[sharp-discuss] SHARP-ARP/wARP and CCP4-ARP/wARP
Clemens Vonrhein
vonrhein at globalphasing.com
Wed Dec 15 11:57:56 GMT 2004
Dear Cholien,
what resolution are you working at? Seems to be fairly low
(Observations/parameters ratio is rather poor). Also, both versions of
ARP/wARP are not really building anything. So my guess is that your
density is rather poor (or too low resolution, i.e. below about
2.5-2.7). No matter what version you are using: this will not work -
and a discussion about R/Rfree values is a bit futile.
The SHARP/autoSHARP version of calling ARP/wARP is maybe a bit more
tuned towards SHARP and the availability of trustworthy experimental
phases. It was first developed for ARP/wARP 5.X and 6.0.
ARP/wARP 6.1.1 has some nice new features, so it is definitely worth
trying both. In easy cases (2A MAD data with a phasing power of 2.0)
both will work equally well I guess. It is the borderline cases, where
you might have greater control using the CCP4 interface to ARP/wARP.
Hope that helps.
Cheers
Clemens
On Wed, Dec 15, 2004 at 07:41:04PM +0800, ???? wrote:
> Dear Sir,
>
> I get eden_flat_XX.Ypc.mtz file from SHARP then use the eden_flat_XX.Ypc.mtz to CCP4/ARP/wARP. The results from SHARP-ARP/wARP and CCP4-ARP/wARP is very different. I don't know how to explain. The result from SHARP-ARP/wARP that R value low stage by stage and Rfree range around: 0.304 ~0.330. But the result from CCP4-ARP/wARP that R value low stage by stage but the Rfree increase even Rfree value is very high. Could you tell me what's wrong?
>
> Thanks in advanced.
>
> cholien.
>
> (1)SHARP-ARP/wARP
> 24792 reflections ( 99.25 % complete ) and 0 restraint used, for refining 5891 atoms.
> Observations/parameters ratio is 1.05 (~1.05 with restraints).
>
>
> --------------------------------------------------------------------------------
>
>
> Starting model : R = 0.322 (Rfree = 0.319)
>
>
> --------------------------------------------------------------------------------
>
>
> Cycle 1 : After refmac [0.50|1.00]: R = 0.283 (Rfree = 0.304)
> Found 38 (38 requested) and removed 19 (19 requested) atoms.
> Cycle 2 : After refmac [0.50|1.00]: R = 0.269 (Rfree = 0.305)
> Found 38 (38 requested) and removed 21 (21 requested) atoms.
> Cycle 3 : After refmac [0.50|1.00]: R = 0.259 (Rfree = 0.308)
> Found 38 (38 requested) and removed 22 (22 requested) atoms.
> Cycle 4 : After refmac [0.50|1.00]: R = 0.253 (Rfree = 0.309)
> Found 39 (39 requested) and removed 25 (25 requested) atoms.
> Cycle 5 : After refmac [0.50|1.00]: R = 0.246 (Rfree = 0.313)
> Found 39 (39 requested) and removed 26 (26 requested) atoms.
> Cycle 6 : After refmac [0.50|1.00]: R = 0.240 (Rfree = 0.309)
> Found 39 (39 requested) and removed 28 (28 requested) atoms.
> Cycle 7 : After refmac [0.50|1.00]: R = 0.236 (Rfree = 0.310)
> Found 39 (39 requested) and removed 29 (29 requested) atoms.
> Cycle 8 : After refmac [0.50|1.00]: R = 0.234 (Rfree = 0.313)
> Found 39 (39 requested) and removed 30 (30 requested) atoms.
> Cycle 9 : After refmac [0.50|1.00]: R = 0.230 (Rfree = 0.309)
> Found 39 (39 requested) and removed 31 (31 requested) atoms.
> Cycle 10 : After refmac [0.50|1.00]: R = 0.228 (Rfree = 0.314)
> Found 39 (39 requested) and removed 31 (31 requested) atoms.
>
>
> --------------------------------------------------------------------------------
>
>
> Building Cycle 1
> Round 1 : 74 peptides in 16 chains.
> Round 2 : 67 peptides in 14 chains.
