![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
#15670 closed defect (wontfix)
Foldseek ligands uses illegal chain id character "_"
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Structure Analysis | Version: | |
| Keywords: | Cc: | Eric Pettersen | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-14.5-arm64-arm-64bit
ChimeraX Version: 1.9.dev202407240247 (2024-07-24 02:47:28 UTC)
Description
The foldseek ligands command is putting underscore in chain identifiers which may be an invalid character. Eric may have changed this to make it a valid character.
Log:
UCSF ChimeraX version: 1.9.dev202407240247 (2024-07-24)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/goddard/Downloads/ChimeraX/Foldseek/8jnb_B/pdb100.m8 format
> foldseek
Summary of feedback from opening
/Users/goddard/Downloads/ChimeraX/Foldseek/8jnb_B/pdb100.m8
---
notes | 8jnb.cif title:
CRAF ras-binding domain chimera, ligand complex [more info...]
| Chain information for 8jnb.cif #1
---
Chain
| Description
| UniProt
B
| RAF proto-oncogene serine/threonine-protein kinase, CRaf
| RAF1_HUMAN 50-101 114-141, BRAF_HUMAN 102-113
Non-standard residues in 8jnb.cif #1
---
USX — 2-[4-[[(2S)-1-ethanoyl-3-oxidanylidene-2H-indol-2-yl]methyl]-2-methoxy-
phenoxy]ethanamide
3 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Foldseek search for similar structures to /B in pdb100 found 845 hits
> time fold lig
> foldseek ligands
Foldseek result 6uyy chain A target sequence
GEYIKLKVIGQDSSEIHFKVKMTTHLKKLKESYAQRQGVPMNSLRFLFEGQRIADNHTPKELGMEEEDVIEVYQEQTGG
does not match sequence from database
GEYIKLKVIGQDSSEIHFKVXMTTHLKKLKESYAQRQGVPMNSLRFLFEGQRIADNHTPKELGMEEEDVIEVYQEQTGG.
Foldseek result 6kbe chain G target sequence
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGAMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLR
does not match sequence from database
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGXMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLR.
Foldseek result 7ooj chain A target sequence
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDTRTLSDYNIQKESTLHLVLRL does
not match sequence from database
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDXRTLSDYNIQKESTLHLVLRL.
Foldseek result 2fcn chain B target sequence
LQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEVIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRL does
not match sequence from database
LQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEXIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRL.
Foldseek result 6qml chain E target sequence
LQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG
does not match sequence from database
XQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG.
Foldseek result pdb100 7w7g chain B number of residues 1711 does not match
residues in structure 1710, sequences
PIQTFLWRQTSAFLRPKLGKQYEASCVSFERVLVENKLHGLSPALSEAIQSISRWELVQAALPHVLHCTATLLSNRNKLGHQDKLGVAETKLLHTLHWMLLENSMATVELFVFLFAPLVHRIKESDLTFRLASGLVIWQPMWEYFDVAVLRCLLQPHWSEEGTQWSLMYYLQRLRHMLLSVVLKAVYLVLNHDISSRICDVALNIVECLLQLGVVPCVEPVSNHRLALTMLIKIVKSLQVFRENAQNCLTKLYKLDKIQFRQTMRDYVNKDSLNNVVDFLHALLGFCMEPNVEGIIVGAMFKSLITRCASTTHELHSPENLGLYCDIRQLVQFIKEAHGNVFRRVALSALLDSANLGRKDFWRKMFKSNVVNLGAIRQGMKRFQFLLNCCEPGTIPDASILAAALDLEAPVVARAALFLECARFVHRCNRGNWPEWMKKRNQKLQWSAAKLFYQWGDAIGIRLNELCHETKRRLRKEDEEEDFLDDSTVNPPFALKMAACQLLLEITTFLRETFSCENYHRNMSWLHVMILLCNQQSFICTHVDYCHPHCYLHHSRSCARLVRAIKLLYSGMLKYIRFQVMSLSPAPLSLLIKAAPILTEEMYGDIQPAAWELLLSMDEHMAGAAAAMFLLCAVKVPDAVSDMLMSEFHHAETVQRLNAVLKFHTLWRFRYQVWPRMEEGAQQIFKIPPPSINFTLPSPVLGMPSVPMFDPPWVPQLKNLQQEEEKKRLGREASLITAIPITQEACYEPQAVFPACICAAVLPIVHLMEDGEVREDGVAVSAVAQQVLWNCLIEDPSTVLRHFLEKLTISNRQDELMYMLRKLLLNIGDFPAQTSHILFNYLVGLIMYFVRTPCEWGMDAISATLTFLWEVVGYVEGLFFKDLKQTMKKEQCEVKLLVTASMPGTKTLVVHGQNECDIPTQLPVHEDTQFEALLKECLEFFNIPESQSTHYFLMDKRWNLIHYNKTYVRDIYPFRRSVSPQLNLVHMHPEKGQELIQKQVFTRKLEEVGRVLFLISLTQKIPTAHKQSHVSMLQEDLLRLPSFPRSAIDAEFSLFSDPQAGKELFGLDTLQKSLWIQLLEEMFLGMPSEFPWGDEIMLFLNVFNGALILHPEDSALLRQYAATVINTAVHFNHLFSLSGYQWILPTMLQVYSDYESNPQLRRAIEFACHQFYILHRKPFVLQLFASVAPLLEFKGVSAQCLFDLLQSLEGETTDILDILELVKAEKPLKSLDFCYGNEDLTFSISEAIKLCVTVVAYAPESFRSLQMLMVLEALVPCYLQKMKRQTSQVETVPAAREEIAATAALATSLQALLYSVEVLTRPMTAPEELDERISREEFRRPRESLLNICTEFYKHCGPRLKILQNLAGEPRVTALELLDVKSHMRLAEIAHSLLKLAPYDTQTMESRGLRRYIMEMLPITDWSAEAVRPALILILKRLDRMFNKIHKMPTLRRQVEWEPASSLIEGVCLTLQRQPIISFLPHLRSLINVCVNLVMGVVGPYLSPPLPFSTAVVRLVALQIQALKEDFPLSHVISPFTNQERREGMLLNLLIPFVLTVGSGSKDSPWLEQPEVQLLLQTVINVLLPLAESTSQAAYLALKVILVCFERQLGSQWYWLSLQVKEMALRKVGGLALWDFLDFIVRTRIPIFVLLRPFIQCKLLAQPAENHEELSARQHISDQLERRFIPRPLCKSSLIAEFNSELKILKEAVHS
and
