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Structure Finder: Troubleshooting Guide

Problem
Possible Solution
Sequence not found
Remove spaces after each residue (e.g. CGCGCG or ALAGLUGLN)
Results list is much smaller/larger than it should be
Incorrect use of Logical Operator "OR" should be indicated when selecting the new constraint (i.e., when looking for structures with publication year 1988 OR 1989, choose the OR Logical Operator when selecting structures from 1989)
Constraint was not selected/Structures not found
Previous search selection was not reset/cleared
Citation report contains too many references for each structure
To limit any citation reports to primary references, Jrnl_Serial_No should be set equal to 1 during the original search (and not during report generation) for the structure.
Report is unordered/ not clear
When creating reports, the row order in the report is first determined by Structure_ID. For reports where there are multiple rows for each structure (such as in the table sugar_phosphate_geometry), the report is then further ordered by the first item selected. To further order reports, first select a item, such as residue_no, by which to order the report output.
Instead of a report, a TIME OUT message appears
Large and complex searches and reports may time out before completion. If you have any questions or queries, please send mail to ndbadmin@ndbserver.rutgers.edu
Rasmol will not display
The remote RasMol viewer (UNIX workstations and X-terminals only) requires that the server know your screen address and has permission to open windows on your screen. To permit the NDB server to display a RasMol window on your screen type at an active UNIX prompt the command:xhost +ndb-mirror-0.rutgers.edu. Your display address should be entered correctly in the space provided on the NDB Search Results page.

The local RasMol display mode returns coordinate files to your local browser with the mime type application/x-rasmol. Check if your browser is set to launch RasMol with this mime type.

 

 

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