id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 2807 'NoneType' object has no attribute 'needs_update' after 2D labels closed shiran.dror@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: Windows-10-10.0.17763 ChimeraX Version: 0.91 (2019-12-23) Description Changed preset to ""Interactive"" got this error, then changed background to white and got it again Log: UCSF ChimeraX version: 0.91 (2019-12-23) © 2016-2019 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""C:/bukau_lab/research proposal/ribosome_structure/chimerax/4U3U.cxc"" > open 4U3U 4u3u title: Crystal structure of Cycloheximide bound to the yeast 80S ribosome [more info...] Chain information for 4u3u #1 --- Chain | Description 1 5 | 25S ribosomal RNA 2 6 | 18S ribosomal RNA 3 7 | 5S ribosomal RNA 4 8 | 5.8S ribosomal RNA C0 c0 | 40S ribosomal protein S10-A C1 c1 | 40S ribosomal protein S11-A C2 c2 | 40S ribosomal protein S12 C3 c3 | 40S ribosomal protein S13 C4 c4 | 40S ribosomal protein S14-A C5 c5 | 40S ribosomal protein S15 C6 c6 | 40S ribosomal protein S16-A C7 c7 | 40S ribosomal protein S17-A C8 c8 | 40S ribosomal protein S18-A C9 c9 | 40S ribosomal protein S19-A D0 d0 | 40S ribosomal protein S20 D1 d1 | 40S ribosomal protein S21-A D2 d2 | 40S ribosomal protein S22-A D3 d3 | 40S ribosomal protein S23-A D4 d4 | 40S ribosomal protein S24-A D5 d5 | 40S ribosomal protein S25-A D6 d6 | 40S ribosomal protein S26-B D7 d7 | 40S ribosomal protein S27-A D8 d8 | 40S ribosomal protein S28-A D9 d9 | 40S ribosomal protein S29-A E0 | 40S ribosomal protein S30-A E1 | Ubiquitin-40S ribosomal protein S31 L2 l2 | 60S ribosomal protein L2-A L3 l3 | 60S ribosomal protein L3 L4 l4 | 60S ribosomal protein L4-A L5 l5 | 60S ribosomal protein L5 L6 l6 | 60S ribosomal protein L6-A L7 l7 | 60S ribosomal protein L7-A L8 l8 | 60S ribosomal protein L8-A L9 l9 | 60S ribosomal protein L9-A M0 m0 | 60S ribosomal protein L10 M1 m1 | 60S ribosomal protein L11-B M3 m3 | 60S ribosomal protein L13-A M4 m4 | 60S ribosomal protein L14-A M5 m5 | 60S ribosomal protein L15-A M6 m6 | 60S ribosomal protein L16-A M7 m7 | 60S ribosomal protein L17-A M8 m8 | 60S ribosomal protein L18-A M9 m9 | 60S ribosomal protein L19-A N0 n0 | 60S ribosomal protein L20-A N1 n1 | 60S ribosomal protein L21-A N2 n2 | 60S ribosomal protein L22-A N3 n3 | 60S ribosomal protein L23-A N4 n4 | 60S ribosomal protein L24-A N5 n5 | 60S ribosomal protein L25 N6 n6 | 60S ribosomal protein L26-A N7 n7 | 60S ribosomal protein L27-A N8 n8 | 60S ribosomal protein L28 N9 n9 | 60S ribosomal protein L29 O0 o0 | 60S ribosomal protein L30 O1 o1 | 60S ribosomal protein L31-A O2 o2 | 60S ribosomal protein L32 O3 o3 | 60S ribosomal protein L33-A O4 o4 | 60S ribosomal protein L34-A O5 o5 | 60S ribosomal protein L35-A O6 o6 | 60S ribosomal protein L36-A O7 o7 | 60S ribosomal protein L37-A O8 o8 | 60S ribosomal protein L38 O9 o9 | 60S ribosomal protein L39 Q0 q0 | Ubiquitin-60S ribosomal protein L40 Q1 q1 | 60S ribosomal protein L41-A Q2 q2 | 60S ribosomal protein L42-A Q3 q3 | 60S ribosomal protein L43-A S0 s0 | 40S ribosomal protein S0-A S1 s1 | 40S ribosomal protein S1-A S2 s2 | 40S ribosomal protein S2 S3 s3 | 40S ribosomal protein S3 S4 s4 | 40S ribosomal protein S4-A S5 s5 | 40S ribosomal protein S5 S6 s6 | 40S ribosomal protein S6-A S7 s7 | 40S ribosomal protein S7-A S8 s8 | 40S ribosomal protein S8-A S9 s9 | 40S ribosomal protein S9-A SM sM | Suppressor protein STM1 SR sR | Guanine nucleotide-binding protein subunit beta-like protein e0 | 40S ribosomal protein S30-A e1 | Ubiquitin-40S ribosomal protein S31 m2 | UNKNOWN PROTEIN m2 p0 | 60S acidic ribosomal protein P0 p1 | UNKNOWN PROTEIN p1 p2 | UNKNOWN PROTEIN p2 Non-standard residues in 4u3u #1 --- 3HE — 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione MG — magnesium ion OHX — osmium (III) hexammine (osmium(6+) hexaazanide) ZN — zinc ion 4u3u mmCIF Assemblies --- 1| software_defined_assembly 2| software_defined_assembly > hide atoms > hide ribbons > show surfaces > color gray > select protein 179694 atoms, 182766 bonds, 15 pseudobonds, 2 models selected > color sel white > select /L0-Q9 49865 atoms, 50591 bonds, 129 pseudobonds, 3 models selected > color sel #aaffff > select /C0-D9,S0-S9 34555 atoms, 35067 bonds, 51 pseudobonds, 3 models selected > color sel #fad0ff > select protein sequence .