, /gM SER 177, /hM SER 164, /iM SER 177, /jM SER 164, /kM SER 177,
/lM SER 164, /mM SER 177, /1N ILE 222, /2N LEU 202, /3N GLY 210, /4N SER 208,
/5N LEU 212, /6N LYS 215, /7N PRO 201, /8N ALA 213, /iO SER 177, /jO SER 164,
/kO SER 177, /lO SER 164, /mO SER 177, /aO SER 177, /bO SER 164, /cO SER 177,
/dO SER 164, /eO SER 177, /fO SER 164, /gO SER 177, /hO SER 164, /Z9 TYR 299,
/M9 TYR 299, /Y3 LYS 61, /53 LYS 57, /46 UNK 118, /16 UNK 118, /4L UNK 118,
/1L UNK 118  
Chain-final residues that are not actual C termini: /KB GLY 261, /UB GLY 261,
/WB ALA 317, /AC UNK 150, /BH MET 228, /MI SER 310, /ZI SER 310, /AL ALA 344,
/BL GLY 507, /EL LYS 81, /IL LYS 35, /ML SER 42, /QL GLY 204, /YL ASN 33, /ZL
PHE 60, /DN SER 135, /EN GLU 60, /FN SER 183, /IN GLN 32, /JN PHE 40, /BO GLY
231, /YP SER 403, /B1 MET 228, /D2 SER 135, /E2 GLU 60, /F2 SER 183, /I2 GLN
32, /J2 PHE 40, /33 VAL 288, /43 PRO 250, /a3 VAL 288, /b3 PRO 250, /63 ASN
117, /63 ASN 878, /73 MET 106, /73 ASN 878, /B4 GLY 231, /A6 ALA 344, /B6 GLY
507, /E6 LYS 81, /I6 LYS 35, /M6 SER 42, /Q6 GLY 204, /S6 UNK 69, /Y6 ASN 33,
/Z6 PHE 60, /a6 ALA 344, /b6 GLY 507, /e6 LYS 81, /g6 THR 206, /h6 GLY 66, /i6
LYS 35, /m6 SER 42, /n6 UNK 27, /q6 GLY 204, /y6 ASN 33, /z6 PHE 60, /A8 UNK
150, /a8 UNK 87, /fB MET 285, /cB ALA 317, /hB MET 285, /aC UNK 87, /dD SER
333, /zF GLY 489, /bJ SER 407, /zK ASP 490, /aL ALA 344, /bL GLY 507, /eL LYS
81, /gL THR 206, /hL GLY 66, /iL LYS 35, /mL SER 42, /nL UNK 27, /qL GLY 204,
/yL ASN 33, /zL PHE 60, /bM ARG 405, /bP SER 403, /dQ SER 333  
Missing OXT added to C-terminal residue /YA TYR 298  
Missing OXT added to C-terminal residue /AB LEU 424  
Missing OXT added to C-terminal residue /EB LEU 424  
Missing OXT added to C-terminal residue /AD TYR 298  
Missing OXT added to C-terminal residue /AE TYR 298  
171 messages similar to the above omitted  
119551 hydrogen bonds  
Adding 'H' to /YA ARG 62  
Adding 'H' to /AB ASP 322  
Adding 'H' to /DB ALA 32  
Adding 'H' to /EB ASP 322  
Adding 'H' to /HB ALA 4  
176 messages similar to the above omitted  
/KB GLY 261 is not terminus, removing H atom from 'C'  
/UB GLY 261 is not terminus, removing H atom from 'C'  
/WB ALA 317 is not terminus, removing H atom from 'C'  
/AC UNK 150 is not terminus, removing H atom from 'C'  
/BH MET 228 is not terminus, removing H atom from 'C'  
73 messages similar to the above omitted  
1239533 hydrogens added  
  

> clipper associate #2 toModel #1

Opened emdb 33618 as #1.1.1.1, grid size 384,384,384, pixel 1.63, shown at
level 1.61, step 1, values float32  
7y5e title:  
In situ single-PBS-PSII-PSI-LHCs megacomplex. [more info...]  
  
