Hi Jordan, you can first intra_fit the multi-state object and then align its first state to the input structure.
# this will fit all states to the first state intra_fit multimodel # align first state to input structure align multimodel, input, mobile_state=1 http://pymolwiki.org/index.php/intra_fit http://pymolwiki.org/index.php/align (PyMOLWiki seems to be down at the moment?) A nicer fit might be possible with theseus, which does a down-weighting of flexible parts of your structure. http://www.theseus3d.org/ Regarding your question "is their a command that can add a bunch of states back together", there is "join_states" if you have psico installed. http://pymolwiki.org/index.php/Psico Cheers, Thomas Jordan Willis wrote, On 07/09/12 03:21: > Hi Pymol! > > I have a question about movies, but has nothing to do with the movie > commands, so don't worry. > > I have 750 states that are dumped directly into pymol where each > "move" from my modeling program, is a new state. I want to compare > this to the input structure which only has one state. > > If I align the 750 states to the 1 input, it sort of gives me a > "global" fit that seems to be a consensus among all 750 states. What > I would like however is each state to be aligned to my input > structure separately. Then when I hit play I won't see such huge > moves away from the input and a bad alignment. > > My plan was to write a script that can do one of the following: > > Make 750 states of the input structure even though they all will be > the same and align state1 from the output to state 1 to the input. > > or: > > split all out to a separate object, align each one separately then > zip up all the objects into one state. > > Usually when I do this, there turns out to be some command that can > do this for me. Does anyone know of an easier way of doing this? Or > perhaps have some tips for me in my scripts? For instance, is their a > command that can add a bunch of states back together? > > Thanks so much, Jordan > > PS. In the newest release of pymol for mac, I have noticed that when > I click on a letter in the sequence (when the s option is toggled) it > selects the entire chain rather than the individual amino acid. -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ PyMOL-users mailing list ([email protected]) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/[email protected]