{1}$ 904 atoms, 809 bonds, 1 model selected > color sel red > show sel atoms > select protein sequence w(b) 264 atoms, 276 bonds, 1 model selected > color sel green > show sel atoms > hide /c0-s9 surfaces > hide /c0-s9 atoms > hide /5-9 surfaces > hide /5-9 atoms > hide /sM,sR surfaces > hide /sM,sR atoms > ~select Nothing selected > view executed 4U3U.cxc > set bgColor white > close session > open ""C:\bukau_lab\research proposal\ribosome_structure\chimerax\4U3U.cxc"" > open 4U3U 4u3u title: Crystal structure of Cycloheximide bound to the yeast 80S ribosome [more info...] Chain information for 4u3u #1 --- Chain | Description 1 5 | 25S ribosomal RNA 2 6 | 18S ribosomal RNA 3 7 | 5S ribosomal RNA 4 8 | 5.8S ribosomal RNA C0 c0 | 40S ribosomal protein S10-A C1 c1 | 40S ribosomal protein S11-A C2 c2 | 40S ribosomal protein S12 C3 c3 | 40S ribosomal protein S13 C4 c4 | 40S ribosomal protein S14-A C5 c5 | 40S ribosomal protein S15 C6 c6 | 40S ribosomal protein S16-A C7 c7 | 40S ribosomal protein S17-A C8 c8 | 40S ribosomal protein S18-A C9 c9 | 40S ribosomal protein S19-A D0 d0 | 40S ribosomal protein S20 D1 d1 | 40S ribosomal protein S21-A D2 d2 | 40S ribosomal protein S22-A D3 d3 | 40S ribosomal protein S23-A D4 d4 | 40S ribosomal protein S24-A D5 d5 | 40S ribosomal protein S25-A D6 d6 | 40S ribosomal protein S26-B D7 d7 | 40S ribosomal protein S27-A D8 d8 | 40S ribosomal protein S28-A D9 d9 | 40S ribosomal protein S29-A E0 | 40S ribosomal protein S30-A E1 | Ubiquitin-40S ribosomal protein S31 L2 l2 | 60S ribosomal protein L2-A L3 l3 | 60S ribosomal protein L3 L4 l4 | 60S ribosomal protein L4-A L5 l5 | 60S ribosomal protein L5 L6 l6 | 60S ribosomal protein L6-A L7 l7 | 60S ribosomal protein L7-A L8 l8 | 60S ribosomal protein L8-A L9 l9 | 60S ribosomal protein L9-A M0 m0 | 60S ribosomal protein L10 M1 m1 | 60S ribosomal protein L11-B M3 m3 | 60S ribosomal protein L13-A M4 m4 | 60S ribosomal protein L14-A M5 m5 | 60S ribosomal protein L15-A M6 m6 | 60S ribosomal protein L16-A M7 m7 | 60S ribosomal protein L17-A M8 m8 | 60S ribosomal protein L18-A M9 m9 | 60S ribosomal protein L19-A N0 n0 | 60S ribosomal protein L20-A N1 n1 | 60S ribosomal protein L21-A N2 n2 | 60S ribosomal protein L22-A N3 n3 | 60S ribosomal protein L23-A N4 n4 | 60S ribosomal protein L24-A N5 n5 | 60S ribosomal protein L25 N6 n6 | 60S ribosomal protein L26-A N7 n7 | 60S ribosomal protein L27-A N8 n8 | 60S ribosomal protein L28 N9 n9 | 60S ribosomal protein L29 O0 o0 | 60S ribosomal protein L30 O1 o1 | 60S ribosomal protein L31-A O2 o2 | 60S ribosomal protein L32 O3 o3 | 60S ribosomal protein L33-A O4 o4 | 60S ribosomal protein L34-A O5 o5 | 60S ribosomal protein L35-A O6 o6 | 60S ribosomal protein L36-A O7 o7 | 60S ribosomal protein L37-A O8 o8 | 60S ribosomal protein L38 O9 o9 | 60S ribosomal protein L39 Q0 q0 | Ubiquitin-60S ribosomal protein L40 Q1 q1 | 60S ribosomal protein L41-A Q2 q2 | 60S ribosomal protein L42-A Q3 q3 | 60S ribosomal protein L43-A S0 s0 | 40S ribosomal protein S0-A S1 s1 | 40S ribosomal protein S1-A S2 s2 | 40S ribosomal protein S2 S3 s3 | 40S ribosomal protein S3 S4 s4 | 40S ribosomal protein S4-A S5 s5 | 40S ribosomal protein S5 S6 s6 | 40S ribosomal protein S6-A S7 s7 | 40S ribosomal protein S7-A S8 s8 | 40S ribosomal protein S8-A S9 s9 | 40S ribosomal protein S9-A SM sM | Suppressor protein STM1 SR sR | Guanine nucleotide-binding protein subunit beta-like protein e0 | 40S ribosomal protein S30-A e1 | Ubiquitin-40S ribosomal protein S31 m2 | UNKNOWN PROTEIN m2 p0 | 60S acidic ribosomal protein P0 p1 | UNKNOWN PROTEIN p1 p2 | UNKNOWN PROTEIN p2 Non-standard residues in 4u3u #1 --- 3HE — 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione MG — magnesium ion OHX — osmium (III) hexammine (osmium(6+) hexaazanide) ZN — zinc ion 4u3u mmCIF Assemblies --- 1| software_defined_assembly 2| software_defined_assembly > hide atoms > hide ribbons > show surfaces > color gray > select protein 179694 atoms, 182766 bonds, 15 pseudobonds, 2 models selected > color sel white > select /L0-Q9 49865 atoms, 50591 bonds, 129 pseudobonds, 3 models selected > color sel #aaffff > select /C0-D9,S0-S9 34555 atoms, 35067 bonds, 51 pseudobonds, 3 models selected > color sel #fad0ff > select protein sequence .