Hi Pietro, It looks as though SFALL thinks you have fractional coords and has coverted them into orthog ones. Does the PDB have a CRYST1 and SCALEi cards?
Adam On Thu, 24 Apr 2008, Pietro Roversi wrote: > Dear everyone, > > I am using sfall in "MODE ATMMAP RESMOD" to compute a > tagged map with > which to score a model against a map. The input PDB is OK and regularly > read by all programs - but sfall seems to interpret the coordinates > wrongly (see the list of the first 10 atoms coordinates that the program > outputs, both in orthogonal and fractional): > > First 10 atoms of atsort - orthog coordinates > 1N CYS 140283.0180251.2380115.7960 1.00 500.00 3 > fractional coordinates 1.57127 1.39484 0.64288 > > > First 10 atoms of atsort - orthog coordinates > 2CA CYS 140281.9190250.4390115.2740 1.00 500.00 2 > fractional coordinates 1.56517 1.39040 0.63998 > 3C CYS 140280.7020251.2870114.8740 1.00 500.00 2 > fractional coordinates 1.55842 1.39511 0.63776 > 4O CYS 140279.7890250.8050114.1860 1.00 500.00 4 > fractional coordinates 1.55335 1.39243 0.63394 > 5CB CYS 140281.5250249.4400116.3580 1.00 500.00 2 > fractional coordinates 1.56299 1.38485 0.64600 > 6SG CYS 140280.3360248.2280115.8470 1.00 500.00 5 > fractional coordinates 1.55638 1.37813 0.64317 > 7N SER 141280.6900252.5440115.3270 1.00 500.00 3 > fractional coordinates 1.55835 1.40209 0.64028 > 8CA SER 141279.5620253.4720115.1380 1.00 500.00 2 > fractional coordinates 1.55209 1.40724 0.63923 > 9CB SER 141279.7800254.7110116.0260 1.00 500.00 2 > fractional coordinates 1.55330 1.41412 0.64416 > 10OG SER 141280.9710255.4130115.6440 1.00 500.00 4 > fractional coordinates 1.55991 1.41802 0.64204 > 11C SER 141279.3470253.9090113.6680 1.00 500.00 2 > fractional coordinates 1.55089 1.40967 0.63107 > First 10 atoms of sorted file in asym unit - > 10.55639 0.64317 0.37813 699.89 1.00 5 102SG > CYS > 10.56299 0.64600 0.38485 599.89 1.00 2 102CB > CYS > 10.56517 0.63998 0.39040 299.89 1.00 2 102CA > CYS > 10.55335 0.63394 0.39243 499.89 1.00 4 102O > CYS > 10.57127 0.64288 0.39484 199.89 1.00 3 102N > CYS > 10.55842 0.63776 0.39511 399.89 1.00 2 102C > CYS > 10.55835 0.64028 0.40209 799.89 1.00 3 103N > SER > 10.55209 0.63923 0.40724 899.89 1.00 2 103CA > SER > 10.55330 0.64416 0.41412 999.89 1.00 2 103CB > SER > 10.55991 0.64204 0.41802 1099.89 1.00 4 103OG > SER > > As a result of course the tagged map is completely screwed. > > Has anyone encountered this problem and if so how did they solve it? I > would rather avoid digging into the code if I can! > > Best regards > > Pietro > -- > Pietro Roversi > Sir William Dunn School of Pathology, Oxford University > South Parks Road, Oxford OX1 3ER, England UK > Tel. 0044-1865-275385 >
