Re: [COOT] drawing symmetry
Hi Eleanor, this is the first action that I do after loading a molecule: I display symmetry-related ones. So, I agree, that displaying symmetry-related copies of a molecule should be set to default (as a user-preference, maybe). Dirk. Am 16.12.2008 um 11:01 schrieb Eleanor Dodson: Am I alone in thinkingthat the default should be to display symmetry related molecules - not to have it turned off? Eleanor *** Dirk Kostrewa Gene Center, A 5.07 Ludwig-Maximilians-University Feodor-Lynen-Str. 25 81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr...@lmb.uni-muenchen.de ***
Re: [COOT] [ccp4bb] superpose structures .ssm or lsq which is better
junfeng liu wrote: Dear All, I am overlaying several structures using coot. There are two ways SSM or LSQ can be used in that package. But I got clearly different result form the two methods. In my opinion SSM only works on the secondary structures and LSQ can works on the whole atoms ,main chain or CA. So the question is which one is better to overlay structures, LSQ or SSM ? Dear Liu, Depends on what you are trying to do. If you are trying to overlay proteins that are homologous but have low sequence identity, then finding which atoms/residues match with which can be pretty difficult - hence you would use SSM. If, however, your protein chains are similar (for example, because they are NCS-related perhaps) then LSQ over a particular residue range is probably a better option. Paul.
[COOT] drawing symmetry
Am I alone in thinkingthat the default should be to display symmetry related molecules - not to have it turned off? Eleanor
Re: [COOT] [ccp4bb] superpose structures .ssm or lsq which is better
Thanks Paul and Edwin, I will use SSM first . It looks little better than LSQ . ta liu Paul Emsley wrote: junfeng liu wrote: Dear All, I am overlaying several structures using coot. There are two ways SSM or LSQ can be used in that package. But I got clearly different result form the two methods. In my opinion SSM only works on the secondary structures and LSQ can works on the whole atoms ,main chain or CA. So the question is which one is better to overlay structures, LSQ or SSM ? Dear Liu, Depends on what you are trying to do. If you are trying to overlay proteins that are homologous but have low sequence identity, then finding which atoms/residues match with which can be pretty difficult - hence you would use SSM. If, however, your protein chains are similar (for example, because they are NCS-related perhaps) then LSQ over a particular residue range is probably a better option. Paul.
