id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
16325	Modeller mismatch failure	jmsstarlight@…	Eric Pettersen	"I still have some problems with the reconstructions of the loop fragments for the structures containing ligands. I've just tested the latest ChimeraX (1.9) and the problem is still there: where I fetch a PDB with the ligand and use it SEQRES to reconstruct the missed loop it produces the error indicating the sequence mismatch. When I remove all ligands, everything is OK. 

Example 1  - no problems with loop reconstructions
open 8OU9 ( the chain C contains 5 missed residues)
sequence chain #1/C
modeller refine 1/C:1:all-missing numModels 3 fast true adjacentFlexible 1 protocol standard

Everything works OK - in spite of the presence of the ligand and ZN in the chain C



Example 2 - the similar system with ligand and ZN, which has a problem in loop reconstruction with modeller

open 6BN7 (the chain B contains a gap of 9 residues)

Here is the example I've just tested with a new pdb where the chain B contains the 9 a.a missed fragments

open 6BN7
sequence chain #1/B
modeller refine 1/B:1:230-238 numModels 3 fast true adjacentFlexible 1 protocol standard

this produces the following error

modeller refine 1/B:1:230-238 numModels 1 fast true adjacentFlexible 1 protocol standard:

Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1514284 1478.793 1.444
read_te_290E> Number of residues in the alignment and pdb files are different: 1305 1178
For alignment entry: 1 6bn7_1
x (mismatch at alignment position 1179)
Alignment DMSPQKFWGLTRSALLPTIP/SMNPPPPETSNPNKPKRQTNQLQYLLRVVLKTLWKHQFA
PDB DMSPQKFWGLTRSALLPTIP/
Match *********************

I've tried to assosiate the sequence with the structure and it did not find any mismatches:

Disassociated 6bn7 chain B from chain B
Associated 6bn7 chain B to chain B with 0 mismatches

One I removed all ligands- everything works OK:

delete ~protein
modeller refine 1/B:1:230-238 numModels 1 fast true adjacentFlexible 1 protocol standardWebservices job id: 602MBGXI5OKGYO2Z
Modeller job (ID 602MBGXI5OKGYO2Z) finished
Computing secondary structure

"	defect	closed	moderate		Structure Prediction		fixed						all	ChimeraX