- Posts: 8
create sekundär struktur and limitation when not
- Newguy
-
Topic Author
- Offline
- Fresh Boarder
Less
More
5 years 8 months ago #7760
by Newguy
create sekundär struktur and limitation when not was created by Newguy
Moin everybody :D
This question would be a little bit between the topics.
For the moment I am having a problem with the definition of the secondary structure of a 10 AS long peptide. (something new)
The working group would like it to be beta-string extended (do not know how to do it in martinize. The explizit creation with Amber xleap and the command -p backbone in martinize seems to work somehow butttttt.....
Sometimes it forms rings.....)
How do I create this secondary structure?
So the secondary structure seems to be not correct (but my professor would really like it to be more flexible and said nice!!!)
Yeah.... that is not correct any more or?
In the review it said every secondary structure needs to be given
(my data would be bul§$shi"§$ or?)
Thanks for your thoughts and expertize :)
This question would be a little bit between the topics.
For the moment I am having a problem with the definition of the secondary structure of a 10 AS long peptide. (something new)
The working group would like it to be beta-string extended (do not know how to do it in martinize. The explizit creation with Amber xleap and the command -p backbone in martinize seems to work somehow butttttt.....
Sometimes it forms rings.....)
How do I create this secondary structure?
So the secondary structure seems to be not correct (but my professor would really like it to be more flexible and said nice!!!)
Yeah.... that is not correct any more or?
In the review it said every secondary structure needs to be given
(my data would be bul§$shi"§$ or?)
Thanks for your thoughts and expertize :)
Please Log in or Create an account to join the conversation.
- Newguy
-
Topic Author
- Offline
- Fresh Boarder
Less
More
- Posts: 8
5 years 8 months ago #7761
by Newguy
Replied by Newguy on topic create sekundär struktur and limitation when not
didn't know if the limitation part would be in the philosophy. Kinds of connect to martinize.py but the limitation part seemed to be more important.
Please Log in or Create an account to join the conversation.
- peterkroon
-
- Offline
- Gold Boarder
Less
More
- Posts: 210
5 years 8 months ago #7762
by peterkroon
Replied by peterkroon on topic create sekundär struktur and limitation when not
Hi!
In general, Martini proteins (and peptides) can not change secondary structure, since the different structure elements have different parameters.
As for Martinize, you can give an secondary structure as a string with the `-ss` option. An extended beta-sheet is probably described as 'E', so just feed `-ss EEEEEEEEEE...` (with the same number of E's as amino acids) to martinize.
Usually these secondary structures are also enforced using an elastic network, but depending on how large your peptide is this may not be too usefull. Experiment with the `-ed` flag.
In general, Martini proteins (and peptides) can not change secondary structure, since the different structure elements have different parameters.
As for Martinize, you can give an secondary structure as a string with the `-ss` option. An extended beta-sheet is probably described as 'E', so just feed `-ss EEEEEEEEEE...` (with the same number of E's as amino acids) to martinize.
Usually these secondary structures are also enforced using an elastic network, but depending on how large your peptide is this may not be too usefull. Experiment with the `-ed` flag.
Please Log in or Create an account to join the conversation.
- Newguy
-
Topic Author
- Offline
- Fresh Boarder
Less
More
- Posts: 8
5 years 8 months ago #7763
by Newguy
Replied by Newguy on topic create sekundär struktur and limitation when not
thanks going to try that :D
Please Log in or Create an account to join the conversation.
Time to create page: 0.099 seconds