Prime User Manual - ISP

!UNUSABLE: SEQRES numbering is wrong
Appendix D: Error Messages and Warnings
• The number of residues in a particular chain does not agree with the number of residues
shown in columns 14 to 17 of SEQRES.
D.3 Edit Alignment
Check Alignment
When you click Next at the end of the Edit Alignment step, the Check Alignment warning may
appear. The warning lists possible alignment problems that you may want to fix before
continuing to the next step. For example, there may be gaps in secondary structure elements of
the template, or gaps in the query that are aligned to secondary structure elements of the
template.
If you do not want to make corrections to the alignment, click Continue to go to the next step.
To make corrections based on the information in the error message, make a note of the gap
locations given, click Cancel to close the message box while remaining in Edit Alignment, and
change the alignment accordingly.
D.4 Build Structure
Error messages and warnings for this generally appear in the log of a running job. The log can
be viewed in the job Monitor panel until the job is completed.
D.5 Refinement
Error messages for Refinement generally appear in the log of a running job. The following is
an example of a warning in the log of a loop refinement.
Invalid Features
When a loop refinement begins, a validation program checks the loop features of the structure.
Apparent errors are reported in a warning dialog box. You may choose to Run All Features,
Run Only Valid Features, orCancel. It is recommended that you make a note of the invalid
features, click Cancel, and correct the structure if appropriate.
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