PIQTFLWRQTSAFLRPKLGKQYEASCVSFERVLVENKLHGLSPALSEAIQSISRWELVQAALPHVLHCTATLLSNRNKLGHQDKLGVAETKLLHTLHWMLLENSMATVELFVFLFAPLVHRIKESDLTFRLASGLVIWQPMWEYFDVAVLRCLLQPHWSEEGTQWSLMYYLQRLRHMLSVVLKAVYLVLNHDISSRICDVALNIVECLLQLGVVPCVEPVSNHRLALTMLIKIVKSLQVFRENAQNCLTKLYKLDKIQFRQTMRDYVNKDSLNNVVDFLHALLGFCMEPNVEGIIVGAMFKSLITRCASTTHELHSPENLGLYCDIRQLVQFIKEAHGNVFRRVALSALLDSANLGRKDFWRKMFKSNVVNLGAIRQGMKRFQFLLNCCEPGTIPDASILAAALDLEAPVVARAALFLECARFVHRCNRGNWPEWMKKRNQKLQWSAAKLFYQWGDAIGIRLNELCHETKRRLRKEDEEEDFLDDSTVNPPFALKMAACQLLLEITTFLRETFSCENYHRNMSWLHVMILLCNQQSFICTHVDYCHPHCYLHHSRSCARLVRAIKLLYSGMLKYIRFQVMSLSPAPLSLLIKAAPILTEEMYGDIQPAAWELLLSMDEHMAGAAAAMFLLCAVKVPDAVSDMLMSEFHHAETVQRLNAVLKFHTLWRFRYQVWPRMEEGAQQIFKIPPPSINFTLPSPVLGMPSVPMFDPPWVPQLKNLQQEEEKKRLGREASLITAIPITQEACYEPQAVFPACICAAVLPIVHLMEDGEVREDGVAVSAVAQQVLWNCLIEDPSTVLRHFLEKLTISNRQDELMYMLRKLLLNIGDFPAQTSHILFNYLVGLIMYFVRTPCEWGMDAISATLTFLWEVVGYVEGLFFKDLKQTMKKEQCEVKLLVTASMPGTKTLVVHGQNECDIPTQLPVHEDTQFEALLKECLEFFNIPESQSTHYFLMDKRWNLIHYNKTYVRDIYPFRRSVSPQLNLVHMHPEKGQELIQKQVFTRKLEEVGRVLFLISLTQKIPTAHKQSHVSMLQEDLLRLPSFPRSAIDAEFSLFSDPQAGKELFGLDTLQKSLWIQLLEEMFLGMPSEFPWGDEIMLFLNVFNGALILHPEDSALLRQYAATVINTAVHFNHLFSLSGYQWILPTMLQVYSDYESNPQLRRAIEFACHQFYILHRKPFVLQLFASVAPLLEFKGVSAQCLFDLLQSLEGETTDILDILELVKAEKPLKSLDFCYGNEDLTFSISEAIKLCVTVVAYAPESFRSLQMLMVLEALVPCYLQKMKRQTSQVETVPAAREEIAATAALATSLQALLYSVEVLTRPMTAPEELDERISREEFRRPRESLLNICTEFYKHCGPRLKILQNLAGEPRVTALELLDVKSHMRLAEIAHSLLKLAPYDTQTMESRGLRRYIMEMLPITDWSAEAVRPALILILKRLDRMFNKIHKMPTLRRQVEWEPASSLIEGVCLTLQRQPIISFLPHLRSLINVCVNLVMGVVGPYLSPPLPFSTAVVRLVALQIQALKEDFPLSHVISPFTNQERREGMLLNLLIPFVLTVGSGSKDSPWLEQPEVQLLLQTVINVLLPLAESTSQAAYLALKVILVCFERQLGSQWYWLSLQVKEMALRKVGGLALWDFLDFIVRTRIPIFVLLRPFIQCKLLAQPAENHEELSARQHISDQLERRFIPRPLCKSSLIAEFNSELKILKEAVHS.
Because of a sequence mismatch between the database structure {name} and the
Foldseek output, the alignment and residue pairing of this structure is
probably wrong, and ChimeraX did not trim the structure.
Foldseek result pdb100 3u8z chain C number of residues 266 does not match
residues in structure 265, sequences
KTFTVRIVTMDAEMEFNCEMKWKGKDLFDLVCRTLGLRETWFFGLQYTIKDTVAWLKMDKKVLPVTFHFLAKFYPENAEEELVQEITQHLFFLQVKKQILDEKIYCPPEASVLLASYAVQAKYGDYDPSVHQMTPEMWEERITAWYAEHRGRARDEAEMEYLKIAQDLEMYGVNYFAIRNKKGTELLLGVDALGLHIYDPENRLTPKISFPWNEIRNISYSDKEFTIKPLDKKIDVFKFNSSKLRVNKLILQLCIGNHDLFMRRRK
and
TFTVRIVTMDAEMEFNCEMKWKGKDLFDLVCRTLGLRETWFFGLQYTIKDTVAWLKMDKKVLPVTFHFLAKFYPENAEEELVQEITQHLFFLQVKKQILDEKIYCPPEASVLLASYAVQAKYGDYDPSVHQMTPEMWEERITAWYAEHRGRARDEAEMEYLKIAQDLEMYGVNYFAIRNKKGTELLLGVDALGLHIYDPENRLTPKISFPWNEIRNISYSDKEFTIKPLDKKIDVFKFNSSKLRVNKLILQLCIGNHDLFMRRRK.
Because of a sequence mismatch between the database structure {name} and the
Foldseek output, the alignment and residue pairing of this structure is
probably wrong, and ChimeraX did not trim the structure.
