Hi Andrea / Bernard Can you provide a more detailed report of the issue with these entries? i.e. which residue numbers are duplicated.
Looking at 5lza are these the lines which are causing problems? ATOM 52209 P P . C V 22 17 ? 159.390 157.935 201.808 1.00 179.95 ? 17 C v P 1 ATOM 52210 O OP1 . C V 22 17 ? 160.558 157.192 201.304 1.00 163.34 ? 17 C v OP1 1 ATOM 52211 O OP2 . C V 22 17 ? 159.494 158.645 203.105 1.00 179.22 ? 17 C v OP2 1 ATOM 52212 O "O5'" . C V 22 17 ? 158.977 158.995 200.693 1.00 174.80 ? 17 C v "O5'" 1 ATOM 52213 C "C5'" . C V 22 17 ? 159.798 159.197 199.552 1.00 185.33 ? 17 C v "C5'" 1 ATOM 52214 C "C4'" . C V 22 17 ? 159.648 160.575 198.959 1.00 196.84 ? 17 C v "C4'" 1 ATOM 52215 O "O4'" . C V 22 17 ? 158.451 160.646 198.143 1.00 206.86 ? 17 C v "O4'" 1 ATOM 52216 C "C3'" . C V 22 17 ? 159.504 161.733 199.935 1.00 202.96 ? 17 C v "C3'" 1 ATOM 52217 O "O3'" . C V 22 17 ? 160.757 162.140 200.486 1.00 209.64 ? 17 C v "O3'" 1 ATOM 52218 C "C2'" . C V 22 17 ? 158.838 162.799 199.077 1.00 196.77 ? 17 C v "C2'" 1 ATOM 52219 O "O2'" . C V 22 17 ? 159.799 163.469 198.274 1.00 196.27 ? 17 C v "O2'" 1 ATOM 52220 C "C1'" . C V 22 17 ? 157.939 161.961 198.163 1.00 212.57 ? 17 C v "C1'" 1 ATOM 52221 N N1 . C V 22 17 ? 156.526 161.937 198.609 1.00 203.47 ? 17 C v N1 1 ATOM 52222 C C2 . C V 22 17 ? 155.711 163.078 198.470 1.00 201.22 ? 17 C v C2 1 ATOM 52223 O O2 . C V 22 17 ? 156.148 164.134 197.982 1.00 180.18 ? 17 C v O2 1 ATOM 52224 N N3 . C V 22 17 ? 154.425 163.025 198.884 1.00 183.62 ? 17 C v N3 1 ATOM 52225 C C4 . C V 22 17 ? 153.931 161.906 199.405 1.00 174.69 ? 17 C v C4 1 ATOM 52226 N N4 . C V 22 17 ? 152.656 161.902 199.796 1.00 172.63 ? 17 C v N4 1 ATOM 52227 C C5 . C V 22 17 ? 154.726 160.737 199.532 1.00 163.94 ? 17 C v C5 1 ATOM 52228 C C6 . C V 22 17 ? 156.004 160.794 199.140 1.00 190.30 ? 17 C v C6 1 ATOM 52229 P P . U V 22 18 A 160.906 163.453 201.425 1.00 213.16 ? 17 U v P 1 ATOM 52230 O OP1 . U V 22 18 A 160.755 164.734 200.686 1.00 209.40 ? 17 U v OP1 1 ATOM 52231 O OP2 . U V 22 18 A 162.184 163.267 202.150 1.00 212.78 ? 17 U v OP2 1 ATOM 52232 O "O5'" . U V 22 18 A 159.749 163.307 202.511 1.00 198.92 ? 17 U v "O5'" 1 ATOM 52233 C "C5'" . U V 22 18 A 159.897 162.389 203.589 1.00 176.83 ? 17 U v "C5'" 1 ATOM 52234 C "C4'" . U V 22 18 A 159.052 162.761 204.784 1.00 178.19 ? 17 U v "C4'" 1 ATOM 52235 O "O4'" . U V 22 18 A 157.733 163.175 204.336 1.00 176.36 ? 17 U v "O4'" 1 ATOM 52236 C "C3'" . U V 22 18 A 158.780 161.634 205.775 1.00 201.36 ? 17 U v "C3'" 1 ATOM 52237 O "O3'" . U V 22 18 A 159.838 161.426 206.700 1.00 203.24 ? 17 U v "O3'" 1 ATOM 52238 C "C2'" . U V 22 18 A 157.454 162.045 206.411 1.00 198.91 ? 17 U v "C2'" 1 ATOM 52239 O "O2'" . U V 22 18 A 157.661 163.011 207.432 1.00 188.97 ? 17 U v "O2'" 1 ATOM 52240 C "C1'" . U V 22 18 A 156.743 162.726 205.237 1.00 181.84 ? 17 U v "C1'" 1 ATOM 52241 N N1 . U V 22 18 A 155.810 161.824 204.513 1.00 214.12 ? 17 U v N1 1 ATOM 52242 C C2 . U V 22 18 A 154.489 161.753 204.929 1.00 205.79 ? 17 U v C2 1 ATOM 52243 O O2 . U V 22 18 A 154.048 162.398 205.865 1.00 184.59 ? 17 U v O2 1 ATOM 52244 N N3 . U V 22 18 A 153.688 160.903 204.200 1.00 201.99 ? 17 U v N3 1 ATOM 52245 C C4 . U V 22 18 A 154.063 160.125 203.123 1.00 187.09 ? 