Chain information for 7y5e  
---  
Chain | Description | UniProt  
1.2/12 1.2/1N | Chlorophyll a-b binding protein, chloroplastic |
A0A5J4Z6J3_PORPP 49-222  
1.2/16 1.2/1L 1.2/46 1.2/4L | CNT |  
1.2/18 1.2/1C 1.2/B5 1.2/B7 1.2/B9 1.2/BA 1.2/BB 1.2/BF 1.2/BI 1.2/BK 1.2/BP
1.2/CB 1.2/CD 1.2/CQ 1.2/D5 1.2/D7 1.2/D9 1.2/DA 1.2/DB 1.2/DF 1.2/DI 1.2/DJ
1.2/DK 1.2/DM 1.2/DP 1.2/ED 1.2/EQ 1.2/F5 1.2/F7 1.2/F9 1.2/FA 1.2/FB 1.2/FF
1.2/FI 1.2/FJ 1.2/FK 1.2/FM 1.2/FP 1.2/GB 1.2/GD 1.2/GQ 1.2/H5 1.2/H7 1.2/H9
1.2/HA 1.2/HB 1.2/HF 1.2/HI 1.2/HJ 1.2/HK 1.2/HM 1.2/HP 1.2/IB 1.2/ID 1.2/IQ
1.2/J5 1.2/J7 1.2/J9 1.2/JA 1.2/JF 1.2/JI 1.2/JJ 1.2/JK 1.2/JM 1.2/JP 1.2/KD
1.2/KQ 1.2/L5 1.2/L7 1.2/L9 1.2/LA 1.2/LB 1.2/LF 1.2/LI 1.2/LJ 1.2/LK 1.2/LM
1.2/LP 1.2/MB 1.2/MD 1.2/MQ 1.2/N7 1.2/NA 1.2/NB 1.2/NF 1.2/NJ 1.2/NK 1.2/NM
1.2/NP 1.2/O5 1.2/O9 1.2/OB 1.2/OD 1.2/OI 1.2/OQ 1.2/P1 1.2/P4 1.2/P7 1.2/PA
1.2/PB 1.2/PE 1.2/PF 1.2/PG 1.2/PH 1.2/PJ 1.2/PK 1.2/PM 1.2/PO 1.2/PP 1.2/Q5
1.2/Q9 1.2/QB 1.2/QD 1.2/QI 1.2/QQ 1.2/R1 1.2/R4 1.2/R7 1.2/RA 1.2/RB 1.2/RE
1.2/RF 1.2/RG 1.2/RH 1.2/RJ 1.2/RK 1.2/RM 1.2/RO 1.2/RP 1.2/S5 1.2/S9 1.2/SB
1.2/SD 1.2/SI 1.2/SQ 1.2/T1 1.2/T4 1.2/T7 1.2/TA 1.2/TE 1.2/TF 1.2/TG 1.2/TH
1.2/TJ 1.2/TK 1.2/TM 1.2/TO 1.2/TP 1.2/U5 1.2/U9 1.2/UD 1.2/UI 1.2/UQ 1.2/V1
1.2/V4 1.2/V7 1.2/VA 1.2/VB 1.2/VE 1.2/VF 1.2/VG 1.2/VH 1.2/VJ 1.2/VK 1.2/VM
1.2/VO 1.2/VP 1.2/W5 1.2/W9 1.2/WD 1.2/WI 1.2/WQ 1.2/X7 1.2/XA 1.2/XB 1.2/XF
1.2/XJ 1.2/XK 1.2/XM 1.2/XP 1.2/Y1 1.2/Y4 1.2/Y5 1.2/Y9 1.2/YB 1.2/YD 1.2/YE
1.2/YG 1.2/YH 1.2/YI 1.2/YO 1.2/YQ 1.2/ZB 1.2/ZF 1.2/ZJ 1.2/ZK 1.2/ZM 1.2/a1
1.2/a4 1.2/aB 1.2/aE 1.2/aG 1.2/aH 1.2/aO 1.2/bB 1.2/bF 1.2/bK 1.2/c1 1.2/c4
1.2/cE 1.2/cG 1.2/cH 1.2/cJ 1.2/cM 1.2/cO 1.2/dB 1.2/dF 1.2/dK 1.2/e1 1.2/e4
1.2/eB 1.2/eE 1.2/eG 1.2/eH 1.2/eJ 1.2/eM 1.2/eO 1.2/fF 1.2/fK 1.2/g1 1.2/g4
1.2/gB 1.2/gE 1.2/gG 1.2/gH 1.2/gJ 1.2/gM 1.2/gO 1.2/hF 1.2/hK 1.2/i1 1.2/i4
1.2/iE 1.2/iG 1.2/iH 1.2/iJ 1.2/iM 1.2/iO 1.2/jF 1.2/jK 1.2/k1 1.2/k4 1.2/kE
1.2/kG 1.2/kH 1.2/kJ 1.2/kM 1.2/kO 1.2/lF 1.2/lK 1.2/m1 1.2/m4 1.2/mE 1.2/mG
1.2/mH 1.2/mJ 1.2/mM 1.2/mO 1.2/nF 1.2/nK 1.2/pF 1.2/pK 1.2/q8 1.2/qC 1.2/rF
1.2/rK 1.2/s8 1.2/sC 1.2/tF 1.2/tK 1.2/u8 1.2/uC 1.2/vF 1.2/vK 1.2/w8 1.2/wC
1.2/y8 1.2/yC | B-phycoerythrin beta chain | PHEB_PORPP 1-177  
1.2/22 1.2/2N | Chlorophyll a-b binding protein of LHCII type III,
chloroplastic | P93450_PORPP 37-202  
1.2/23 1.2/Z3 | Lrc4 | A0A5J4YTV6_PORPP 20-178  
1.2/32 1.2/3N | Chlorophyll a-b binding protein, chloroplastic |
A0A5J4YYC4_PORPP 42-210  
1.2/33 1.2/a3 | LRC5 | A0A5J4Z2M2_PORPP 10-297  
1.2/42 1.2/4N | Chlorophyll a-b binding protein 1B-21, chloroplastic |
A0A5J4ZAY0_PORPP 37-208  
1.2/43 1.2/b3 | FAS1 domain-containing protein | A0A5J4ZA95_PORPP 6-258  
1.2/52 1.2/5N | Chlorophyll a-b binding protein 1B-21, chloroplastic |
A0A5J4YSS5_PORPP 39-212  
1.2/53 1.2/Y3 | LPP2 | A0A5J4Z365_PORPP -104-57 -100-61  
1.2/62 1.2/6N | Chlorophyll a-b binding protein 1B-21, chloroplastic |
A0A5J4YN76_PORPP 47-215  
1.2/63 1.2/73 | Phycobiliprotein ApcE | A0A343KPB8_PORPP 1-879  
1.2/72 1.2/7N | Fucoxanthin-chlorophyll a-c binding protein, chloroplastic |
A0A5J4YKR2_PORPP 38-201  
1.2/82 1.2/8N | RedCAP | A0A5J4YP51_PORPP 34-213  
1.2/A1 1.2/A4 1.2/AD 1.2/AE 1.2/AG 1.2/AH 1.2/AO 1.2/AQ 1.2/Y7 1.2/YA |
R-phycoerythrin gamma chain, chloroplastic | A0A5J4YX19_PORPP 9-298  
1.2/A2 1.2/AN | PsaA | W0S1N1_PORPP 1-752  
1.2/A3 1.2/C3 1.2/E3 1.2/G3 1.2/J3 1.2/K3 1.2/N3 1.2/P3 1.2/R3 1.2/T3 1.2/c3
1.2/e3 1.2/g3 1.2/i3 1.2/l3 1.2/m3 1.2/p3 1.2/r3 1.2/t3 1.2/v3 |
Allophycocyanin alpha subunit | W0RYM0_PORPP 1-161  
1.2/A5 1.2/A7 1.2/A9 1.2/AA 1.2/AF 1.2/AI 1.2/AK 1.2/AP 1.2/BD 1.2/BQ 1.2/C5
1.2/C7 1.2/C9 1.2/CA 1.2/CF 1.2/CI 1.2/CJ 1.2/CK 1.2/CM 1.2/CP 1.2/DD 1.2/DQ