{1}$ 904 atoms, 809 bonds, 1 model selected > color sel red > show sel atoms > select protein sequence w(b) 264 atoms, 276 bonds, 1 model selected > color sel green > show sel atoms > hide /c0-s9 surfaces > hide /c0-s9 atoms > hide /5-9 surfaces > hide /5-9 atoms > hide /sM,sR surfaces > hide /sM,sR atoms > ~select Nothing selected > view executed 4U3U.cxc > select /E1 567 atoms, 577 bonds, 4 pseudobonds, 2 models selected > select clear > close session > open ""C:\bukau_lab\research proposal\ribosome_structure\chimerax\ribosome > model (PDB 6T4Q).cxs"" format session opened ChimeraX session > view > lighting full > save C:\Users\Shiran\Desktop\image1.png supersample 3 > save C:\Users\Shiran\Desktop\image1.png supersample 5 Expected a models specifier or a keyword Expected a models specifier or a keyword > save C:\Users\Shiran\Desktop\ribosomal_proteins_c_terminal.png supersample 5 > save C:\Users\Shiran\Desktop\ribosomal_proteins_c_terminal_2.png supersample > 5 > close session > open ""C:/bukau_lab/research proposal/ribosome_structure/chimerax/6T4Q.cxc"" > open 6T4Q 6t4q title: Structure of yeast 80S ribosome stalled on the CGA-CCG inhibitory codon combination. [more info...] Chain information for 6t4q #1 --- Chain | Description 5 | mRNA 6 | ICG tRNA Arg (P/P) 7 | tRNA (E/E) 8 | nascent chain C1 | 25S rRNA C2 | 18S rRNA C3 | 5.8S rRNA C4 | 5S rRNA LA | 60S ribosomal protein L2-A LB | 60S ribosomal protein L3 LC | 60S ribosomal protein L4-A LD | 60S ribosomal protein L5 LE | 60S ribosomal protein L6-B LF | 60S ribosomal protein L7-A LG | 60S ribosomal protein L8-A LH | 60S ribosomal protein L9-A LI | 60S ribosomal protein L10 LJ | 60S ribosomal protein L11-B LL | 60S ribosomal protein L13-A LM | 60S ribosomal protein L14-A LN | 60S ribosomal protein L15-A LO | 60S ribosomal protein L16-A LP | 60S ribosomal protein L17-A LQ | 60S ribosomal protein L18-A LR | 60S ribosomal protein L19-A LS | 60S ribosomal protein L20-A LT | 60S ribosomal protein L21-A LU | 60S ribosomal protein L22-A LV | 60S ribosomal protein L23-A LW | 60S ribosomal protein L24-A LX | 60S ribosomal protein L25 LY | 60S ribosomal protein L26-A LZ | 60S ribosomal protein L27-A La | 60S ribosomal protein L28 Lb | 60S ribosomal protein L29 Lc | 60S ribosomal protein L30 Ld | 60S ribosomal protein L31-A Le | 60S ribosomal protein L32 Lf | 60S ribosomal protein L33-A Lg | 60S ribosomal protein L34-A Lh | 60S ribosomal protein L35-A Li | 60S ribosomal protein L36-A Lj | 60S ribosomal protein L37-A Lk | 60S ribosomal protein L38 Ll | 60S ribosomal protein L39 Lm | Ubiquitin-60S ribosomal protein L40 Ln | 60S ribosomal protein L41-A Lo | 60S ribosomal protein L42-A Lp | 60S ribosomal protein L43-A SA | 40S ribosomal protein S0-A SB | 40S ribosomal protein S1-A SC | 40S ribosomal protein S2 SD | 40S ribosomal protein S3 SE | 40S ribosomal protein S4-A SF | Rps5p SG | 40S ribosomal protein S6-A SH | 40S ribosomal protein S7-A SI | 40S ribosomal protein S8-A SJ | 40S ribosomal protein S9-A SK | 40S ribosomal protein S10-A SL | 40S ribosomal protein S11-A SM | 40S ribosomal protein S12 SN | 40S ribosomal protein S13 SO | 40S ribosomal protein S14-B SP | 40S ribosomal protein S15 SQ | 40S ribosomal protein S16-A SR | 40S ribosomal protein S17-A SS | 40S ribosomal protein S18-A ST | 40S ribosomal protein S19-A SU | 40S ribosomal protein S20 SV | 40S ribosomal protein S21-A SW | 40S ribosomal protein S22-A SX | 40S ribosomal protein S23-A SY | 40S ribosomal protein S24-A SZ | 40S ribosomal protein S25-A Sa | 40S ribosomal protein S26-B Sb | 40S ribosomal protein S27-A Sc | 40S ribosomal protein S28-A Sd | 40S ribosomal protein S29-A Se | 40S ribosomal protein S30-A Sf | Ubiquitin-40S ribosomal protein S31 Sg | Guanine nucleotide-binding protein subunit beta-like protein Non-standard residues in 6t4q #1 --- MG — magnesium ion ZN — zinc ion > hide atoms > hide ribbons > show surfaces > color gray > select protein 87780 atoms, 89304 bonds, 4 pseudobonds, 2 models selected > color sel white > select /L* 49852 atoms, 50717 bonds, 35 pseudobonds, 3 models selected > color sel #aaffff > select /S* 37899 atoms, 38533 bonds, 13 pseudobonds, 3 models selected > color sel #fad0ff > select protein sequence .