> Chains 7, Residues 33 [out of 668], Connectivity Index 0.58
>
>
> --------------------------------------------------------------------------------
>
>
> Cycle 11 : After refmac [0.60|0.95]: R = 0.252 (Rfree = 0.333)
> Found 37 (37 requested) and removed 18 (18 requested) atoms.
> Cycle 12 : After refmac [0.72|0.95]: R = 0.238 (Rfree = 0.325)
> Found 37 (37 requested) and removed 18 (18 requested) atoms.
> Cycle 13 : After refmac [0.86|0.95]: R = 0.232 (Rfree = 0.326)
> Found 37 (37 requested) and removed 18 (18 requested) atoms.
> Cycle 14 : After refmac [0.95|0.95]: R = 0.229 (Rfree = 0.322)
> Found 37 (37 requested) and removed 18 (18 requested) atoms.
> Cycle 15 : After refmac [0.95|0.95]: R = 0.237 (Rfree = 0.326)
> Found 37 (37 requested) and removed 18 (18 requested) atoms.
> Cycle 16 : After refmac [0.95|0.95]: R = 0.235 (Rfree = 0.327)
> Found 38 (38 requested) and removed 19 (19 requested) atoms.
> Cycle 17 : After refmac [0.95|0.95]: R = 0.234 (Rfree = 0.326)
> Found 38 (38 requested) and removed 19 (19 requested) atoms.
> Cycle 18 : After refmac [0.95|0.95]: R = 0.241 (Rfree = 0.331)
> Found 38 (38 requested) and removed 19 (19 requested) atoms.
> Cycle 19 : After refmac [0.95|0.95]: R = 0.245 (Rfree = 0.331)
> Found 38 (38 requested) and removed 19 (19 requested) atoms.
> Cycle 20 : After refmac [0.95|0.95]: R = 0.241 (Rfree = 0.329)
> Found 38 (38 requested) and removed 19 (19 requested) atoms.
>
>
> --------------------------------------------------------------------------------
>
>
> Building Cycle 2
> Round 1 : 65 peptides in 15 chains.
> Round 2 : 65 peptides in 14 chains.
> Chains 7, Residues 31 [out of 668], Connectivity Index 0.57
>
>
> --------------------------------------------------------------------------------
>
>
>
> Note: Switching side-chain docking ON for next building cycle.
>
>
>
> Cycle 21 : After refmac [0.95|0.95]: R = 0.258 (Rfree = 0.338)
> Found 36 (36 requested) and removed 18 (18 requested) atoms.
> Cycle 22 : After refmac [0.95|0.95]: R = 0.254 (Rfree = 0.335)
> Found 37 (37 requested) and removed 18 (18 requested) atoms.
> Cycle 23 : After refmac [0.95|0.95]: R = 0.257 (Rfree = 0.340)
> Found 37 (37 requested) and removed 18 (18 requested) atoms.
> Cycle 24 : After refmac [0.95|0.95]: R = 0.246 (Rfree = 0.335)
> Found 37 (37 requested) and removed 18 (18 requested) atoms.
> Cycle 25 : After refmac [0.95|0.95]: R = 0.255 (Rfree = 0.335)
> Found 37 (37 requested) and removed 18 (18 requested) atoms.
> Cycle 26 : After refmac [0.95|0.95]: R = 0.244 (Rfree = 0.334)
> Found 37 (37 requested) and removed 18 (18 requested) atoms.
> Cycle 27 : After refmac [0.95|0.95]: R = 0.245 (Rfree = 0.329)
> Found 37 (37 requested) and removed 18 (18 requested) atoms.
> Cycle 28 : After refmac [0.95|0.95]: R = 0.254 (Rfree = 0.334)
> Found 37 (37 requested) and removed 18 (18 requested) atoms.
> Cycle 29 : After refmac [0.95|0.95]: R = 0.250 (Rfree = 0.328)
> Found 37 (37 requested) and removed 18 (18 requested) atoms.