1.2/E5 1.2/E7 1.2/E9 1.2/EA 1.2/EF 1.2/EI 1.2/EJ 1.2/EK 1.2/EM 1.2/EP 1.2/FD
1.2/FQ 1.2/G5 1.2/G7 1.2/G9 1.2/GA 1.2/GF 1.2/GI 1.2/GJ 1.2/GK 1.2/GM 1.2/GP
1.2/HD 1.2/HQ 1.2/I5 1.2/I7 1.2/I9 1.2/IA 1.2/IF 1.2/II 1.2/IJ 1.2/IK 1.2/IM
1.2/IP 1.2/JB 1.2/JD 1.2/JQ 1.2/K5 1.2/K7 1.2/K9 1.2/KA 1.2/KF 1.2/KI 1.2/KJ
1.2/KK 1.2/KM 1.2/KP 1.2/LD 1.2/LQ 1.2/M7 1.2/MA 1.2/MF 1.2/MJ 1.2/MK 1.2/MM
1.2/MP 1.2/N5 1.2/N9 1.2/ND 1.2/NI 1.2/NQ 1.2/O1 1.2/O4 1.2/O7 1.2/OA 1.2/OE
1.2/OF 1.2/OG 1.2/OH 1.2/OJ 1.2/OK 1.2/OM 1.2/OO 1.2/OP 1.2/P5 1.2/P9 1.2/PD
1.2/PI 1.2/PQ 1.2/Q1 1.2/Q4 1.2/Q7 1.2/QA 1.2/QE 1.2/QF 1.2/QG 1.2/QH 1.2/QJ
1.2/QK 1.2/QM 1.2/QO 1.2/QP 1.2/R5 1.2/R9 1.2/RD 1.2/RI 1.2/RQ 1.2/S1 1.2/S4
1.2/S7 1.2/SA 1.2/SE 1.2/SF 1.2/SG 1.2/SH 1.2/SJ 1.2/SK 1.2/SM 1.2/SO 1.2/SP
1.2/T5 1.2/T9 1.2/TB 1.2/TD 1.2/TI 1.2/TQ 1.2/U1 1.2/U4 1.2/U7 1.2/UA 1.2/UE
1.2/UF 1.2/UG 1.2/UH 1.2/UJ 1.2/UK 1.2/UM 1.2/UO 1.2/UP 1.2/V5 1.2/V9 1.2/VD
1.2/VI 1.2/VQ 1.2/W1 1.2/W4 1.2/W7 1.2/WA 1.2/WE 1.2/WF 1.2/WG 1.2/WH 1.2/WJ
1.2/WK 1.2/WM 1.2/WO 1.2/WP 1.2/X5 1.2/X9 1.2/XD 1.2/XI 1.2/XQ 1.2/YF 1.2/YJ
1.2/YK 1.2/YM 1.2/Z1 1.2/Z4 1.2/ZE 1.2/ZG 1.2/ZH 1.2/ZO 1.2/aF 1.2/aJ 1.2/aK
1.2/aM 1.2/b1 1.2/b4 1.2/bE 1.2/bG 1.2/bH 1.2/bO 1.2/cF 1.2/cK 1.2/d1 1.2/d4
1.2/dE 1.2/dG 1.2/dH 1.2/dJ 1.2/dM 1.2/dO 1.2/eF 1.2/eK 1.2/f1 1.2/f4 1.2/fE
1.2/fG 1.2/fH 1.2/fJ 1.2/fM 1.2/fO 1.2/gF 1.2/gK 1.2/h1 1.2/h4 1.2/hE 1.2/hG
1.2/hH 1.2/hJ 1.2/hM 1.2/hO 1.2/iF 1.2/iK 1.2/j1 1.2/j4 1.2/jE 1.2/jG 1.2/jH
1.2/jJ 1.2/jM 1.2/jO 1.2/kF 1.2/kK 1.2/l1 1.2/l4 1.2/lE 1.2/lG 1.2/lH 1.2/lJ
1.2/lM 1.2/lO 1.2/mF 1.2/mK 1.2/oF 1.2/oK 1.2/p8 1.2/pC 1.2/qF 1.2/qK 1.2/r8
1.2/rC 1.2/sF 1.2/sK 1.2/t8 1.2/tC 1.2/uF 1.2/uK 1.2/v8 1.2/vC 1.2/x8 1.2/xC
1.2/z8 1.2/zC | Phycoerythrin alpha subunit | E2IH77_PORPP 1-164  
1.2/A6 1.2/AL 1.2/a6 1.2/aL | Photosystem II protein D1 | W0RZ08_PORPP 1-360  
1.2/A8 1.2/AC 1.2/a8 1.2/aC | LRH |  
1.2/AB 1.2/EB | Linker4 | A0A5J4YXP2_PORPP 287-424  
1.2/AJ 1.2/AM 1.2/wF 1.2/wK 1.2/xF 1.2/xK | R-phycoerythrin gamma chain,
chloroplastic | A0A5J4YZM7_PORPP 11-283  
1.2/B1 1.2/B4 1.2/BE 1.2/BG 1.2/BH 1.2/BO | Phycobilisome rod-core linker
polypeptide | W0RZ90_PORPP 1-232  
1.2/B2 1.2/BN | Photosystem I P700 chlorophyll a apoprotein A2 | W0RYU6_PORPP
3-734  
1.2/B3 1.2/D3 1.2/F3 1.2/H3 1.2/I3 1.2/L3 1.2/M3 1.2/O3 1.2/Q3 1.2/S3 1.2/U3
1.2/d3 1.2/f3 1.2/h3 1.2/j3 1.2/k3 1.2/n3 1.2/o3 1.2/q3 1.2/s3 1.2/u3 1.2/w3 |
Allophycocyanin beta subunit | W0S279_PORPP 1-161  
1.2/B6 1.2/BL 1.2/b6 1.2/bL | Photosystem II CP47 reaction center protein |
W0RZ84_PORPP 1-509  
1.2/BJ 1.2/BM 1.2/yF 1.2/yK | R-phycoerythrin gamma chain, chloroplastic |
A0A5J4YZH3_PORPP 8-297  
1.2/C1 1.2/C4 1.2/CE 1.2/CG 1.2/CH 1.2/CO 1.2/E1 1.2/E4 1.2/EE 1.2/EG 1.2/EH
1.2/EO 1.2/G1 1.2/G4 1.2/GE 1.2/GG 1.2/GH 1.2/GO 1.2/I1 1.2/I4 1.2/IE 1.2/IG
1.2/IH 1.2/IO 1.2/K1 1.2/K4 1.2/KE 1.2/KG 1.2/KH 1.2/KO 1.2/M1 1.2/M4 1.2/ME
1.2/MG 1.2/MH 1.2/MO | C-phycocyanin alpha subunit | W0RYI4_PORPP 1-162  
1.2/C2 1.2/CN | Photosystem I iron-sulfur center | W0S231_PORPP 1-81  
1.2/C6 1.2/CL 1.2/c6 1.2/cL | Photosystem II CP43 reaction center protein |
W0RYK4_PORPP 1-473  
1.2/D1 1.2/D4 1.2/DE 1.2/DG 1.2/DH 1.2/DO 1.2/F1 1.2/F4 1.2/FE 1.2/FG 1.2/FH
1.2/FO 1.2/H1 1.2/H4 1.2/HE 1.2/HG 1.2/HH 1.2/HO 1.2/J1 1.2/J4 1.2/JE 1.2/JG
1.2/JH 1.2/JO 1.2/L1 1.2/L4 1.2/LE 1.2/LG 1.2/LH 1.2/LO 1.2/N1 1.2/N4 1.2/NE
1.2/NG 1.2/NH 1.2/NO | C-phycocyanin beta subunit | W0RZB2_PORPP 1-172  
1.2/D2 1.2/DN | Photosystem I reaction center subunit II | W0RZ23_PORPP -2-139  
1.2/D6 1.2/DL 1.2/d6 1.2/dL | Photosystem II D2 protein | W0RYZ0_PORPP 2-352  
1.2/E2 1.2/EN | Photosystem I reaction center subunit IV | W0RYG1_PORPP 1-61  