Foldseek result pdb100 3u8z chain D number of residues 237 does not match
residues in structure 236, sequences
KTFTVRIVTMDAEMEFNCEMKWKGKDLFDLVCRTLGLRETWFFGLQYTIKDTVAWLKMDKKVLPVTFHFLAKFYPENAEEELVQEITQHLFFLQVKKQILDEKIYCPPEASVLLASYAVQAKYARDEAEMEYLKIAQDLEMYGVNYFAIRNKKGTELLLGVDALGLHIYDPENRLTPKISFPWNEIRNISYSDKEFTIKPLDKKIDVFKFNSSKLRVNKLILQLCIGNHDLFMRRRK
and
TFTVRIVTMDAEMEFNCEMKWKGKDLFDLVCRTLGLRETWFFGLQYTIKDTVAWLKMDKKVLPVTFHFLAKFYPENAEEELVQEITQHLFFLQVKKQILDEKIYCPPEASVLLASYAVQAKYARDEAEMEYLKIAQDLEMYGVNYFAIRNKKGTELLLGVDALGLHIYDPENRLTPKISFPWNEIRNISYSDKEFTIKPLDKKIDVFKFNSSKLRVNKLILQLCIGNHDLFMRRRK.
Because of a sequence mismatch between the database structure {name} and the
Foldseek output, the alignment and residue pairing of this structure is
probably wrong, and ChimeraX did not trim the structure.
Foldseek result pdb100 3u8z chain B number of residues 260 does not match
residues in structure 259, sequences
KTFTVRIVTMDAEMEFNCEMKWKGKDLFDLVCRTLGLRETWFFGLQYTIKDTVAWLKMDKKVLPVTFHFLAKFYPENAEEELVQEITQHLFFLQVKKQILDEKIYCPPEASVLLASYAVQAKYGDQMTPEMWEERITAWYAEHRGRARDEAEMEYLKIAQDLEMYGVNYFAIRNKKGTELLLGVDALGLHIYDPENRLTPKISFPWNEIRNISYSDKEFTIKPLDKKIDVFKFNSSKLRVNKLILQLCIGNHDLFMRRRK
and
TFTVRIVTMDAEMEFNCEMKWKGKDLFDLVCRTLGLRETWFFGLQYTIKDTVAWLKMDKKVLPVTFHFLAKFYPENAEEELVQEITQHLFFLQVKKQILDEKIYCPPEASVLLASYAVQAKYGDQMTPEMWEERITAWYAEHRGRARDEAEMEYLKIAQDLEMYGVNYFAIRNKKGTELLLGVDALGLHIYDPENRLTPKISFPWNEIRNISYSDKEFTIKPLDKKIDVFKFNSSKLRVNKLILQLCIGNHDLFMRRRK.
Because of a sequence mismatch between the database structure {name} and the
Foldseek output, the alignment and residue pairing of this structure is
probably wrong, and ChimeraX did not trim the structure.
Foldseek result 7c3m chain A target sequence
SSWELRVFVGEEDPEAESVTLRVTGESHIGGVLLKIVEQINRKQDWSDHAIWWEQKRQWLLQTHWTLDKYGILADARLFFGPQHRPVILRLPNRRALRLRASFSQPLFQAVAAICRLLSIRHPEELSLLRAPVAPALFRGMPAHFSDSAQTEACYHMLSRPQPPPDPLLLQRLPRPSSLSDKTQLHSRWLDSSRCLMQQGIKAGDALWLRFKYYSFFDLDPKTDPVRLTQLYEQARWDLLLEEIDCTEEEMMVFAALQYHINKLSQSXXXXXXXPELKDHLRIFRIPRRPRKLTLKGYRQHWVVFKETTLSYYKSQDEAPGDPIQQLNLKGCEVVPDVNVSGQKFCIKLLVPSPEGMSEIYLRCQDEQQYARWMAGCRLASKGRTMADSSYTSEVQAILAFLSLQRTGSEGLNPYGLVAPRFQRKFKAKQLTPRILEAHQNVAQLSLAEAQLRFIQAWQSLPDFGISYVMVRFKGSRKDEILGIANNRLIRIDLAVGDVVKTWRFSNMRQWNVNWDIRQVAIEFDEHINVAFSCVSASCRIVHEYIGGYIFLSTRERARGEELDEDLFLQLTGGHEA
does not match sequence from database
SSWELRVFVGEEDPEAESVTLRVTGESHIGGVLLKIVEQINRKQDWSDHAIWWEQKRQWLLQTHWTLDKYGILADARLFFGPQHRPVILRLPNRRALRLRASFSQPLFQAVAAICRLLSIRHPEELSLLRAPVAPALFRGMPAHFSDSAQTEACYHMLSRPQPPPDPLLLQRLPRPSSLSDKTQLHSRWLDSSRCLMQQGIKAGDALWLRFKYYSFFDLDPKTDPVRLTQLYEQARWDLLLEEIDCTEEEMMVFAALQYHINKLSQS???????PELKDHLRIFRIPRRPRKLTLKGYRQHWVVFKETTLSYYKSQDEAPGDPIQQLNLKGCEVVPDVNVSGQKFCIKLLVPSPEGMSEIYLRCQDEQQYARWMAGCRLASKGRTMADSSYTSEVQAILAFLSLQRTGSEGLNPYGLVAPRFQRKFKAKQLTPRILEAHQNVAQLSLAEAQLRFIQAWQSLPDFGISYVMVRFKGSRKDEILGIANNRLIRIDLAVGDVVKTWRFSNMRQWNVNWDIRQVAIEFDEHINVAFSCVSASCRIVHEYIGGYIFLSTRERARGEELDEDLFLQLTGGHEA.
