Dear community,
having searched the whole of the manual as well as past posts, I could find helpful contributions, so I'm trying to find help here. I'm facing to questions:
1. RESTRAINTS: I didn't get the idea of how to *ADD* restraints to those modeller makes itself. Actually, I didn't get the idea of how manually add restraints with modeller, at all (remark: I'm a Charmm-User). So here is what I want to do, maybe some could help me with a little script: I'd like to fix the coordinates of all atoms of a slice of residues (e.g. Res 10-23). All the rest of the restraints are supposed to be calculated by modeller.
2. RAND_SEED: Is there a way to define the random seed for the "CALL ROUTINE = 'model'" command?
Thank you very much in advance
could the administrator construct a online bbs?
So people can post their message online. and maybe for most questions, people can find the answer from the discussion of previous messages on the BBS.
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Dear Sascha,
> 1. RESTRAINTS: I didn't get the idea of how to *ADD* restraints to those > modeller makes itself. Actually, I didn't get the idea of how manually add > restraints with modeller, at all.
I do not have a reply to your first question (in fact, all the syntax is in the documentation, but how to apply this is another question - if you find a good MODELLER tutorial for advanced applications - or someone on the list knows one, I would be happy to learn about it).
> 2. RAND_SEED: Is there a way to define the random seed for the "CALL > ROUTINE = 'model'" command?
As for the second one, just insert this before calling 'model'.
SET RAND_SEED = -12345
But be particularry CAREFUL to use NEGATIVE seeds (positive won't work ;-)
Kind regards, Karsten.
On Thu, Jul 01, 2004 at 10:15:53AM -0700, zjnjuct wrote: > could the administrator construct a online bbs? > > So people can post their message online. and maybe for > most questions, people can find the answer from the > discussion of previous messages on the BBS.
You can post your messages with the email client of your choice using the current mailing list list system, or search the previous messages at http://salilab.org/archives/modeller_usage/2004/threads.html. What doesn't this do that a 'BBS' would do?
Of course, this is the appropriate place to suggest improvements or new features, if they are desired; any further discussion on the topic is welcome.
Ben Webb, Modeller Caretaker
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Karsten Suhre -
Modeller Caretaker -
Sascha Tayefeh -
zjnjuct