1.2/E6 1.2/EL 1.2/e6 1.2/eL | Cytochrome b559 subunit alpha | W0RYH5_PORPP
0-83  
1.2/F2 1.2/FN | Photosystem I reaction center subunit III | W0RZ71_PORPP 1-185  
1.2/F6 1.2/FL 1.2/f6 1.2/fL | Cytochrome b559 subunit beta | W0S1X0_PORPP 2-45  
1.2/G2 1.2/GN | Cytochrome c6 | W0S1L8_PORPP 7-110  
1.2/G6 1.2/GL 1.2/g6 1.2/gL | PSII_Pbs31 domain-containing protein |
A0A5J4Z270_PORPP 1-213  
1.2/H6 1.2/HL 1.2/h6 1.2/hL | Photosystem II reaction center protein H |
W0RYU5_PORPP 1-67  
1.2/I2 1.2/IN | Photosystem I reaction center subunit VIII | W0RZ51_PORPP 1-37  
1.2/I6 1.2/IL 1.2/i6 1.2/iL | Photosystem II reaction center protein I |
W0RYJ5_PORPP 1-38  
1.2/J2 1.2/JN | Photosystem I reaction center subunit IX | W0RYG9_PORPP 1-42  
1.2/J6 1.2/JL 1.2/j6 1.2/jL | Photosystem II reaction center protein J |
W0RYQ6_PORPP 2-40  
1.2/K2 1.2/KN | Photosystem I reaction center subunit PsaK | W0RZ04_PORPP 1-70  
1.2/K6 1.2/KL 1.2/k6 1.2/kL | Photosystem II reaction center protein K |
W0RZ28_PORPP 1-45  
1.2/KB 1.2/UB | CaRSPs1 | A0A5J4YJY8_PORPP 1-288  
1.2/L2 1.2/LN | Photosystem I reaction center subunit XI | W0S1Z0_PORPP 3-142  
1.2/L6 1.2/LL 1.2/l6 1.2/lL | PsbL | W0RZ31_PORPP 0-37  
1.2/M2 1.2/MN | Photosystem I reaction center subunit XII | W0S1Z9_PORPP 1-30  
1.2/M5 1.2/M9 1.2/Z5 1.2/Z9 | R-phycoerythrin gamma chain, chloroplastic |
A0A5J4YNU6_PORPP -34-298 -33-299  
1.2/M6 1.2/ML 1.2/m6 1.2/mL | PsbM | A0A5J4YYD7_PORPP -56-44  
1.2/MI 1.2/ZI | Phycobilisome 27.9 kDa linker polypeptide, phycoerythrin-
associated, rod | A0A5J4Z323_PORPP 1-316  
1.2/N2 1.2/NN | Ferredoxin | W0RYF9_PORPP 1-99  
1.2/N6 1.2/NL 1.2/n6 1.2/nL | Psb34 |  
1.2/O2 1.2/ON | Photosystem I subunit O | A0A5J4YUC8_PORPP 46-137  
1.2/O6 1.2/OL 1.2/o6 1.2/oL | Oxygen-evolving enhancer protein | E5RPB3_PORPP
-32-254  
1.2/Q6 1.2/QL 1.2/q6 1.2/qL | PsbQ' | A0A5J4Z679_PORPP 1-205  
1.2/R2 1.2/RN | PsaR | A0A5J4YR43_PORPP 44-121  
1.2/R6 1.2/RL 1.2/r6 1.2/rL | Photosystem II protein Y | W0S1X5_PORPP 2-34  
1.2/S6 1.2/SL | LPP1 |  
1.2/T6 1.2/TL 1.2/t6 1.2/tL | Photosystem II reaction center protein T |
W0RYV0_PORPP 1-31  
1.2/U6 1.2/UL 1.2/u6 1.2/uL | PS II complex 12 kDa extrinsic protein |
A0A5J4YLQ6_PORPP -46-103 -46-105  
1.2/V3 1.2/x3 | Allophycocyanin gamma subunit | W0S1U6_PORPP 1-161  
1.2/V6 1.2/VL 1.2/v6 1.2/vL | Cytochrome c550 | W0RYZ6_PORPP -24-137  
1.2/W3 1.2/y3 | Allophycocyanin beta 18 subunit | W0RZE2_PORPP 1-173  
1.2/W6 1.2/WL 1.2/w6 1.2/wL | PsbW |  
1.2/WB 1.2/cB | CaRSP2 | A0A5J4YX67_PORPP 1-327  
1.2/X1 1.2/X4 1.2/XE 1.2/XG 1.2/XH 1.2/XO | Phycobilisome 31.8 kDa linker
polypeptide, phycoerythrin-associated, rod | A0A5J4YM59_PORPP 9-371  
1.2/X3 1.2/z3 | Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-
associated, core | A0A5J4YVZ2_PORPP 40-132  
1.2/X6 1.2/XL 1.2/x6 1.2/xL | Photosystem II reaction center X protein |
W0RZ76_PORPP 3-41  
1.2/Y6 1.2/YL 1.2/y6 1.2/yL | Photosystem II reaction center protein Ycf12 |
W0RZ91_PORPP 1-34  
1.2/YP 1.2/bP | Phycobilisome 31.8 kDa linker polypeptide, phycoerythrin-
associated, rod | A0A5J4YMI8_PORPP -16-409  
1.2/Z2 1.2/ZN | LPS1 |  
1.2/Z6 1.2/ZL 1.2/z6 1.2/zL | Photosystem II reaction center protein Z |
W0RZ40_PORPP 1-62  
1.2/bJ 1.2/bM | Phycobilisome 32.1 kDa linker polypeptide, phycocyanin-
associated, rod | A0A5J4YX63_PORPP -28-461  
1.2/dD 1.2/dQ | Phycobilisome 27.9 kDa linker polypeptide, phycoerythrin-
associated, rod | A0A5J4Z162_PORPP 5-346  
1.2/e7 1.2/eA | Phycobilisome 31.8 kDa linker polypeptide, phycoerythrin-
associated, rod | A0A5J4Z7F4_PORPP -12-290  
1.2/fB 1.2/hB | FAS1 domain-containing protein | A0A5J4Z027_PORPP 0-287  
1.2/zF 1.2/zK | Phycobilisome 31.8 kDa linker polypeptide, phycoerythrin-
associated, rod | A0A5J4YI31_PORPP 1-498  
  