Foldseek result pdb100 4im0 chain A number of residues 619 does not match
residues in structure 618, sequences
GSMQSTSNHLWLLSDILGQGATANVFRGRHKKTGDLFAIKVFNNRPVDVQMREFEVLKKLNHKNIVKLFAIEEETTTRHKVLIMEFCPCGSLYTVLEEPSNAYGLPESEFLIVLRDVVGGMNHLRENGIVHRNIKPGNIMRVIGEDGQSVYKLTDFGTEEYLHPDMYERVLRKDHATVDLWSIGVTFYHAATGSLPFRPFEGPRRNKEVMYKIITGKPSGAISGVQKAENGPIDWSGDMPVSCSLSRGLQVLLTPVLANILEADQEKCWGFDQFFAETSDILHRMVIHVFSLQQMTAHKIYIHSYNTATIFHELVYKQTKIISSNQELIYEGRRLVLEPGRLAQHFPKTTEENPIFVVSREPLNTIGLIYEKISLPKVHPRYDLDGDASMAKAITGVVCYACRIASTLLLYQELMRKGIRWLIELIKDDYNETVHKKTEVVITLDFCIRNIEKTVKVMEISDIHTKLLRLSSSQGTIETSLQDIDSRLSPGGSLADAWAHQEGTHPKDRNVEKLQVLLNCMTEIYYQFKKDKAERRLAYNEEQIHKFDKQKLYYHATKAMTHFTDECVKKYEAFLNKSEEWIRKMLHLRKQLLSLTNQCFDIEEEVSKYQEYTNELQET
and
GSMQSTSNHLWLLSDILGQGATANVFRGRHKKTGDLFAIKVFNNPVDVQMREFEVLKKLNHKNIVKLFAIEEETTTRHKVLIMEFCPCGSLYTVLEEPSNAYGLPESEFLIVLRDVVGGMNHLRENGIVHRNIKPGNIMRVIGEDGQSVYKLTDFGTEEYLHPDMYERVLRKDHATVDLWSIGVTFYHAATGSLPFRPFEGPRRNKEVMYKIITGKPSGAISGVQKAENGPIDWSGDMPVSCSLSRGLQVLLTPVLANILEADQEKCWGFDQFFAETSDILHRMVIHVFSLQQMTAHKIYIHSYNTATIFHELVYKQTKIISSNQELIYEGRRLVLEPGRLAQHFPKTTEENPIFVVSREPLNTIGLIYEKISLPKVHPRYDLDGDASMAKAITGVVCYACRIASTLLLYQELMRKGIRWLIELIKDDYNETVHKKTEVVITLDFCIRNIEKTVKVMEISDIHTKLLRLSSSQGTIETSLQDIDSRLSPGGSLADAWAHQEGTHPKDRNVEKLQVLLNCMTEIYYQFKKDKAERRLAYNEEQIHKFDKQKLYYHATKAMTHFTDECVKKYEAFLNKSEEWIRKMLHLRKQLLSLTNQCFDIEEEVSKYQEYTNELQET.
Because of a sequence mismatch between the database structure {name} and the
Foldseek output, the alignment and residue pairing of this structure is
probably wrong, and ChimeraX did not trim the structure.
