Dear Wenhe, lsqkab, which is also part of ccp4, can be adjusted for its output. It includes the option to print RMSD values for all atoms that the program matched.
If you need even more fine-tuning, you might take a look at lsqman from the Uppsala Software Factory. Best, Tim On Monday, October 31, 2016 10:14:12 AM Clement Angkawidjaja wrote: > Dear Wenhe, > > Have you looked at the Additional Log File from Superpose? > > Cheers, > Clement > > -----Original Message----- > From: WENHE ZHONG > Sent: Sunday, October 30, 2016 12:47 AM > To: CCP4BB@JISCMAIL.AC.UK > Subject: [ccp4bb] Superpose program in CCP4 > > Dear all, > > I always use the SUPERPOSE tool in CCP4 to superpose molecules. This time I > want to use the RMSD values of superposed C-alpha atoms to plot a RMSD graph > (instead of using the graph automatically made by the program). However, > there are many atoms missing in the RMSD list. > > In the settings I chose “Superpose specific atoms/residues”, checked > “Output all distances to a file”, fit “C-alpha atoms”. The superposed > structures have exactly the same sequence. > > My question is: is there any way to get the completed list of RMSD value for > each C-alpha atom? Or is there any other program for this purpose? > > Thank you! > > Kind regards, > Wenhe -- -- Paul Scherrer Institut Dr. Tim Gruene - persoenlich - Principal Investigator Biology and Chemistry OFLC/102 CH-5232 Villigen PSI Phone: +41 (0)56 310 5297 GPG Key ID = A46BEE1A
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