Hello there, I have a question regarding MODELLER in Chimera and the ability of chimera to adjust the model using some inbuilt features quickly(i.e. automatically, instead of interactively) Firstly, I am trying to model the "holo" form of an enzyme with known apo-form structure. I did this usinig the two independent domains of the apo form as a template (in a bid to get the domains accurate) and for the holo-form closure I used a very similar homologue that has been solved in the holo form. The results were good and I got a decent model that had closed up like the homolog. However, I noticed that in the model a lot of the sidechains have not been modelled with the right rotamer. This is odd, as I gave it the two independent domains as a template, so it had all the information it needed to get that perfectly right. Either way, this means, I need to manually "copy" the rotamers from the apo form onto the "holo model", which is time consuming. I know from the homolog that only two or three residues in the active site change rotamer upon apo-holo conformational change. So, I just want an easy way to edit the rotamers in the holo-model to copy the rotamers of the apo-form for all residues. Is there an easy way to do this, is it possible to this with a script? I have no idea how to script, mind you! Ahir
I have attached a script that, if you have exactly two models open and they have the same residues, will copy the chi angles of the lower- numbered model into the higher-numbered model. You can run the script simply by opening it with File->Open. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Feb 6, 2012, at 10:51 AM, Ahir Pushpanath wrote:
Hello there, I have a question regarding MODELLER in Chimera and the ability of chimera to adjust the model using some inbuilt features quickly(i.e. automatically, instead of interactively)
Firstly, I am trying to model the "holo" form of an enzyme with known apo-form structure. I did this usinig the two independent domains of the apo form as a template (in a bid to get the domains accurate) and for the holo-form closure I used a very similar homologue that has been solved in the holo form. The results were good and I got a decent model that had closed up like the homolog.
However, I noticed that in the model a lot of the sidechains have not been modelled with the right rotamer. This is odd, as I gave it the two independent domains as a template, so it had all the information it needed to get that perfectly right.
Either way, this means, I need to manually "copy" the rotamers from the apo form onto the "holo model", which is time consuming. I know from the homolog that only two or three residues in the active site change rotamer upon apo-holo conformational change. So, I just want an easy way to edit the rotamers in the holo-model to copy the rotamers of the apo-form for all residues.
Is there an easy way to do this, is it possible to this with a script? I have no idea how to script, mind you!
Ahir _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
It works like a charm! Absolute genius Eric! Fourth time I have a question with brilliantly helpful answers from USCF. Thanks Ahir On Mon, Feb 6, 2012 at 7:55 PM, Eric Pettersen <pett@cgl.ucsf.edu> wrote:
I have attached a script that, if you have exactly two models open and they have the same residues, will copy the chi angles of the lower-numbered model into the higher-numbered model. You can run the script simply by opening it with File->Open.
--Eric
Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
On Feb 6, 2012, at 10:51 AM, Ahir Pushpanath wrote:
Hello there, I have a question regarding MODELLER in Chimera and the ability of chimera to adjust the model using some inbuilt features quickly(i.e. automatically, instead of interactively)
Firstly, I am trying to model the "holo" form of an enzyme with known apo-form structure. I did this usinig the two independent domains of the apo form as a template (in a bid to get the domains accurate) and for the holo-form closure I used a very similar homologue that has been solved in the holo form. The results were good and I got a decent model that had closed up like the homolog.
However, I noticed that in the model a lot of the sidechains have not been modelled with the right rotamer. This is odd, as I gave it the two independent domains as a template, so it had all the information it needed to get that perfectly right.
Either way, this means, I need to manually "copy" the rotamers from the apo form onto the "holo model", which is time consuming. I know from the homolog that only two or three residues in the active site change rotamer upon apo-holo conformational change. So, I just want an easy way to edit the rotamers in the holo-model to copy the rotamers of the apo-form for all residues.
Is there an easy way to do this, is it possible to this with a script? I have no idea how to script, mind you!
Ahir _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Don't make me blush! :-) --Eric On Feb 7, 2012, at 3:01 AM, Ahir Pushpanath wrote:
It works like a charm! Absolute genius Eric! Fourth time I have a question with brilliantly helpful answers from USCF.
Thanks Ahir
On Mon, Feb 6, 2012 at 7:55 PM, Eric Pettersen <pett@cgl.ucsf.edu> wrote: I have attached a script that, if you have exactly two models open and they have the same residues, will copy the chi angles of the lower-numbered model into the higher-numbered model. You can run the script simply by opening it with File->Open.
--Eric
Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
On Feb 6, 2012, at 10:51 AM, Ahir Pushpanath wrote:
Hello there, I have a question regarding MODELLER in Chimera and the ability of chimera to adjust the model using some inbuilt features quickly(i.e. automatically, instead of interactively)
Firstly, I am trying to model the "holo" form of an enzyme with known apo-form structure. I did this usinig the two independent domains of the apo form as a template (in a bid to get the domains accurate) and for the holo-form closure I used a very similar homologue that has been solved in the holo form. The results were good and I got a decent model that had closed up like the homolog.
However, I noticed that in the model a lot of the sidechains have not been modelled with the right rotamer. This is odd, as I gave it the two independent domains as a template, so it had all the information it needed to get that perfectly right.
Either way, this means, I need to manually "copy" the rotamers from the apo form onto the "holo model", which is time consuming. I know from the homolog that only two or three residues in the active site change rotamer upon apo-holo conformational change. So, I just want an easy way to edit the rotamers in the holo-model to copy the rotamers of the apo-form for all residues.
Is there an easy way to do this, is it possible to this with a script? I have no idea how to script, mind you!
Ahir _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (2)
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Ahir Pushpanath -
Eric Pettersen