Found 6587 ligands in 424 hits: 17F, ACT, AR6, ARS, BEN, CA, CBY, CD, CL, EDO,
EIB, EPE, FB1, FES, GA, GOL, HOH, IPA, K, MG, MLI, MTN, NA, NAG, NO3, PCW,
PO4, RIB, SO4, TRS, ZN
Remapping chain ID '2n2k_A' in 2n2k_A #209 to '2n2k_B'
Remapping chain ID '2n2k_A' in 2n2k_A #210 to '2n2k_C'
Remapping chain ID '2n2k_A' in 2n2k_A #211 to '2n2k_D'
Remapping chain ID '2n2k_A' in 2n2k_A #212 to '2n2k_E'
Remapping chain ID '2n2k_A' in 2n2k_A #213 to '2n2k_F'
Remapping chain ID '2n2k_A' in 2n2k_A #214 to '2n2k_G'
Remapping chain ID '2n2k_A' in 2n2k_A #215 to '2n2k_H'
Remapping chain ID '2n2k_A' in 2n2k_A #217 to '2n2k_I'
Remapping chain ID '2n2k_A' in 2n2k_A #218 to '2n2k_J'
Remapping chain ID '2n2k_A' in 2n2k_A #219 to '2n2k_K'
Remapping chain ID '2n2k_A' in 2n2k_A #220 to '2n2k_L'
Remapping chain ID '2n2k_A' in 2n2k_A #221 to '2n2k_M'
Remapping chain ID '2n2k_A' in 2n2k_A #222 to '2n2k_N'
Remapping chain ID '2n2k_A' in 2n2k_A #223 to '2n2k_O'
Remapping chain ID '2n2k_A' in 2n2k_A #224 to '2n2k_P'
Remapping chain ID '2n2k_A' in 2n2k_A #225 to '2n2k_Q'
Remapping chain ID '2n2k_A' in 2n2k_A #226 to '2n2k_R'
Remapping chain ID '2n2k_A' in 2n2k_A #227 to '2n2k_S'
Remapping chain ID '2n2k_A' in 2n2k_A #229 to '2n2k_T'
Remapping chain ID '2n2k_A' in 2n2k_A #230 to '2n2k_U'
Remapping chain ID '2n2k_A' in 2n2k_A #231 to '2n2k_V'
Remapping chain ID '2n2k_A' in 2n2k_A #232 to '2n2k_W'
Remapping chain ID '2n2k_A' in 2n2k_A #233 to '2n2k_X'
Remapping chain ID '2n2k_A' in 2n2k_A #234 to '2n2k_Y'
Remapping chain ID '2n2k_A' in 2n2k_A #235 to '2n2k_Z'
Remapping chain ID '2n2k_A' in 2n2k_A #236 to '2n2k_a'
Remapping chain ID '2n2k_A' in 2n2k_A #237 to '2n2k_b'
Remapping chain ID '2n2k_A' in 2n2k_A #238 to '2n2k_c'
Remapping chain ID '2n2k_A' in 2n2k_A #239 to '2n2k_d'
Remapping chain ID '2n2k_A' in 2n2k_A #240 to '2n2k_e'
Remapping chain ID '2n2k_A' in 2n2k_A #241 to '2n2k_f'
Remapping chain ID '2n2k_A' in 2n2k_A #242 to '2n2k_g'
Remapping chain ID '2n2k_A' in 2n2k_A #243 to '2n2k_h'
Remapping chain ID '2n2k_A' in 2n2k_A #244 to '2n2k_i'
Remapping chain ID '2n2k_A' in 2n2k_A #245 to '2n2k_j'
Remapping chain ID '2n2k_A' in 2n2k_A #246 to '2n2k_k'
Remapping chain ID '2n2k_A' in 2n2k_A #247 to '2n2k_l'
Remapping chain ID '2n2k_A' in 2n2k_A #248 to '2n2k_m'
Remapping chain ID '2n2k_A' in 2n2k_A #250 to '2n2k_n'
Remapping chain ID '2n2k_A' in 2n2k_A #251 to '2n2k_o'
Remapping chain ID '2n2k_A' in 2n2k_A #252 to '2n2k_p'
Remapping chain ID '2n2k_A' in 2n2k_A #253 to '2n2k_q'
Remapping chain ID '2n2k_A' in 2n2k_A #254 to '2n2k_r'
Remapping chain ID '2n2k_A' in 2n2k_A #255 to '2n2k_s'
Remapping chain ID '2n2k_A' in 2n2k_A #256 to '2n2k_t'
Remapping chain ID '2n2k_A' in 2n2k_A #257 to '2n2k_u'
Remapping chain ID '2n2k_A' in 2n2k_A #258 to '2n2k_v'
Remapping chain ID '2n2k_A' in 2n2k_A #259 to '2n2k_w'
Remapping chain ID '2n2k_A' in 2n2k_A #260 to '2n2k_x'
Remapping chain ID '2n2k_A' in 2n2k_A #261 to '2n2k_y'
Remapping chain ID '2n2k_A' in 2n2k_A #262 to '2n2k_z'
Remapping chain ID '2n2k_A' in 2n2k_A #264 to '2n2k_1'
Remapping chain ID '2n2k_A' in 2n2k_A #265 to '2n2k_2'
Remapping chain ID '2n2k_A' in 2n2k_A #266 to '2n2k_3'
Remapping chain ID '2n2k_A' in 2n2k_A #267 to '2n2k_4'
Remapping chain ID '2n2k_A' in 2n2k_A #268 to '2n2k_5'
Remapping chain ID '2n2k_A' in 2n2k_A #269 to '2n2k_6'
Remapping chain ID '2n2k_A' in 2n2k_A #270 to '2n2k_7'
Remapping chain ID '2n2k_A' in 2n2k_A #271 to '2n2k_8'
Remapping chain ID '2n2k_A' in 2n2k_A #272 to '2n2k_9'
Remapping chain ID '2n2k_A' in 2n2k_A #273 to '2n2k_0'
Traceback (most recent call last):
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molobject.py", line 1447, in next_chain_id
next_index = _cid_index[cid[col]] + 1
~~~~~~~~~~^^^^^^^^^^
KeyError: '_'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute
cmd.run(cmd_text)
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/std_commands/time.py", line 30, in time
