Validation of Consensus Run: Difference between revisions
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=== '''Verification of Consensus Assignments''' === | === '''Verification of Consensus Assignments''' === | ||
1. Create a working subdirectory, for example, <tt>cyana21/calc2</tt>. | 1. Create a working subdirectory, for example, <tt>cyana21/calc2</tt>. | ||
2. Copy consensus peaklists (<tt>n_cons.peaks</tt>, <tt>ali_cons.peaks</tt> and <tt>aro_cons.peaks</tt>) into this subdirectory. | 2. Copy consensus peaklists (<tt>n_cons.peaks</tt>, <tt>ali_cons.peaks</tt> and <tt>aro_cons.peaks</tt>) into this subdirectory. | ||
*If using CARA, re-integrate the peakslist and export them. | *If using CARA, re-integrate the peakslist and export them. | ||
3. Copy <tt>init.cya</tt>, <tt>XXXX.seq</tt>, <tt>XXXX.prot</tt> and <tt>stereofound.cya</tt> from the CYANA automated run (<tt>cyana21/calc2</tt>). Rename <tt>stereofound.cya</tt> into <tt>stereo.cya</tt> | 3. Copy <tt>init.cya</tt>, <tt>XXXX.seq</tt>, <tt>XXXX.prot</tt> and <tt>stereofound.cya</tt> from the CYANA automated run (<tt>cyana21/calc2</tt>). Rename <tt>stereofound.cya</tt> into <tt>stereo.cya</tt> | ||
4. Copy <tt>GridSearch.cya</tt>, <tt>CALC.cya</tt> and <tt>talos.aco</tt> from the <tt>found</tt> subdirectory. Modify <tt>GridSearch.cya</tt> to read <tt>cons.upl</tt> instead of <tt>short.upl</tt>. | 4. Copy <tt>GridSearch.cya</tt>, <tt>CALC.cya</tt> and <tt>talos.aco</tt> from the <tt>found</tt> subdirectory. Modify <tt>GridSearch.cya</tt> to read <tt>cons.upl</tt> instead of <tt>short.upl</tt>. | ||
5. Create UPL file <tt>cons.upl</tt> using run_caliba.cya (see below). | 5. Create UPL file <tt>cons.upl</tt> using run_caliba.cya (see below). | ||
6. In CYANA 2.1 run <tt>GridSearch.cya</tt> | 6. In CYANA 2.1 run <tt>GridSearch.cya</tt> | ||
7. In CYANA 2.1 run CALC.cya for manual structure calculation with only consensus constraints. | 7. In CYANA 2.1 run CALC.cya for manual structure calculation with only consensus constraints. | ||
8. Clean violations the same was is in [[NESG:UsingFOUNDakaHABAS|Verifying Local NOE Network with FOUND (HABAS)]] and try to keep TF < 1.0. | 8. Clean violations the same was is in [[NESG:UsingFOUNDakaHABAS|Verifying Local NOE Network with FOUND (HABAS)]] and try to keep TF < 1.0. | ||
*For the violated NOE, re-integrate the peaks first if it is overintegrated (in XEASY). | *For the violated NOE, re-integrate the peaks first if it is overintegrated (in XEASY). | ||
*Unassign peaks, which appear at spectral artifacts. | *Unassign peaks, which appear at spectral artifacts. | ||
*If violation persisit while peak integrals are correct, then modify the calibration parameters. | *If violation persisit while peak integrals are correct, then modify the calibration parameters. | ||
9. Verify the additional stereospecific assignments made in this run. Swap the atom groups if needed. | 9. Verify the additional stereospecific assignments made in this run. Swap the atom groups if needed. | ||
You may want to run an additional iteration of consensus assignment, though it is usually not necessary: | You may want to run an additional iteration of consensus assignment, though it is usually not necessary: | ||
=== | |||
=== '''Acceptance Criteria''' === | === '''Acceptance Criteria''' === | ||
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#The manual run of CYANA structure calculation with distance constraints from consensus assigned NOEs delivers converged structure, the pairwise RMSD of the structure family shall be less than 3A. | #The manual run of CYANA structure calculation with distance constraints from consensus assigned NOEs delivers converged structure, the pairwise RMSD of the structure family shall be less than 3A. | ||
#The yield of consensus assigned NOEs shall be large than 50%. | #The yield of consensus assigned NOEs shall be large than 50%. | ||
=== | |||
=== '''Example scripts''' === | === '''Example scripts''' === | ||
| Line 61: | Line 63: | ||
write upl cons.upl | write upl cons.upl | ||
protocol:=</pre> | protocol:=</pre> | ||
<br> <br> -- GaohuaLiu - 26 Jan 2007 | |||
<br> -- GaohuaLiu - 26 Jan 2007 | |||
-- Edited by JimAramini - Nov 2009 | -- Edited by JimAramini - Nov 2009 | ||
Revision as of 20:28, 4 November 2009
Validation of Consensus Run
Verification of Consensus Assignments
1. Create a working subdirectory, for example, cyana21/calc2.
2. Copy consensus peaklists (n_cons.peaks, ali_cons.peaks and aro_cons.peaks) into this subdirectory.
- If using CARA, re-integrate the peakslist and export them.
3. Copy init.cya, XXXX.seq, XXXX.prot and stereofound.cya from the CYANA automated run (cyana21/calc2). Rename stereofound.cya into stereo.cya
4. Copy GridSearch.cya, CALC.cya and talos.aco from the found subdirectory. Modify GridSearch.cya to read cons.upl instead of short.upl.
5. Create UPL file cons.upl using run_caliba.cya (see below).
6. In CYANA 2.1 run GridSearch.cya
7. In CYANA 2.1 run CALC.cya for manual structure calculation with only consensus constraints.
8. Clean violations the same was is in Verifying Local NOE Network with FOUND (HABAS) and try to keep TF < 1.0.
- For the violated NOE, re-integrate the peaks first if it is overintegrated (in XEASY).
- Unassign peaks, which appear at spectral artifacts.
- If violation persisit while peak integrals are correct, then modify the calibration parameters.
9. Verify the additional stereospecific assignments made in this run. Swap the atom groups if needed.
You may want to run an additional iteration of consensus assignment, though it is usually not necessary:
===
Acceptance Criteria
A successful consensus run shall satisfy:
- Both program CYANA and AutoStructure automatic structure calculation deliver converged structure.
- The structures from program CYANA and AutoStructure are similar, the RMSD value between the mean structures from both programs should be less than the sum of pairwise RMSD values of the two structure families.
- The manual run of CYANA structure calculation with distance constraints from consensus assigned NOEs delivers converged structure, the pairwise RMSD of the structure family shall be less than 3A.
- The yield of consensus assigned NOEs shall be large than 50%.
===
Example scripts
run_caliba.cya
protocol:=caliba.log read prot $name read peaks n_cons peaks select "**" peaks set volume=abs(volume) caliba bb=1.7E+06 read peaks ali_cons peaks select "**" peaks set volume=abs(volume) caliba bb=1.7E+06 read peaks aro_cons peaks select "**" peaks set volume=abs(volume) caliba bb=1.7E+06 write upl cons.upl protocol:=
-- GaohuaLiu - 26 Jan 2007
-- Edited by JimAramini - Nov 2009