Real space refinment keeps messing up my taxol conformation
I used elbow to generate restraints for taxol using chemical componenet and sdf file. I posted before to the list and Oleg was kind enough to provide restraints generated by readyset. No matter what restraints I use, the taxol is messed up! The other thing is, the refinement keeps breaking the peptide bond at a specific location! I would like to send some files to someone privately to investigate! Please let me know. Regards.
Hi Ahmad,
I used elbow to generate restraints for taxol using chemical componenet and sdf file. I posted before to the list and Oleg was kind enough to provide restraints generated by readyset. No matter what restraints I use, the taxol is messed up!
The other thing is, the refinement keeps breaking the peptide bond at a specific location! I would like to send some files to someone privately to investigate!
please send me files that show the issue: - model before and after refinement, and tell what residue number in what chain I need to look at; - map file and ligand CIF. Pavel
I'm still having issues with taxol ligand (TA1), check out attached
screenshot, despite using different methods (readyset, elbow,...etc) to
generate the restraints and upgrading from v1.14 to v1.16.
I would appreciate your prompt feedback with this!
On Mon, Jul 15, 2019 at 1:00 PM Pavel Afonine
Hi Ahmad,
I used elbow to generate restraints for taxol using chemical componenet and sdf file. I posted before to the list and Oleg was kind enough to provide restraints generated by readyset. No matter what restraints I use, the taxol is messed up!
The other thing is, the refinement keeps breaking the peptide bond at a specific location! I would like to send some files to someone privately to investigate!
please send me files that show the issue:
- model before and after refinement, and tell what residue number in what chain I need to look at; - map file and ligand CIF.
Pavel
participants (2)
-
Ahmad Khalifa -
Pavel Afonine