run(session, command)
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/foldseek/ligands.py", line 94, in foldseek_ligands
cmodel =_combine_structures(session, keep_structs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/foldseek/ligands.py", line 143, in _combine_structures
cmodel = run(session, cmd, log = False)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/cmd.py", line 79, in combine_cmd
new_id = next_chain_id(new_id)
^^^^^^^^^^^^^^^^^^^^^
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molobject.py", line 1449, in next_chain_id
raise ValueError("Illegal chain ID character: %s" % repr(cid[col]))
ValueError: Illegal chain ID character: '_'
ValueError: Illegal chain ID character: '_'
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molobject.py", line 1449, in next_chain_id
raise ValueError("Illegal chain ID character: %s" % repr(cid[col]))
See log for complete Python traceback.
OpenGL version: 4.1 Metal - 88.1
OpenGL renderer: Apple M2 Ultra
OpenGL vendor: Apple
Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: Mac Studio
Model Identifier: Mac14,14
Model Number: Z1800003VLL/A
Chip: Apple M2 Ultra
Total Number of Cores: 24 (16 performance and 8 efficiency)
Memory: 64 GB
System Firmware Version: 10151.121.1
OS Loader Version: 10151.121.1
Software:
System Software Overview:
System Version: macOS 14.5 (23F79)
Kernel Version: Darwin 23.5.0
Time since boot: 36 days, 23 hours, 59 minutes
Graphics/Displays:
Apple M2 Ultra:
Chipset Model: Apple M2 Ultra
Type: GPU
Bus: Built-In
Total Number of Cores: 60
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
PHL 278B1:
Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 2.4.1
Babel: 2.14.0
beautifulsoup4: 4.12.3
biopython: 1.83
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.3
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.17
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.6
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.58.3
ChimeraX-AtomicLibrary: 14.0.3
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.4.5
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.3
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-Clipper: 0.23.0
ChimeraX-clix: 0.1.4
ChimeraX-ColorActions: 1.0.4
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.5
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.9.dev202407240247
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-DeepMutationalScan: 1.0
ChimeraX-Dicom: 1.2
ChimeraX-DiffPlot: 1.0
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-Foldseek: 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: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.10
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.7
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.2
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-maskChains: 1.1
ChimeraX-MatchMaker: 2.1.3
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.15
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.1
ChimeraX-NIHPresets: 1.1.19
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.1
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.4
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.5
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.1
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.4.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 1.0.4
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.16.4
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.39.8
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.1
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.3
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.2.1
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.1
decorator: 5.1.1
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.4
fonttools: 4.51.0
fsspec: 2024.3.1
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.11.0
html2text: 2024.2.26