{1}$ 548 atoms, 482 bonds, 1 model selected > color sel red > show sel atoms > select protein sequence w(b) 132 atoms, 138 bonds, 1 model selected > color sel green > show sel atoms > ~select Nothing selected > view executed 6T4Q.cxc > select /6 1622 atoms, 1811 bonds, 73 pseudobonds, 3 models selected > color sel gold > select /7 1589 atoms, 1773 bonds, 72 pseudobonds, 2 models selected > color sel gold > select /5 644 atoms, 721 bonds, 6 pseudobonds, 2 models selected > color sel orange > close session > open ""C:\bukau_lab\research proposal\ribosome_structure\chimerax\6T4Q.cxc"" > open 6T4Q 6t4q title: Structure of yeast 80S ribosome stalled on the CGA-CCG inhibitory codon combination. [more info...] Chain information for 6t4q #1 --- Chain | Description 5 | mRNA 6 | ICG tRNA Arg (P/P) 7 | tRNA (E/E) 8 | nascent chain C1 | 25S rRNA C2 | 18S rRNA C3 | 5.8S rRNA C4 | 5S rRNA LA | 60S ribosomal protein L2-A LB | 60S ribosomal protein L3 LC | 60S ribosomal protein L4-A LD | 60S ribosomal protein L5 LE | 60S ribosomal protein L6-B LF | 60S ribosomal protein L7-A LG | 60S ribosomal protein L8-A LH | 60S ribosomal protein L9-A LI | 60S ribosomal protein L10 LJ | 60S ribosomal protein L11-B LL | 60S ribosomal protein L13-A LM | 60S ribosomal protein L14-A LN | 60S ribosomal protein L15-A LO | 60S ribosomal protein L16-A LP | 60S ribosomal protein L17-A LQ | 60S ribosomal protein L18-A LR | 60S ribosomal protein L19-A LS | 60S ribosomal protein L20-A LT | 60S ribosomal protein L21-A LU | 60S ribosomal protein L22-A LV | 60S ribosomal protein L23-A LW | 60S ribosomal protein L24-A LX | 60S ribosomal protein L25 LY | 60S ribosomal protein L26-A LZ | 60S ribosomal protein L27-A La | 60S ribosomal protein L28 Lb | 60S ribosomal protein L29 Lc | 60S ribosomal protein L30 Ld | 60S ribosomal protein L31-A Le | 60S ribosomal protein L32 Lf | 60S ribosomal protein L33-A Lg | 60S ribosomal protein L34-A Lh | 60S ribosomal protein L35-A Li | 60S ribosomal protein L36-A Lj | 60S ribosomal protein L37-A Lk | 60S ribosomal protein L38 Ll | 60S ribosomal protein L39 Lm | Ubiquitin-60S ribosomal protein L40 Ln | 60S ribosomal protein L41-A Lo | 60S ribosomal protein L42-A Lp | 60S ribosomal protein L43-A SA | 40S ribosomal protein S0-A SB | 40S ribosomal protein S1-A SC | 40S ribosomal protein S2 SD | 40S ribosomal protein S3 SE | 40S ribosomal protein S4-A SF | Rps5p SG | 40S ribosomal protein S6-A SH | 40S ribosomal protein S7-A SI | 40S ribosomal protein S8-A SJ | 40S ribosomal protein S9-A SK | 40S ribosomal protein S10-A SL | 40S ribosomal protein S11-A SM | 40S ribosomal protein S12 SN | 40S ribosomal protein S13 SO | 40S ribosomal protein S14-B SP | 40S ribosomal protein S15 SQ | 40S ribosomal protein S16-A SR | 40S ribosomal protein S17-A SS | 40S ribosomal protein S18-A ST | 40S ribosomal protein S19-A SU | 40S ribosomal protein S20 SV | 40S ribosomal protein S21-A SW | 40S ribosomal protein S22-A SX | 40S ribosomal protein S23-A SY | 40S ribosomal protein S24-A SZ | 40S ribosomal protein S25-A Sa | 40S ribosomal protein S26-B Sb | 40S ribosomal protein S27-A Sc | 40S ribosomal protein S28-A Sd | 40S ribosomal protein S29-A Se | 40S ribosomal protein S30-A Sf | Ubiquitin-40S ribosomal protein S31 Sg | Guanine nucleotide-binding protein subunit beta-like protein Non-standard residues in 6t4q #1 --- MG — magnesium ion ZN — zinc ion > hide atoms > hide ribbons > show surfaces > color gray > select protein 87780 atoms, 89304 bonds, 4 pseudobonds, 2 models selected > color sel white > select /L* 49852 atoms, 50717 bonds, 35 pseudobonds, 3 models selected > color sel #aaffff > select /S* 37899 atoms, 38533 bonds, 13 pseudobonds, 3 models selected > color sel #fad0ff > select protein sequence .{1}$ 548 atoms, 482 bonds, 1 model selected > color sel red > show sel atoms > select protein sequence w(b) 132 atoms, 138 bonds, 1 model selected > color sel green > show sel atoms > color /5-8 gold > color /Sf,sf,Sg,Lm white > ~select Nothing selected > view executed 6T4Q.cxc > select /LX 964 atoms, 979 bonds, 1 model selected > close session > open ""C:\bukau_lab\research proposal\ribosome_structure\chimerax\6T4Q.cxc"" > open 6T4Q 6t4q title: Structure of yeast 80S ribosome stalled on the CGA-CCG inhibitory codon combination. [more info...] Chain information for 6t4q #1 --- Chain | Description 5 | mRNA 6 | ICG tRNA Arg (P/P) 7 | tRNA (E/E) 8 | nascent chain C1 | 25S rRNA C2 | 18S rRNA C3 | 5.8S rRNA C4 | 5S rRNA LA | 60S ribosomal protein L2-A LB | 60S ribosomal protein L3 LC | 60S ribosomal protein L4-A LD | 60S ribosomal protein L5 LE | 60S ribosomal protein L6-B LF | 60S ribosomal