Non-standard residues in 7y5e #1.2  
---  
3XQ — (2S)-2,3-dihydroxypropyl octadecanoate  
BCR — β-carotene  
BCT — bicarbonate ion  
BGC — beta-D-glucopyranose (beta-D-glucose; D-glucose; glucose)  
CL — chloride ion  
CLA — chlorophyll A  
CYC — phycocyanobilin  
DGD — digalactosyl diacyl glycerol (DGDG)  
FE — Fe (III) ion  
FES — FE2/S2 (inorganic) cluster  
GOL — glycerol (glycerin; propane-1,2,3-triol)  
HEM — protoporphyrin IX containing Fe (HEME)  
LHG — 1,2-dipalmitoyl-phosphatidyl-glycerole  
LMG — 1,2-distearoyl-monogalactosyl-diglyceride  
OEX — Ca-MN4-O5 cluster  
PEB — phycoerythrobilin  
PHO — pheophytin A  
PL9 —
2,3-dimethyl-5-(3,7,11,15,19,23,27,31,35-nonamethyl-2,6,10,14,18,22,26,30,34-hexatriacontanonaenyl-2,5-cyclohexadiene-1,4-dione-2,3-dimethyl-5-solanesyl-1,4-benzoquinone
(plastoquinone 9)  
PQN — phylloquinone (vitamin K1; 2-methyl-3-phytyl-1,4-naphthoquinone)  
PUB — phycourobilin  
SF4 — iron/sulfur cluster  
ZEX —
(1R,2S)-4-{(1E,3E,5E,7E,9E,11E,13E,15E,17E)-18-[(4S)-4-hydroxy-2,6,6-trimethylcyclohex-1-en-1-yl]-3,7,12,16-tetramethyloctadeca-1,3,5,7,9,11,13,15,17-nonaen-1-yl}-2,5,5-trimethylcyclohex-3-en-1-ol  
  

