Hi John,
not sure if we have to discuss this on list (we can continue private
after this if you wish).
Coot, better mmdb, picks up _atom_site.auth_seq_id in the first instance
as residue number. So, here we have 17 twice. Of course we have an
insertion code but in the "strict" setting of Coot we do not allow this
at the moment and warn of duplicated residues (see FAQ). I am not sure
if this has ever been an issue with cif files, certainly for pdb files
therefore the pedantry at the moment.
HTH,
B
On 13/12/2018 10:05, John Berrisford wrote:
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
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Div. Molecular Structural Biology
Dept. of Medical Biochemistry and Biophysics (MBB) |
Karolinska Institutet
SE-17177 Stockholm
Sweden
+46 8 52487695
[email protected] | ki.se
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