protein L7-A LG | 60S ribosomal protein L8-A LH | 60S ribosomal protein L9-A LI | 60S ribosomal protein L10 LJ | 60S ribosomal protein L11-B LL | 60S ribosomal protein L13-A LM | 60S ribosomal protein L14-A LN | 60S ribosomal protein L15-A LO | 60S ribosomal protein L16-A LP | 60S ribosomal protein L17-A LQ | 60S ribosomal protein L18-A LR | 60S ribosomal protein L19-A LS | 60S ribosomal protein L20-A LT | 60S ribosomal protein L21-A LU | 60S ribosomal protein L22-A LV | 60S ribosomal protein L23-A LW | 60S ribosomal protein L24-A LX | 60S ribosomal protein L25 LY | 60S ribosomal protein L26-A LZ | 60S ribosomal protein L27-A La | 60S ribosomal protein L28 Lb | 60S ribosomal protein L29 Lc | 60S ribosomal protein L30 Ld | 60S ribosomal protein L31-A Le | 60S ribosomal protein L32 Lf | 60S ribosomal protein L33-A Lg | 60S ribosomal protein L34-A Lh | 60S ribosomal protein L35-A Li | 60S ribosomal protein L36-A Lj | 60S ribosomal protein L37-A Lk | 60S ribosomal protein L38 Ll | 60S ribosomal protein L39 Lm | Ubiquitin-60S ribosomal protein L40 Ln | 60S ribosomal protein L41-A Lo | 60S ribosomal protein L42-A Lp | 60S ribosomal protein L43-A SA | 40S ribosomal protein S0-A SB | 40S ribosomal protein S1-A SC | 40S ribosomal protein S2 SD | 40S ribosomal protein S3 SE | 40S ribosomal protein S4-A SF | Rps5p SG | 40S ribosomal protein S6-A SH | 40S ribosomal protein S7-A SI | 40S ribosomal protein S8-A SJ | 40S ribosomal protein S9-A SK | 40S ribosomal protein S10-A SL | 40S ribosomal protein S11-A SM | 40S ribosomal protein S12 SN | 40S ribosomal protein S13 SO | 40S ribosomal protein S14-B SP | 40S ribosomal protein S15 SQ | 40S ribosomal protein S16-A SR | 40S ribosomal protein S17-A SS | 40S ribosomal protein S18-A ST | 40S ribosomal protein S19-A SU | 40S ribosomal protein S20 SV | 40S ribosomal protein S21-A SW | 40S ribosomal protein S22-A SX | 40S ribosomal protein S23-A SY | 40S ribosomal protein S24-A SZ | 40S ribosomal protein S25-A Sa | 40S ribosomal protein S26-B Sb | 40S ribosomal protein S27-A Sc | 40S ribosomal protein S28-A Sd | 40S ribosomal protein S29-A Se | 40S ribosomal protein S30-A Sf | Ubiquitin-40S ribosomal protein S31 Sg | Guanine nucleotide-binding protein subunit beta-like protein Non-standard residues in 6t4q #1 --- MG — magnesium ion ZN — zinc ion > hide atoms > hide ribbons > show surfaces > color gray > color protein white > color /L* #aaffff > color /S* #fad0ff > color /LX,LO #00aaff > select protein sequence .{1}$ 548 atoms, 482 bonds, 1 model selected > color sel red > show sel atoms > select protein sequence w(b) 132 atoms, 138 bonds, 1 model selected > color sel green > show sel atoms > color /5-8 gold > color /Sf,sf,Sg,Lm white > ~select Nothing selected > view executed 6T4Q.cxc > toolshed show ""Side View"" > lighting simple > select /SM 875 atoms, 883 bonds, 1 model selected > select /SM 875 atoms, 883 bonds, 1 model selected > select /SC 1626 atoms, 1656 bonds, 1 model selected > select /LR 1517 atoms, 1532 bonds, 1 pseudobond, 2 models selected > select /LI 1764 atoms, 1801 bonds, 1 model selected > select /Lk 612 atoms, 618 bonds, 1 model selected > select /Lk 612 atoms, 618 bonds, 1 model selected > select /LD 2351 atoms, 2400 bonds, 1 model selected > select /Le 1019 atoms, 1038 bonds, 4 pseudobonds, 2 models selected > select /LB 3077 atoms, 3146 bonds, 2 pseudobonds, 2 models selected > select /Ll 436 atoms, 443 bonds, 1 model selected > select /La 1174 atoms, 1204 bonds, 1 pseudobond, 2 models selected > select /Lb 462 atoms, 473 bonds, 1 model selected > select /LX 964 atoms, 979 bonds, 1 model selected > select /SD 1729 atoms, 1754 bonds, 1 model selected > show sel atoms > show sel atoms > hide sel surfaces > style sel stick Changed 1729 atom styles > hbonds sel The following atoms were skipped as donors/acceptors due to missing heavy-atom bond partners: /SK PRO 88 N 187 hydrogen bonds found > select /Sg 2383 atoms, 2436 bonds, 1 model selected > show sel atoms > hide sel surfaces > style sel stick Changed 2383 atom styles > select up 2 atoms, 1 bond, 1 model selected > select up 12 atoms, 12 bonds, 2 models selected > select up 1729 atoms, 1754 bonds, 2 models selected > select down 12 atoms, 12 bonds, 2 models selected > hbonds sel The following atoms were skipped as donors/acceptors due to missing heavy-atom bond partners: /SK PRO 