> isolde start

> set selectionWidth 4

Removed all altlocs in #1.2 and reset associated occupancies to 1.  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 8849 residues in model #1.2 to IUPAC-
IUB standards.  

> select clear

> graphics quality ribbon

Expected keyword "ribbonDivisions" or "ribbonSides"  

> graphics quality ribbonDivisions

Missing "ribbonDivisions" keyword's argument  

> graphics quality ribbonDivisions

Missing "ribbonDivisions" keyword's argument  

> graphics quality

Quality 1, atom triangles 2000, bond triangles 160, ribbon divisions 2  

> graphics quality ribbonDivisions 5

> ui tool show "Ramachandran Plot"

> hide HC

> view name clash1

> hide HC

> view name clash2

> view name clash3

> hide HC

> clipper isolate #1

> select clear

> view name overview

> ui tool show "Volume Viewer"

> volume #1.1.1.1 step 1

> movie record

> movie stop

> movie reset

> view name overview

> movie record

> view clash1 frames 120

> rock y 30 60 cycle 60

> view overview frames 30

> view clash2 frames 120

> rock y 30 60 cycle 60

> movie stop

> movie reset

> graphics quality

Quality 1, atom triangles 10, bond triangles 24, ribbon divisions 5  

> graphics quality atomTriangles 32 bondTriangles 32

> clipper isolate #1 maskRadius 5

> volume #1.1.1.1 step 1

> clashes #1

85684 clashes  

> view name clash2

> view clash1

> view name clash1

> view clash3

> view name clash4

> view overview

> movie record

> view clash1 frames 120

> rock y 30 60 cycle 60

> view overview frames 30

> movie duplicate 10

> view clash2 frames 120

> movie stop

[Repeated 1 time(s)]Not currently recording  

> movie stop

Not currently recording  

> movie stop

Not currently recording  

> movie stop

Not currently recording  

> movie stop

Not currently recording  

> movie stop

Not currently recording  

> movie stop

Not currently recording  

> movie stop

Not currently recording  

> movie stop

Not currently recording  

> movie stop

Not currently recording  

> view overview

> movie reset

> usage movie rec

movie record [directory name of a folder to save/write; a name of 'browse'
will bring up a file browser] [pattern a text string] [format format] [size
size] [supersample an integer] [limit an integer]  
— Start saving frames of a movie to image files  
format: one of JPEG, PNG, or PPM  
size: some integers  

> windowsize

window size 1287 828  

> windowsize

window size 2439 1476  

> movie record

> view clash1 frames 90

> movie stop

> movie reset

> cofr showPivot false

> view overview

> movie record

> view clash1 frames 90

> rock y 30 60 cycle 60

> view overview frames 30

> movie duplicate 10

> view clash2 frames 90

> movie stop

[Repeated 1 time(s)]Not currently recording  

> movie stop

Not currently recording  

> movie stop

Not currently recording  

> stopstop

Unknown command: movie stopstop  

> stop

[Repeated 2 time(s)]

> view overview

> view clash1 frames 3

> view overview

> view clash2 frames 3

> view overview

> ui tool show Shell

> view clash2 frames 5

> view overview

> view clash2 frames 3

Profile for last activation of new frame trigger:  
25892913 function calls (25593577 primitive calls) in 31.241 seconds  
  
Ordered by: internal time  
List reduced from 127 to 20 due to restriction <20>  
  
ncalls tottime percall cumtime percall filename:lineno(function)  
748330/448998 9.560 0.000 9.910 0.000 C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\geometry\matrix.py:157(multiply_matrices)  
149667 4.311 0.000 5.116 0.000 C:\Program Files\ChimeraX\bin\lib\site-
packages\numpy\linalg\linalg.py:483(inv)  
149666 3.475 0.000 4.763 0.000 C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\geometry\matrix.py:479(rotation_transform)  
1496679 1.628 0.000 1.628 0.000 {built-in method numpy.array}  
149667 1.151 0.000 7.474 0.000 C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\geometry\matrix.py:120(invert_matrix)  
1945708 1.068 0.000 1.592 0.000 <frozen
importlib._bootstrap>:1033(_handle_fromlist)  
898033 1.053 0.000 6.568 0.000 {built-in method
numpy.core._multiarray_umath.implement_array_function}  
149666 1.004 0.000 14.468 0.000 C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\geometry\matrix.py:710(fractional_transform)  
299340 0.928 0.000 3.168 0.000 C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\geometry\matrix.py:18(apply_matrix)  
149666 0.775 0.000 1.386 0.000 C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\geometry\matrix.py:561(R_to_axis_angle)  
299332 0.361 0.000 0.999 0.000 C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\geometry\matrix.py:68(translation_matrix)  
3592075 0.325 0.000 0.325 0.000 {built-in method builtins.hasattr}  
1 0.310 0.310 30.803 30.803 C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\std_commands\view.py:425(<listcomp>)  
149665 0.301 0.000 0.301 0.000 {built-in method
chimerax.geometry._geometry.same_matrix}  
149666 0.289 0.000 27.664 0.000 C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\geometry\matrix.py:701(interpolate_transforms)  
2394656 0.287 0.000 0.287 0.000 C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\geometry\matrix.py:168(<genexpr>)  
149666 0.286 0.000 28.534 0.000 C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\geometry\place.py:244(interpolate)  
149675 0.270 0.000 1.897 0.000 C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\geometry\place.py:100(__mul__)  
4190780 0.262 0.000 0.262 0.000 {built-in method builtins.isinstance}  
149666 0.259 0.000 1.216 0.000 C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\geometry\matrix.py:427(normalize_vector)  
  
  
  

> view clash2 frames 3

Profile for last activation of new frame trigger:  
25892915 function calls (25593579 primitive calls) in 31.464 seconds  
  
Ordered by: cumulative time  
List reduced from 127 to 20 due to restriction <20>  
  
ncalls tottime percall cumtime percall filename:lineno(function)  
1 0.000 0.000 31.464 31.464 C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py:221(_activate)  
8 0.000 0.000 31.464 3.933 C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py:134(invoke)  
1 0.000 0.000 31.464 31.464 C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\motion.py:36(__call__)  
1 0.000 0.000 31.464 31.464 C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\std_commands\view.py:354(frame_cb)  
1 0.000 0.000 31.464 31.464 C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\std_commands\view.py:365(_interpolate_views)  
1 0.028 0.028 31.463 31.463 C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\std_commands\view.py:414(_interpolate_model_positions)  
1 0.001 0.001 31.079 31.079 C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\std_commands\view.py:423(_interpolated_positions)  
1 0.306 0.306 31.077 31.077 C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\std_commands\view.py:425(<listcomp>)  
149666 0.295 0.000 28.812 0.000 C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\geometry\place.py:244(interpolate)  
149666 0.290 0.000 27.928 0.000 C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\geometry\matrix.py:701(interpolate_transforms)  
149666 1.017 0.000 14.604 0.000 C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\geometry\matrix.py:710(fractional_transform)  
748330/448998 9.653 0.000 10.010 0.000 C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\geometry\matrix.py:157(multiply_matrices)  
149667 1.147 0.000 7.529 0.000 C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\geometry\matrix.py:120(invert_matrix)  
898033 1.059 0.000 6.627 0.000 {built-in method
numpy.core._multiarray_umath.implement_array_function}  
149667 0.096 0.000 5.414 0.000 <__array_function__ internals>:177(inv)  
149667 4.346 0.000 5.171 0.000 C:\Program Files\ChimeraX\bin\lib\site-
packages\numpy\linalg\linalg.py:483(inv)  
149666 3.501 0.000 4.799 0.000 C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\geometry\matrix.py:479(rotation_transform)  
299340 0.940 0.000 3.179 0.000 C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\geometry\matrix.py:18(apply_matrix)  
149675 0.270 0.000 1.903 0.000 C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\geometry\place.py:100(__mul__)  
1496679 1.624 0.000 1.624 0.000 {built-in method numpy.array}  
  
