Lines Matching refs:oligomer
191 like an oligomer, that is, it gets its left and right end caps
353 phase fragmentation of the currently selected oligomer;
785 selection behaves as an oligomer, and thus should normally be capped
789 oligomer is capped on both its ends;
792 selection behaves as a residual chain, and thus the oligomer
795 simulating partial cleavages by first selecting an oligomer,
797 oligomer resulting from a partial cleavage. Also, the situation
1179 cleavage of a selected oligomer using a different cleavage agent. In
1194 \guilabel{Sequence} tab widget displays the sequence of the oligomer
1216 to the clipboard or to a file or even to drag the displayed oligomer
1220 For oligomer data filtering, please refer to
1221 section~\ref{sect:oligomer-data-filtering}, page
1222 \pageref{sect:oligomer-data-filtering}.
1252 oligomer. Instead, a single peak will be calculated, based either on
1253 the monoisotopic or on the average mass of the oligomer that is used
1274 an isotopic cluster for each oligomer.
1278 Computing isotopic cluster for oligomer 1
1288 Computing isotopic cluster for oligomer 2
1344 \index{\xpe!simulations!oligomer~fragmentation}
1351 those fragmentations \textit{in silico}. Let's see how an oligomer
1361 oligomer fragmentation is performed. One or more fragmentation
1373 definition corresponding to the polymer sequence of which an oligomer
1388 monomers contained in the oligomer. Only cross-links that are fully
1389 contained in the oligomer are taken into account. Partial cross-links,
1391 of the oligomer, are ignored.
1433 If we select the oligomer region [38--77] and that we ask for a
1465 {figures/xpertedit-fragmentation-cross-linked-oligomer.png}
1469 cross-linking situation with an oligomer that has five
1470 cross-links, four of which are fully encompassed by the oligomer
1471 and one that involves a monomer outside of the oligomer.}
1472 \label{fig:xpertedit-fragmentation-cross-linked-oligomer}
1476 The calculation of the fragments for this oligomer involves the
1481 \item Calculate regions of the oligomer that involve cross-links
1485 outside of the oligomer;
1487 \item For fragments that have the left end of the oligomer (``Left-end
1513 \item For fragments that have the right end of the oligomer (Right-end
1537 the cross-links of the oligomer.
1544 that involve monomer(s) outside of the oligomer are ignored. The user
1552 displayed oligomer items in a text editor.
1554 For oligomer data filtering, please refer to
1555 section~\ref{sect:oligomer-data-filtering}, page
1556 \pageref{sect:oligomer-data-filtering}.
1615 displayed oligomer items in a text editor.
1617 For oligomer data filtering, please refer to
1618 section~\ref{sect:oligomer-data-filtering}, page
1619 \pageref{sect:oligomer-data-filtering}.
1625 \label{sect:oligomer-data-filtering}
1636 Figure~\ref{fig:xpertedit-filtering-oligomer-data}.
1641 {figures/xpertedit-filtering-oligomer-data.png}
1644 This figure shows how oligomer data can be filtered. The
1649 sequence-cleavage oligomer data.}
1650 \label{fig:xpertedit-filtering-oligomer-data}
1656 (Figure~\ref{fig:xpertedit-filtering-oligomer-data},
1657 page~\pageref{fig:xpertedit-filtering-oligomer-data}). For any
1678 with other oligomer data : \guilabel{Mono}, \guilabel{Avg},
2152 cleavages, oligomer fragmentations): 5;