88 N 1 hydrogen bonds found > ui mousemode rightMode label > label #1/SD:225 > style sel ball Changed 12 atom styles > color sel byhetero > select /SD 1729 atoms, 1754 bonds, 1 model selected > select /SD:225@CA 1 atom, 1 model selected > select /SD 1729 atoms, 1754 bonds, 1 model selected > show sel surfaces > select /Sg 2383 atoms, 2436 bonds, 1 model selected > show sel surfaces > select /SD:225@C 1 atom, 1 model selected > select up 12 atoms, 12 bonds, 2 models selected > hide sel surfaces > select /SD 1729 atoms, 1754 bonds, 1 model selected > ui mousemode rightMode label > label delete residues > 2dlabels S3 > 2dlabels text S3 > label #1/SR:23 > ui mousemode rightMode ""move label"" > 2dlabels #2.1 xpos 0.468 ypos 0.502 > hide #1.8 models > select clear > view > 2dlabels #2.1 xpos 0.338 ypos 0.405 > select /SD 1729 atoms, 1754 bonds, 1 model selected > style sel ball Changed 1729 atom styles > show sel cartoons > hide sel atoms > show sel atoms > hide sel cartoons > select clear > select /SD 1729 atoms, 1754 bonds, 1 model selected Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword > color sel indigo > show sel surfaces > 2dlabels #2.1 xpos 0.330 ypos 0.425 > select /SD:225@OH 1 atom, 1 model selected > select up 12 atoms, 12 bonds, 2 models selected > color sel red > select clear > 2dlabels text uS3 color red > close #2.1 > 2dlabels #2.2 xpos 0.319 ypos 0.448 > 2dlabels text uS3 color red bgColor black > close #2.1 > undo > undo > redo > close #2 > 2dlabels text uS3 color red bgColor black > 2dlabels #2.1 xpos 0.311 ypos 0.423 > select clear > 2dlabels #2.1 xpos 0.316 ypos 0.467 > save C:\Users\Shiran\Desktop\image2.png supersample 3 > save C:\Users\Shiran\Desktop\uS3.png supersample 5 > 2dlabels #2.1 xpos 0.316 ypos 0.467 > hide #!2 models > select /SD:225@CE1 1 atom, 1 model selected > select up 12 atoms, 12 bonds, 2 models selected > hide sel surfaces > select /SD:224@O 1 atom, 1 model selected > select up 8 atoms, 7 bonds, 2 models selected > hide sel surfaces > select /SD:225@O 1 atom, 1 model selected > color sel blue > select clear > select /SD:225@CB 1 atom, 1 model selected > select up 12 atoms, 12 bonds, 2 models selected > label sel color red bgColor black Expected a keyword > label sel color red bgColor black size 50 > label defaultHeight 50 > label defaultHeight 28.0 Invalid ""size"" argument: Expected 'default' or an integer > label sel color red bgColor black size 50 > label delete > label sel color red bgColor black size 50 > label delete > label sel color red bgColor black size 25 > label delete > label defaultHeight 25 > label defaultHeight 25.0 > label sel color red bgColor black size 25 > label delete > label sel color red bgColor black size 10 > label delete > label sel color red bgColor black size 10 defaultHeight 10 > label defaultHeight 10.0 > label sel color red bgColor black size 50 defaultHeight 10 > label sel color red bgColor black size 50 defaultHeight 5 > label defaultHeight 5.0 > label delete > label sel color red bgColor black size 50 defaultHeight 5 > label delete > label sel color red bgColor black size 50 defaultHeight 5 onTop false > label sel color red bgColor black size 25 defaultHeight 5 onTop false > label delete > label sel color red bgColor black size 25 defaultHeight 5 onTop false > label sel color red bgColor black size 10 defaultHeight 5 onTop false > label delete > label sel color red bgColor black size 10 defaultHeight 5 onTop false > label sel color red bgColor black size 10 defaultHeight 1 onTop false > label defaultHeight 1.0 > label delete > label sel color red bgColor black size 10 defaultHeight 1 onTop false > label sel color red bgColor black size 10 defaultHeight 3 onTop false > label defaultHeight 3.0 > label delete > label sel color red bgColor black size 10 defaultHeight 3 onTop false > label sel color red bgColor black size 50 defaultHeight 3 onTop false > select /SD:225@O 1 atom, 1 model selected > label sel color red bgColor black size 50 defaultHeight 3 onTop false > label sel atoms color red bgColor black size 50 defaultHeight 3 onTop false > label delete > label sel color red bgColor black size 50 defaultHeight 3 onTop false > select clear > save C:\Users\Shiran\Desktop\uS3_zoom.png supersample 5 > select up 2 atoms, 1 bond, 1 model selected > select up 12 atoms, 12 bonds, 2 models selected > select up 