idna: 3.7
ihm: 1.0
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.2
jedi: 0.19.1
Jinja2: 3.1.3
joblib: 1.4.2
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.10
kiwisolver: 1.4.5
line-profiler: 4.1.2
llvmlite: 0.42.0
lxml: 5.2.1
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.4
matplotlib-inline: 0.1.7
mpmath: 1.3.0
mrcfile: 1.5.0
msgpack: 1.0.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numba: 0.59.1
numexpr: 2.10.0
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.3.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.1
prompt-toolkit: 3.0.43
psutil: 5.9.8
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pygments: 2.17.2
pynmrstar: 3.3.4
pynndescent: 0.5.12
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.1.2
pyproject-hooks: 1.1.0
PyQt6: 6.6.1
PyQt6-Qt6: 6.6.3
PyQt6-sip: 13.6.0
PyQt6-WebEngine: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.3
python-dateutil: 2.9.0.post0
pytz: 2024.1
pyzmq: 26.0.3
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scikit-learn: 1.4.2
scipy: 1.13.0
setuptools: 69.5.1
setuptools-scm: 8.0.4
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 7.2.6
sphinx-autodoc-typehints: 2.0.1
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.6.3
sympy: 1.12
tables: 3.8.0
tcia-utils: 1.5.1
threadpoolctl: 3.5.0
tifffile: 2024.1.30
tinyarray: 1.2.4
torch: 2.3.0
tornado: 6.4
tqdm: 4.66.4
traitlets: 5.14.2
typing-extensions: 4.11.0
tzdata: 2024.1
umap-learn: 0.5.6
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.10
Change History (6)
comment:1 by , 15 months ago
| Component: | Unassigned → Structure Analysis |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Foldseek ligands uses illegal chain id character "_" |
comment:2 by , 15 months ago
comment:3 by , 15 months ago
| Cc: | added |
|---|
I don't think many programs will allow non-alphanumeric chain IDs. As per https://www.rcsb.org/docs/general-help/identifiers-in-pdb, chain IDs are "commonly 1- or 2-character alphanumeric". Obviously many non-alphanumeric chain IDs would badly foul up atom specifiers, so ChimeraX couldn't possibly allow them. I could (should?) change the next_chain_id code to accept non-alphanumeric IDs while never generating anything other than alphanumeric chain IDs.
comment:4 by , 15 months ago
The mmCIF file where I am saving with chain ids with underscore "_" characters is intended for use in ChimeraX. It is a file containing ligands derived from different PDB files and I make the chain ids indicate the ligand source, for example chain id "8abc_B" means the ligand came from PDB 8abc chain B. I could make it 8abcB but that is not as readable. And the main point is readability in mouse hover popup atom specs in ChimeraX. This bug happens when the combine command needs to choose new chain ids to avoid overlaps. My code wasn't supposed to combine any duplicate chain ids, but due to the wrong handling of chain ids for NMR ensembles where I wanted 2n2k_A_1, 2n2k_A_2 to handle ensemble model number but instead used 2n2k for all I got the error reported in this ticket. I added the ensemble number in the chain id and combine now works without error.
While the "_" in chain ids is not officially supported by ChimeraX I no longer encounter problems with it so I think I will stick with it for now since I don't have a nice alternative to track where my ligands came from.
comment:5 by , 15 months ago
| Resolution: | → wontfix |
|---|---|
| Status: | assigned → closed |
comment:6 by , 15 months ago
Yes, if the chain IDs you are combining are all unique then this problem will never occur.
Note:
See TracTickets
for help on using tickets.
Another problem in this report is that apparently there was an NMR ensemble 2n2k and the foldseek ligands command used the same chain name for every ensemble member. It should have added a model number to avoid combine trying to rename all those.