CCP4 Scaling

If one writes york format files with Denzo, what is the appropriate keyword to use with Scalepack? I thought Denzo_york worked, but it seems to fail. (The error is "ERROR: Unable to open 1 for reading", but if the format is changed to Denzo _ip, the file is opened correctly, but, of course, the data format is incorrect.)

Use Denzo_york1 instead. Scalepack will read also concatenated Denzo_york1 format (but not Denzo _ip). Denzo _york is another creation by Eleanor Dodson that hopefully died by now. The error is "ERROR: Unable to open 1 for reading" comes from the fact that Denzo _york and Denzo _york1 do not require staring batch number, as it is coded in the header of Denzo _york formats. The "1" is interpreted as file name with hkl's instead and Scalepack cannot open it if (unless you called output from Denzo "1").

Comment: To go to CCP4 format you should use different option in Denzo: york output file. That will produce somewhat different *.x file that can go into rotaprep (part of ccp4 package). Lack of satisfactory result from Scalepack maybe either from misunderstanding how the program works or from problems in the data collection. Scalepack algorithms are fairly similar to Rotavata/Agrovata and should not give qualitatively different results.


I am still unable to go to SCALA since the ROT information does not carry through rotaprep. Any advice would be appreciated. So far though Scalepack does the same as rotavata and agrovata. Not surprising.

Ask Eleanor Dodson, author of Rotaprep or Phil Evans, author of SCALA.