Hi,
We have used eginput/PSF_generation/addAtoms.py recently to add MTSL (a spin label) to proteins. We find that when addAtoms.py is used with Xplornih 2.15, the backbone of the protein is not altered and occasionally the spin label side chains have bad bond distances and/or angles. When the same addAtoms.py and protein is used with Xplornih 2.18 we get no bad spin label side chain bond distances or angles but the tertiary and secondary structure of the protein is highly altered. We have been able to correct the bad distances and bonds angles obtained with Xplornih 2.15 by using simulated annealing and energy minimization procedures very similar to those found in eginput/prot_prot. Our initial attempt to restore the secondary and tertiary structure to our spin labeled protein obtained with Xplornih 2.18 yielded a good backbone structure but some bad spin label side chain bond distances and angles. We used a reference structure with the correct backbone fold and a harmonic restraining potential (between the reference structure and the spin labeled molecule backbones) with a simulated annealing and energy minimization protocol similar to that mentioned above. There is a small difference in addAtoms.py between 2.15 and 2.18 but this is not what caused the differences discussed above. My main question: Is there a script which will impose a different and defined backbone structure on a protein and maintain reasonable side chain structure? Thanks, Jeff Ellena -------------- next part -------------- An HTML attachment was scrubbed... URL: http://dcb.cit.nih.gov/pipermail/xplor-nih/attachments/20071015/225fb437/attachment.html
