Hi Eric, Thanks for the suggestion. I found out that the problem was that I was trying to associate the FASTA sequence and the structure sequence from the sequence viewer, not from the FASTA sequence. Now it works, no errors! Best Sasha   -----Original Message----- From: Eric <pett@cgl.ucsf.edu> To: Alexandra <alexandra.zahradnikova@savba.sk> Cc: chimerax-users <chimerax-users@cgl.ucsf.edu> Date: Tuesday, 1 April 2025 1:55 AM CEST Subject: Re: [chimerax-users] Model loops with MODELER in ChimeraX Hi again Sasha, You should be able to do this with a FASTA file and a PDB with the SEQRES records removed.  This worked fine for me in a test situation where I had a structure with a missing segment and a FASTA sequence that corresponded except the missing part had been turned into alanines (more residues than the original missing segment).  The fact that this doesn’t work for you suggests to me that the FASTA sequence you opened doesn’t match well to the existing parts of the structure.  If you right click on the sequence and choose “Associations…” and then force the structure to associate with the sequence, do you get a lot of red error boxes on the sequence? You might have to open a ticket for this (Help→Report a Bug) and attach the sequence and structure files for me to offer further advice.  If the data is private, you could email it to me directly.   --Eric   Eric Pettersen UCSF Computer Graphics Lab On Mar 28, 2025, at 7:54 AM, Alexandra Zahradnikova via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote: Hello, I have recently watched a Youtube video (https://www.youtube.com/watch?v=GV6jHhxR5T4) about completing loops with Modeller in ChimeraX. However, the structure I want to model is only a part of the actual molecule, and I want to replace one unresolved segment (300 residues long) with 11 glycines.  When I upload both, the FASTA file with the sequence as it should look after completion of the loops, and the PDB file of the incomplete structure, I am not able to align them together in order to perform the modelling.  - If I use the original PDB file containing the SEQRES part, the association is performed but produces mismatches after the start of the unresolved sequence. - If I use the PDB file without the SEQRES part, I am not able to perform the association. Can anybody help me? Thanks in advance Sasha ________________________________________________________________________ Alexandra Zahradníková, PhD Department of Cell Cardiology Institute of Experimental Endocrinology Biomedical Research Centre SAS Dúbravská cesta 9 845 05 Bratislava Slovakia Mobile: +421 908 069 796           _______________________________________________ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.eduTo unsubscribe send an email to chimerax-users-leave@cgl.ucsf.eduArchives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/