1729 atoms, 1754 bonds, 2 models selected > color sel #fad0ff > show sel surfaces > label delete > select /SD:225@CE2 1 atom, 1 model selected > select up 12 atoms, 12 bonds, 2 models selected > color sel red > select /SM 875 atoms, 883 bonds, 1 model selected > color sel indigo > select /SM:143@O 1 atom, 1 model selected > select up 9 atoms, 8 bonds, 2 models selected > color sel red > hide sel surfaces > style sel ball Changed 9 atom styles > select up 875 atoms, 883 bonds, 2 models selected > hide sel surfaces > show sel atoms > style sel ball Changed 875 atom styles > show sel surfaces > select down 9 atoms, 8 bonds, 2 models selected > select clear > 2dlabels text eS12 color red bgColor black > hide #2.1 models > show #2.1 models > hide #2.1 models > 2dlabels #2.2 xpos 0.332 ypos 0.304 > save C:\Users\Shiran\Desktop\eS12.png supersample 5 > close #2 > select /SM:143@O 1 atom, 1 model selected > select up 9 atoms, 8 bonds, 2 models selected > hide sel surfaces > hbonds sel The following atoms were skipped as donors/acceptors due to missing heavy-atom bond partners: /SK PRO 88 N 0 hydrogen bonds found > select /SM:143@O 1 atom, 1 model selected > color sel blue > select up 9 atoms, 8 bonds, 2 models selected > select up 875 atoms, 883 bonds, 2 models selected > select up 203559 atoms, 218508 bonds, 2 models selected > select up 203559 atoms, 218508 bonds, 418 pseudobonds, 85 models selected > select down 203559 atoms, 218508 bonds, 83 models selected > select down 875 atoms, 883 bonds, 83 models selected > select down 9 atoms, 8 bonds, 2 models selected > label sel color red bgColor black size 50 defaultHeight 3 onTop false > ui mousemode rightMode ""move label"" > select clear > select up Nothing selected > save C:\Users\Shiran\Desktop\eS12_zoom.png supersample 5 > label delete > select /SM:143@CA 1 atom, 1 model selected > select up 9 atoms, 8 bonds, 2 models selected > select up 875 atoms, 883 bonds, 2 models selected > show sel surfaces > color sel #fad0ff > select /SM:143@O 1 atom, 1 model selected > select up 9 atoms, 8 bonds, 2 models selected > color sel red > select /SM 875 atoms, 883 bonds, 1 model selected > select /SN 1192 atoms, 1215 bonds, 1 model selected > select /SP 916 atoms, 936 bonds, 1 model selected > select /SC 1626 atoms, 1656 bonds, 1 model selected > color sel indigo > select /SC:249@CA 1 atom, 1 model selected > select up 5 atoms, 4 bonds, 2 models selected > color sel red > 2dlabels text uS5 color red bgColor black > 2dlabels #2.1 xpos 0.466 ypos 0.246 > select clear > save C:\Users\Shiran\Desktop\uS5.png supersample 5 > close #2 > select /SC:249@O 1 atom, 1 model selected > select up 5 atoms, 4 bonds, 2 models selected > hide sel surfaces > style sel ball Changed 5 atom styles > hbonds sel The following atoms were skipped as donors/acceptors due to missing heavy-atom bond partners: /SK PRO 88 N 0 hydrogen bonds found > select up 39 atoms, 38 bonds, 2 models selected > show sel atoms > style sel ball Changed 39 atom styles > select up 1626 atoms, 1656 bonds, 2 models selected > style sel ball Changed 1626 atom styles > show sel atoms > select /SC:249@O 1 atom, 1 model selected > color sel blue > select up 5 atoms, 4 bonds, 2 models selected > select up 39 atoms, 38 bonds, 2 models selected > hide sel surfaces > select down 5 atoms, 4 bonds, 2 models selected > select up 39 atoms, 38 bonds, 2 models selected > select down 5 atoms, 4 bonds, 2 models selected > label sel color red bgColor black size 50 defaultHeight 3 onTop false > select clear > save C:\Users\Shiran\Desktop\uS5_zoom.png supersample 5 > label delete > select /SC:249@CA 1 atom, 1 model selected > select up 5 atoms, 4 bonds, 2 models selected > select up 39 atoms, 38 bonds, 2 models selected > select up 1626 atoms, 1656 bonds, 2 models selected > hide sel atoms > show sel surfaces > color sel #fad0ff > select down 39 atoms, 38 bonds, 2 models selected > select down 5 atoms, 4 bonds, 2 models selected > color sel red > select /SU 797 atoms, 807 bonds, 1 model selected > color sel indigo > select /SU:119@CB 1 atom, 1 model selected > color sel red > 2dlabels text uS10 color red bgColor black > 2dlabels #2.1 xpos 0.629 ypos 0.646 > select clear > 2dlabels #2.1 xpos 0.567 ypos 0.608 > 2dlabels #2.1 xpos 0.563 ypos 0.551 > 2dlabels #2.1 xpos 0.518 ypos 0.673 > 2dlabels #2.1 xpos 0.516 ypos 0.631 > save C:\Users\Shiran\Desktop\uS10.png supersample 5 > close #2 > select /SU:119@CB 1 atom, 1 model selected > hide sel surfaces > select up 5 atoms, 4 bonds, 2 models selected > hide sel surfaces > style sel ball Changed 5 atom styles > select up 797 atoms, 807 bonds, 2 models selected > select down 5 atoms, 4 bonds, 2 models selected > select up 797 atoms, 807 bonds, 2 models selected > show sel atoms > style sel ball Changed 797 atom styles > hbonds sel The following atoms were skipped as donors/acceptors due to missing heavy-atom bond partners: /SK PRO 88 N 99 hydrogen bonds found > select down 5 atoms, 4 bonds, 2 models selected > interfaces sel & ~solvent 0 buried areas: > color sel red > select /SU:119@O 1 atom, 1 model selected > color sel blue > select clear > select up 2 atoms, 1 bond, 1 model selected > select up 5 atoms, 4 bonds, 2 models selected > label sel color red bgColor black size 50 defaultHeight 3 onTop false > select clear > save C:\Users\Shiran\Desktop\uS10_zoom.png supersample 5 > label delete > select /SU:119@CB 1 atom, 1 model selected > select up 5 atoms, 4 bonds, 2 models selected > select up 797 atoms, 807 bonds, 2 models selected > color sel #fad0ff > show sel surfaces > hide sel atoms > select down 5 atoms, 4 bonds, 2 models selected > select down 1 atom, 2 models selected > select up 5 atoms, 4 bonds, 2 models selected > color sel red > select /SP 916 atoms, 936 bonds, 1 model selected > select /SD 1729 atoms, 1754 bonds, 1 model selected > close session Missing or invalid ""filename"" argument: Expected a file name Unknown command: 6U5T > open 6U5T Summary of feedback from opening 6U5T fetched from pdb --- notes | Fetching compressed mmCIF 6u5t from http://files.rcsb.org/download/6u5t.cif Fetching CCD PNS from http://ligand-expo.rcsb.org/reports/P/PNS/PNS.cif Fetching CCD FMN from http://ligand-expo.rcsb.org/reports/F/FMN/FMN.cif 6u5t title: Electron cryomicroscopy Structure of S. cerevisiae FAS in the Apo state [more info...] Chain information for 6u5t #1 --- Chain | Description A | Fatty acid synthase subunit α G | Fatty acid synthase subunit β Non-standard residues in 6u5t #1 --- FMN — flavin mononucleotide (riboflavin monophosphate) PNS — 4'-phosphopantetheine 6u5t mmCIF Assemblies --- 1| complete point assembly 2| point asymmetric unit 3| point asymmetric unit, std point frame > select /A 12207 atoms, 12429 bonds, 3 pseudobonds, 2 models selected > color sel #b22222 > select /G 16026 atoms, 16393 bonds, 1 pseudobond, 2 models selected Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword > color sel navy > select strand 3718 atoms, 3690 bonds, 1 model selected > select coil 10558 atoms, 10569 bonds, 4 pseudobonds, 2 models selected > select /A&coil 4775 atoms, 4780 bonds, 3 pseudobonds, 2 models selected > toolshed show ""Cage Builder"" > view > preset ""overall look"" interactive Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\label\label2d.py"", line 405, in _background_color_changed l.update_drawing() File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\label\label2d.py"", line 495, in update_drawing d.needs_update = True AttributeError: 'NoneType' object has no attribute 'needs_update' Error processing trigger ""setting changed"": AttributeError: 'NoneType' object has no attribute 'needs_update' File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\label\label2d.py"", line 495, in update_drawing d.needs_update = True See log for complete Python traceback. Preset expands to these ChimeraX commands: ~set bg graphics silhouettes f > set bgColor white Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\label\label2d.py"", line 405, in _background_color_changed l.update_drawing() File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\label\label2d.py"", line 495, in update_drawing d.needs_update = True AttributeError: 'NoneType' object has no attribute 'needs_update' Error processing trigger ""setting changed"": AttributeError: 'NoneType' object has no attribute 'needs_update' File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\label\label2d.py"", line 495, in update_drawing d.needs_update = True See log for complete Python traceback. OpenGL version: 3.3.0 NVIDIA 432.00 OpenGL renderer: GeForce GTX 1050 Ti/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation }}} " defect closed normal Graphics fixed all ChimeraX