> Cycle 30 : After refmac [0.95|0.95]: R = 0.241 (Rfree = 0.330)
> Found 38 (38 requested) and removed 19 (19 requested) atoms.(2)CCP4-ARP/wARP 24771 reflections ( 99.25 % complete ), for refining 6148 atoms. Observations/parameters ratio is 1.01------------------------------------------------------ Starting model: R = 0.405 (Rfree = 0.390). ------------------------------------------------------ Cycle 0: After refmac, R = 0.314 (Rfree = 0.427). Found 39 (39 requested) and removed 36 (36 requested) atoms.------------------------------------------------------ Building Cycle 0 Round 1: 41 peptides in 9 chains. Round 2: 28 peptides in 6 chains. Chains 6, Residues 22, Connectivity Index 0.57------------------------------------------------------ 24771 reflections ( 99.25 % complete ) and 120 restraints for refining 5989 atoms. Observations/parameters ratio is 1.03------------------------------------------------------ Cycle 1: After refmac, R = 0.301 (Rfree = 0.461). Found 38 (38 requested) and removed 19 (19 requested) atoms. Cycle 2: After refmac, R = 0.285 (Rfree = 0.481). Found 38 (38 requested) and removed 19 (19 requested) atoms. Cycle 3: After refmac, R = 0.275 (Rfree = 0.494). Found 39 (39 requested) and removed 19 (19 requested) atoms. Cycle 4: After refmac, R = 0.267 (Rfree = 0.502). Found 32 (39 requested) and removed 19 (19 requested) atoms. Cycle 5: After refmac, R = 0.262 (Rfree = 0.509). Found 22 (39 requested) and removed 19 (19 requested) atoms.------------------------------------------------------ Building Cycle 1 Round 1: 47 peptides in 11 chains. Round 2: 43 peptides in 10 chains. Chains 3, Residues 13, Connectivity Index 0.53------------------------------------------------------ 24771 reflections ( 99.25 % complete ) and 69 restraints for refining 5956 atoms. Observations/parameters ratio is 1.04------------------------------------------------------ Cycle 6: After refmac, R = 0.265 (Rfree = 0.521). Found 36 (38 requested) and removed 19 (19 requested) atoms. Cycle 7: After refmac, R = 0.260 (Rfree = 0.529). Found 32 (38 requested) and removed 19 (19 requested) atoms. Cycle 8: After refmac, R = 0.256 (Rfree = 0.537). Found 22 (38 requested) and removed 19 (19 requested) atoms. Cycle 9: After refmac, R = 0.254 (Rfree = 0.545). Found 25 (38 requested) and removed 19 (19 requested) atoms. Cycle 10: After refmac, R = 0.252 (Rfree = 0.550). Found 23 (38 requested) and removed 19 (19 requested) atoms.------------------------------------------------------ Building Cycle 2 Round 1: 36 peptides in 9 chains. Round 2: 37 peptides in 8 chains. Chains 3, Residues 15, Connectivity Index 0.57------------------------------------------------------ 24771 reflections ( 99.25 % complete ) and 75 restraints for refining 5939 atoms. Observations/parameters ratio is 1.04------------------------------------------------------ Cycle 11: After refmac, R = 0.256 (Rfree = 0.557). Found 38 (38 requested) and removed 19 (19 requested) atoms. Cycle 12: After refmac, R = 0.253 (Rfree = 0.562). Found 14 (38 requested) and removed 19 (19 requested) atoms. Cycle 13: After refmac, R = 0.256 (Rfree = 0.559). Found 21 (38 requested) and removed 19 (19 requested) atoms. Cycle 14: After refmac, R = 0.253 (Rfree = 0.565). Found 23 (38 requested) and removed 19 (19 requested) atoms. Cycle 15: After refmac, R = 0.251 (Rfree = 0.571). Found 21 (38 requested) and removed 19 (19 requested) atoms.