Hello. Thank you for your answer about the modelling loops ( date: 14/02) Now, I have a problem with the different commands. I have the main template I want to use to build the model and several small templates I only want to use to model the loops. My alignment looks like: Main template: -------Leu-His-Gly-Tyr-Phe-Val-Phe-Gly-Pro-Thr-Gly-------------- Loop's templates:------___-Ala-Asn-Trp-Tyr-___-Phe------------------- Loop's templates:---------------------------- Phe-Gly-Asn-Phe-Leu Loop's templates::-------------Asn-Trp-Phe-___-Phe-Gly-Asn Target:--------------Val-Ala-Asn-Trp-Tyr-___-Phe-Gly-Asn-Phe-Leu and I want to run the following commands: MALIGN3D TRANSFER XYZ ( with a CLUSTER_CUT >0) My problems are: 1º) As I have understood, the command MALIGN3D doesn't work because there aren`t equivalent positions during the framework construction betweeen the first template and the rest. Am I wrong? So I try to solve this by superposing the loop's templates with the main template with the command SUPERPOSE. 2º) After, when I run TRANFER XYZ ( CLUSTER_CUT >0), it appears in the .log : transfe_505_> MODEL is an average of the largest cluster: 1.0000 transfe_336E> No template structures. recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 I don't know what's my error. Do I need more templates to make a cluster? Must the loop's templates be similar to the first template in order to have the same topology? Don't they overlap properly? Is TRANFER XYZ ( CLUSTER_CUT =-1.0) the only possibility I have? (because it works) Thanks in advance