id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
1837	modeller cannot use template that differs from its associated sequence	Elaine Meng	Eric Pettersen	"Example 
open http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/super8.msf
open 1muc

try to model any sequence in that alignment, e.g.

modeller comparative super8.msf:1 combineTemplates true numModels 1 fast true hetPreserve false hydrogens false waterPreserve false

Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 519305 507.134 0.495
read_te_291E> Sequence difference between alignment and pdb :
x (mismatch at alignment position 1)
Alignment LEVAWTLASGDTARDIAEARHMLEIRRHRVFKLKIGANPVEQDLKHVVTIKRELG 
PDB ALIERIDAIIVDLPTIRQQQTLVVLRVRCSDGVEGIGEATTIGGLAYGYESPEGI 
Match * * * *
Alignment residue type 10 (L, LEU) does not match pdb
residue type 1 (A, ALA),
for align code 1muc_1/A (atom file 1muc_1), pdb residue number ""4"", chain ""A""

Please check your alignment file header to be sure you correctly specified
the starting and ending residue numbers and chains. The alignment sequence
must match that from the atom file exactly.

Another possibility is that some residues in the atom file are missing,
perhaps because they could not be resolved experimentally. (Note that Modeller
reads only the ATOM and HETATM records in PDB, NOT the SEQRES records.)
In this case, simply replace the section of your alignment corresponding
to these missing residues with gaps.
read_te_288W> Protein not accepted: 1 1muc_1/A

No output models from Modeller; see log for Modeller text output.
"	defect	closed	major		Sequence		fixed						all	ChimeraX