  
  

> view matrix

view matrix camera
-0.93466,-0.29094,0.20436,307.27,-0.13635,0.82416,0.5497,376.21,-0.32836,0.48592,-0.80998,481.36  
view matrix models
#1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1.1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1.1.1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1.1.1.1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1.1.1.2,1,0,0,0,0,1,0,0,0,0,1,0,#1.2,1,0,0,0,0,1,0,0,0,0,1,0,#1.2.3,1,0,0,0,0,1,0,0,0,0,1,0,#1.2.4,1,0,0,0,0,1,0,0,0,0,1,0,#1.2.5,1,0,0,0,0,1,0,0,0,0,1,0,#1.2.5.1,0.98773,0.071822,0.32821,500.49,0.071822,0.80859,-0.93399,265.52,-0.21292,0.60592,1.2075,263.56,#1.2.6,1,0,0,0,0,1,0,0,0,0,1,0,#1.2.6.1,1,0,0,0,0,1,0,0,0,0,1,0,#1.2.6.2,0.5,0,0,499.64,0,0.5,0,265.6,0,0,0.5,256.25,#1.2.7,1,0,0,0,0,1,0,0,0,0,1,0,#1.2.7.1,1,0,0,0,0,1,0,0,0,0,1,0,#1.2.8,1,0,0,0,0,1,0,0,0,0,1,0,#1.2.9,1,0,0,0,0,1,0,0,0,0,1,0,#1.3,1,0,0,0,0,1,0,0,0,0,1,0  
  

> pwd

Current working directory is: C:\Users\Tristan Croll\Desktop  

> save 7y5e_session.cxs

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 285, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\geometry\psession.py", line 46, in take_snapshot  
data = {'shift_and_scale': sas} if sas else {'array': places.array()}  
ValueError: The truth value of an array with more than one element is
ambiguous. Use a.any() or a.all()  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 262, in discovery  
self.processed[key] = self.process(obj, parents)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 290, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'named views' ->
<chimerax.std_commands.view.NamedViews object at 0x0000019FF4376760> ->
<chimerax.std_commands.view.NamedView object at 0x0000019FEC117B50> ->
<chimerax.geometry.place.Places object at 0x000001A06A3029D0>  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 899, in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 625, in save  
mgr.discovery(self._state_containers)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'named views' ->
<chimerax.std_commands.view.NamedViews object at 0x0000019FF4376760> ->
<chimerax.std_commands.view.NamedView object at 0x0000019FEC117B50> ->
<chimerax.geometry.place.Places object at 0x000001A06A3029D0>: Error while
saving session data for 'named views' ->
<chimerax.std_commands.view.NamedViews object at 0x0000019FF4376760> ->
<chimerax.std_commands.view.NamedView object at 0x0000019FEC117B50> ->
<chimerax.geometry.place.Places object at 0x000001A06A3029D0>  
  
ValueError: error processing: 'named views' -> -> -> : Error while saving
session data for 'named views' -> -> ->  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 285, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\geometry\psession.py", line 46, in take_snapshot  
data = {'shift_and_scale': sas} if sas else {'array': places.array()}  
ValueError: The truth value of an array with more than one element is
ambiguous. Use a.any() or a.all()  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 262, in discovery  
self.processed[key] = self.process(obj, parents)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 290, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'named views' ->
<chimerax.std_commands.view.NamedViews object at 0x0000019FF4376760> ->
<chimerax.std_commands.view.NamedView object at 0x0000019FEC117B50> ->
<chimerax.geometry.place.Places object at 0x000001A06A3029D0>  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 319, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 75, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 90, in provider_save  
saver_info.save(session, path, **provider_kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 84, in save  
return cxs_save(session, path, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 899, in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 625, in save  
mgr.discovery(self._state_containers)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'named views' ->
<chimerax.std_commands.view.NamedViews object at 0x0000019FF4376760> ->
<chimerax.std_commands.view.NamedView object at 0x0000019FEC117B50> ->
<chimerax.geometry.place.Places object at 0x000001A06A3029D0>: Error while
saving session data for 'named views' ->
<chimerax.std_commands.view.NamedViews object at 0x0000019FF4376760> ->
<chimerax.std_commands.view.NamedView object at 0x0000019FEC117B50> ->
<chimerax.geometry.place.Places object at 0x000001A06A3029D0>  
  
ValueError: error processing: 'named views' -> -> -> : Error while saving
session data for 'named views' -> -> ->  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 528.24
OpenGL renderer: NVIDIA GeForce RTX 3070 Laptop GPU/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.9.11
Locale: en_GB.cp1252
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: windows

Manufacturer: HP
Model: HP ZBook Studio 15.6 inch G8 Mobile Workstation PC
OS: Microsoft Windows 11 Pro (Build 22621)
Memory: 34,007,068,672
MaxProcessMemory: 137,438,953,344
CPU: 16 11th Gen Intel(R) Core(TM) i7-11800H @ 2.30GHz
OSLanguage: en-GB

