reflecting changes in the CCD

MonomerLibrary / monomers

dictionary of monomers and links

GNU Lesser General Public License v3.0

14 stars 85 forks source link

reflecting changes in the CCD #44

Closed keitaroyam closed 7 months ago

keitaroyam commented 9 months ago

Following #40, inconsistencies from the CCD was checked.

Now, following entries are obsolete:

2VO 39E E7U F3O LL8 M60 ON8 PSD QHD RTV SOC T0Q YYQ

Following entries have been updated, because atomic compositions or bonding patterns were changed.

5Z8 8BA 9NG BP5 CLZ CV6 DG9 DLC ETA N8K O18 PFX Q75 Q78 QFW RHJ T0N X1J YOA

Note 8BA has wrong chemistry (both P-OP1 and P-OP2 were double bond) which was fixed manually.

There are some changes in following entries as well, but they couldn't be updated because of metals or borons.

1CL 39B FSO K3G OEX OEY PTT RAX RUX TPT

Needs testing before merging.

GaribMurshudov commented 9 months ago

Did you report 8BA and others where there are chemistry changes to the PDB. mtals will come soon. borons will have to wait.

keitaroyam commented 9 months ago

~Not yet, will do.~ done

Updated DG9-SER link

LINK: RES-NAME-1 DG9 ATOM-NAME-1 P2A RES-NAME-2 SER ATOM-NAME-2 OG DELETE ATOM O4 1

NOTE: T0N should be fixed; this acedrg seems to have a problem with atom name having two single quotations.

keitaroyam commented 9 months ago

T0N fixed (by a newer acedrg). still needs tests

drlemmus commented 9 months ago

T0N is only in one NMR model so I cannot test in pdb-redo.

keitaroyam commented 9 months ago

N8K is used in 6tg4 and 7pox. 6tg4 is good, but 7pox uses different atom names. I initially thought atom names have not been updated in 7pox, but they are also inconsistent with alt_atom_id (so updating in gemmi didn't help at all).

Similarly, X1J is inconsistent with both PDB entries (5sns and 5s65). Again alt_atom_id didn't help, which is (partly) incorrect.

drlemmus commented 9 months ago

I'll report those to the PDB annotators

keitaroyam commented 8 months ago

@drlemmus any update from the PDB?

drlemmus commented 8 months ago

Not yet, I'm afraid.

keitaroyam commented 8 months ago

7CQ in the CCD was fixed and that in our library was updated accordingly.

keitaroyam commented 8 months ago

In the CCD, now 8NK BJ3 BQG HEK are obsolete, and 6VO and X1J were updated. The X1J issue (inconsistent atom names in the pdb models) has been sorted.

keitaroyam commented 7 months ago

As discussed in #48, single-atom entries ZCM RHF CF BS3 TA0 AM 4TI 0BE have been added.

By the way, should we remove RH RH3 BI TA BE from the library? In the CCD, they don't exist, and RHF BS3 TA0 0BE exist instead.

keitaroyam commented 7 months ago

Redundant and CCD-nonexistent single atom entries RH RH3 BI TA BE ER have been removed

GaribMurshudov commented 7 months ago

Do we have replacements for these single atom monomers?

keitaroyam commented 7 months ago

Yes. They were Rh, Rh, Bi, Ta, Be, Er, respectively. Here is the summary of single-atom entries:

Element	CCD	Monlib
X	UNX
H		H
D	D8U	D8U
He		HE
Li	LI	LI
Be	0BE	0BE
N		UNX
O	O	DUM O
F	F	F
Ne		NE
Na	NA	NA
Mg	MG	MG
Al	AL	AL
Si		SI
S		S
Cl	CL	CL
Ar	AR	AR
K	K	K
Ca	CA	CA
Sc		WSC
Ti	4TI	4TI
V	V	V
Cr	CR	CR
Mn	MN MN3	MN MN3
Fe	FE FE2	FE FE2
Co	3CO CO	3CO CO
Ni	3NI NI	3NI NI
Cu	CU CU1 CU3	CU CU1 CU3
Zn	ZN	ZN
Ga	GA	GA
Ge		GE
As	ARS	ARS
Se	SE	SE
Br	BR	BR
Kr	KR	KR
Rb	RB	RB
Sr	SR	SR
Y	Y1 YT3	Y1 YT3
Zr	ZR	ZR
Nb		NB
Mo	4MO 6MO MO	4MO 6MO MO
Ru	RU	RU
Rh	RH RH3 RHF	RHF
Pd	PD	PD
Ag	AG	AG
Cd	CD	CD
In	IN	IN
Sn		SN
Sb	SB	SB
Te	TE	TE
I	IOD	IOD
Xe	XE	XE
Cs	CS	CS
Ba	BA	BA
La	LA	LA
Ce	CE	CE
Pr	PR	PR
Nd	ND	ND
Pm		PM
Sm	SM	SM
Eu	EU EU3	EU EU3
Gd	GD GD3	GD GD3
Tb	TB	TB
Dy	DY	DY
Ho	HO HO3	HO HO3
Er	ER3	ER3
Tm		TM
Yb	YB YB2	YB YB2
Lu	LU	LU
Hf		HF
Ta	TA0	TA0
W	W	W
Re	RE	RE
Os	OS OS4	OS OS4
Ir	IR IR3	IR IR3
Pt	PT PT4	PT PT4
Au	AU AU3	AU AU3
Hg	HG	HG
Tl	TL	TL
Pb	PB	PB
Bi	BS3	BS3
Po		PO
At		AT
Rn		RN
Fr		FR
Ra		RA
Ac		AC
Th	TH	TH
U	U1	U1
Pu	4PU	4PU
Am	AM	AM
Cm	ZCM	ZCM
Cf	CF	CF