------------------------------------------------------ Building Cycle 3 Round 1: 42 peptides in 10 chains. Round 2: 43 peptides in 9 chains. Chains 6, Residues 29, Connectivity Index 0.58------------------------------------------------------ 24771 reflections ( 99.25 % complete ) and 113 restraints for refining 5927 atoms. Observations/parameters ratio is 1.04------------------------------------------------------ Cycle 16: After refmac, R = 0.256 (Rfree = 0.577). Found 38 (38 requested) and removed 19 (19 requested) atoms. Cycle 17: After refmac, R = 0.254 (Rfree = 0.580). Found 38 (38 requested) and removed 19 (19 requested) atoms. Cycle 18: After refmac, R = 0.253 (Rfree = 0.585). Found 27 (38 requested) and removed 19 (19 requested) atoms. Cycle 19: After refmac, R = 0.251 (Rfree = 0.588). Found 21 (38 requested) and removed 19 (19 requested) atoms. Cycle 20: After refmac, R = 0.251 (Rfree = 0.592). Found 26 (38 requested) and removed 19 (19 requested) atoms.------------------------------------------------------ Building Cycle 4 Round 1: 31 peptides in 7 chains. Round 2: 33 peptides in 7 chains. Chains 5, Residues 23, Connectivity Index 0.58------------------------------------------------------ 24771 reflections ( 99.25 % complete ) and 99 restraints for refining 5952 atoms. Observations/parameters ratio is 1.04------------------------------------------------------ Cycle 21: After refmac, R = 0.253 (Rfree = 0.590). Found 38 (38 requested) and removed 19 (19 requested) atoms. Cycle 22: After refmac, R = 0.252 (Rfree = 0.594). Found 35 (38 requested) and removed 19 (19 requested) atoms. Cycle 23: After refmac, R = 0.251 (Rfree = 0.596). Found 27 (38 requested) and removed 19 (19 requested) atoms. Cycle 24: After refmac, R = 0.250 (Rfree = 0.597). Found 22 (38 requested) and removed 19 (19 requested) atoms. Cycle 25: After refmac, R = 0.250 (Rfree = 0.599). Found 21 (38 requested) and removed 19 (19 requested) atoms.------------------------------------------------------ Building Cycle 5 Round 1: 45 peptides in 10 chains. Round 2: 46 peptides in 10 chains. Chains 5, Residues 21, Connectivity Index 0.57------------------------------------------------------ 24771 reflections ( 99.25 % complete ) and 117 restraints for refining 5971 atoms. Observations/parameters ratio is 1.04------------------------------------------------------ Cycle 26: After refmac, R = 0.253 (Rfree = 0.603). Found 38 (38 requested) and removed 19 (19 requested) atoms. Cycle 27: After refmac, R = 0.251 (Rfree = 0.606). Found 26 (38 requested) and removed 19 (19 requested) atoms. Cycle 28: After refmac, R = 0.251 (Rfree = 0.609). Found 25 (38 requested) and removed 19 (19 requested) atoms. Cycle 29: After refmac, R = 0.250 (Rfree = 0.611). Found 26 (38 requested) and removed 19 (19 requested) atoms. Cycle 30: After refmac, R = 0.254 (Rfree = 0.601). Found 5 (38 requested) and removed 19 (19 requested) atoms.------------------------------------------------------ Building Cycle 6 Round 1: 44 peptides in 10 chains. Round 2: 46 peptides in 9 chains. Chains 7, Residues 32, Connectivity Index 0.61------------------------------------------------------ 24771 reflections ( 99.25 % complete ) and 168 restraints for refining 5960 atoms. Observations/parameters ratio is 1.04------------------------------------------------------ Cycle 31: After refmac, R = 0.258 (Rfree = 0.611). Found 38 (38 requested) and removed 19 (19 requested) atoms. Cycle 32: After refmac, R = 0.255 (Rfree = 0.618). Found 38 (38 requested) and removed 19 (19 requested) atoms. Cycle 33: After refmac, R = 0.255 (Rfree = 0.622). Found 18 (38 requested) and removed 19 (19 requested) atoms. Cycle 34: After refmac, R = 0.255 (Rfree = 0.625). Found 18 (38 requested) and removed 19 (19 requested) atoms. Cycle 35: After refmac, R = 0.256 (Rfree = 0.630). Found 18 (38 requested) and removed 19 (19 requested) atoms.-----------------------------------------------------
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--
***************************************************************
* Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com
*
* Global Phasing Ltd.
* Sheraton House, Castle Park
* Cambridge CB3 0AX, UK
*--------------------------------------------------------------
* BUSTER Development Group (http://www.globalphasing.com)
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