Installed Packages:
    -himerax-isolde: 1.6.dev0
    -himerax-qscore: 1.0
    alabaster: 0.7.13
    appdirs: 1.4.4
    asttokens: 2.2.1
    Babel: 2.12.1
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    build: 0.10.0
    certifi: 2022.12.7
    cftime: 1.6.2
    charset-normalizer: 3.1.0
    ChimeraX-AddCharge: 1.5.9
    ChimeraX-AddH: 2.2.4
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.3.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.9.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.43.10
    ChimeraX-AtomicLibrary: 10.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.8
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
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    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3.1
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    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.6.dev1
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    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    ChimeraX-Map: 1.1.4
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.0.12
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.9
    ChimeraX-ModelPanel: 1.3.7
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.0
    ChimeraX-NRRD: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.10.1
    ChimeraX-PDB: 2.7
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-QScore: 1.0
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 3.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.1
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.8.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.10.2
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Topography: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.28.4
    ChimeraX-uniprot: 2.2.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.1
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.1.3
    comtypes: 1.1.14
    contourpy: 1.0.7
    cxservices: 1.2.2
    cycler: 0.11.0
    Cython: 0.29.33
    debugpy: 1.6.7
    decorator: 5.1.1
    docutils: 0.19
    executing: 1.2.0
    filelock: 3.9.0
    fonttools: 4.39.3
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.8.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.35
    imagecodecs: 2022.9.26
    imagesize: 1.4.1
    importlib-metadata: 6.3.0
    ipykernel: 6.21.1
    ipython: 8.10.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.0.6
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.0.2
    jupyter-core: 5.3.0
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Change History (15)

comment:1 by pett, 3 years ago

Component: Unassigned → Sessions
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Saving shift_and_scale uses numpy array as boolean

comment:2 by Tom Goddard, 2 years ago

Description: modified (diff)

This session saving code would never work if a Places instance is saved that is using shift and scale placement. The only ChimeraX code that uses that placement is atom drawings and those don't save directly in sessions since the structure recreates them. So I guess ISOLDE is what is trying to save shift-and-scale Places in a session. I would like a test case to easily reproduce this if you can provide one, because once I make the trivial fix, there is no telling if it will correctly save and restore in a session since obviously that code path has never been used.

in reply to:  3 ; comment:3 by Tristan Croll, 2 years ago 

Hmm... looks like it's the Ramachandran annotation (uses `shift_and_scale`
to set the indicator positions here:
https://github.com/tristanic/isolde/blob/e40a11e673f8e23917791ac03599329e25bf024a/isolde/src/validation/rama_annotation.py#L246).
Doing "rama #{model}" on an otherwise vanilla structure then creating a
named view is enough to trigger the traceback on session save.

On Wed, May 10, 2023 at 8:30 AM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

comment:4 by Tom Goddard, 2 years ago

That test case works correctly for me with no errors

open 1a0m
show atoms
rama #1
view name test
save test.cxs
open test.cxs

with ChimeraX 1.6.1 and current ISOLDE.

Last edited 2 years ago by Tom Goddard (previous) (diff)

in reply to:  5 ; comment:5 by Tristan Croll, 2 years ago 

Try:

open 1a0m
 show atoms
 rama #1
view name test
 save test.cxs
(should fail here)

On Wed, 10 May 2023 at 18:17, ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

in reply to:  6 ; comment:6 by goddard@…, 2 years ago 

Oops.  I did "view name test" and just forgot to put it in my previous comment.  It works without errors.

in reply to:  7 ; comment:7 by Tristan Croll, 2 years ago 

Weird. On my Windows machine (Apr 25 release candidate) that same set of
commands fails. I’m on the bus right now - will try with 1.6.1 either
this evening or tomorrow.

On Wed, 10 May 2023 at 18:31, ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

in reply to:  8 ; comment:8 by Tristan Croll, 2 years ago 

Did you do the "view name" command before or after the "rama" command? The
traceback only happens in the latter scenario:

open 1a0m
show
view name test
rama
save test.cxs
view name test2
save test.cxs;# kaboom

On Wed, May 10, 2023 at 6:36 PM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

comment:9 by Tom Goddard, 2 years ago

Of course I did the "view name test" after rama. It is mysterious that it produces no error in ChimeraX 1.6.1 on Mac.

in reply to:  10 ; comment:10 by Tristan Croll, 2 years ago 

I updated my Windows machine to 1.6.1 and downgraded ISOLDE to the version
on the ToolShed (1.6.dev1). Still fails for me. Mystifying.

On Wed, May 10, 2023 at 7:20 PM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

comment:11 by Tom Goddard, 2 years ago

I'll try on Windows. Unlikely it is OS specific, but something is weird.

in reply to:  12 ; comment:12 by Tristan Croll, 2 years ago 

Ah - wait... the Mac version on the Toolshed is currently behind the others
(1.6.dev0; Linux and Windows are at .dev1 (slack of me, I know - life has
been somewhat distracting lately). If I downgrade my Mac to the version on
the Toolshed then the problem goes away. That narrows down the issue -
it'll be something to do with my attempts to address #8432 (most likely
promoting the Ramachandran `Drawing` to a `Model`). Since that didn't
really actually fix anything, maybe I should roll it back.

On Wed, May 10, 2023 at 7:46 PM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

comment:13 by Tom Goddard, 2 years ago

It is kind of nice having annotations be models instead of drawings so the user can see them in Model Panel and hide them.

The bug is easy to fix and should be fixed since the session save code is broken. I will test the simple fix on Windows and if it works commit it.

in reply to:  14 ; comment:14 by Tristan Croll, 2 years ago 

Well… they could do that before anyway. The `RamaAnnotator` was always a
`Model`, but it has to manage two drawings (one for the CA indicators, one
for the cis/twisted peptide bonds). Those were `Drawing`s before, and are
now `Model`s. I guess it doesn’t truly matter either way, so if the fix
works I may as well leave it as is.

On Wed, 10 May 2023 at 20:53, ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

comment:15 by Tom Goddard, 2 years ago

Resolution: → fixed
Status: assigned → closed

Fixed.

The session saving code for shift and scale positioning of graphics instances did a test "if sas" where sas was either None or a numpy array and it gives an error for a numpy array, a standard numpy pitfall, so I corrected it to "if sas is not None" and tested with ISOLDE Ramachandran plots on Windows and session save and restore worked.

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