17 U v C4 1 ATOM 52246 O O4 . U V 22 18 A 153.241 159.399 202.562 1.00 178.92 ? 17 U v O4 1 ATOM 52247 C C5 . U V 22 18 A 155.438 160.245 202.771 1.00 179.05 ? 17 U v C5 1 ATOM 52248 C C6 . U V 22 18 A 156.225 161.075 203.437 1.00 200.82 ? 17 U v C6 1 The auth_seq_id is the same for these two residues, the second one has an insert code. Thanks John PDBe -----Original Message----- From: Mailing list for users of COOT Crystallographic Software <[email protected]> On Behalf Of Bernhard Lohkamp Sent: 13 December 2018 08:55 To: [email protected] Subject: Re: Problem loading PDBx/mmCIF files for EM in Coot Hi Andrea, as Huw pointed out there are duplicated sequence numbers which Coot (mmdb) does not allow. The work around is the command: python: allow_duplicate_sequence_numbers() guile: (allow-duplicate-sequencenumbers) and have a look at the FAQ (https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/docs/coot-faq.html#How-do-I-read-a-coordinates-file-with-duplicate-residue-numbers_003f) HTH, Bernhard On 13/12/2018 09:48, Andrea Thorn wrote: > Thank you for pointing this out. The file came from PDBe - and I have > a few dozens where this happens. So just fixing the CIF file in my > download folder does not help the underlying problem. I basically want > to find out if I did something wrong - or if I need to ask the PDB > people to fix the PDBx/mmCIF files - or if it's Coot doing something > it is not supposed to (bug report)... > > Best wishes > > > Andrea. > > On 11/12/2018 17:35, Huw Jenkins wrote: >>> On 11 Dec 2018, at 15:32, Andrea Thorn <[email protected]> wrote: >>> >>> Can someone point out if the files for these entries are broken >>> somehow, or if there is a bug in Coot? >> 5lza for me: >> >> There was an error reading 5lza.cif. >> ERROR 42 READ: Duplicate sequence number and insertion code. >> CIF ITEM: loop _atom_site.B_iso_or_equiv_esd row 52227 data >> [NULL] >> >> There was a coordinates read error >> >> looks like duplicate atom_site.auth_seq_id >> >> >> Huw >> ##################################################################### >> ### >> >> To unsubscribe from the COOT list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=COOT&A=1 >> > -- *************************************************** Dr. Bernhard Lohkamp | Associate Professor/Docent Div. Molecular Structural Biology Dept. of Medical Biochemistry and Biophysics (MBB) | Karolinska Institutet SE-17177 Stockholm Sweden +46 8 52487695 [email protected] | ki.se När du skickar e-post till Karolinska Institutet (KI) innebär detta att KI kommer att behandla dina personuppgifter. Här finns information om hur KI behandlar personuppgifter<https://ki.se/medarbetare/integritetsskyddspolicy>. Sending email to Karolinska Institutet (KI) will result in KI processing your personal data. You can read more about KI’s processing of personal data here<https://ki.se/en/staff/data-protection-policy>. ######################################################################## To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=COOT&A=1 ######################################################################## To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=COOT&A=1
