[Chimera-users] Command Patch problem

[mahad iou muddei addò]

Dear Elaine, thank you so much because i understand my mistakes, but i'm
afraid i have to ask you something again. I've done as you said, so i
selected the residues and then used join models function but the apply
button cannot be clicked. I don't understand if this happens because:

-of the selected residues
-the 2 proteins have to be already in position for the bond
-something to be done before using join models

I'm sorry to trouble you so much
Sincererly

Mahad

2013/1/25 Elaine Meng <meng at cgl.ucsf.edu>

> Hi Mahad,
> If I read your mail correctly, there is no overlap between the two
> sequences.  You would only use "match" to overlap structures, i.e. to try
> to put one group of atoms on top of another group of atoms (with exactly
> the same number of atoms).  As the error message said,
>
> > match #0:422 #1:442
> > Unequal numbers of atoms chosen for evaluation
>
> ... residue 422 in #0 and residue 442 in #1 do not have the same numbers
> of atoms, which is not surprising if one is an "R" and the other is "D."
> You could specify using backbone atoms only to get the same numbers, for
> example:
>
> match #0:422 at n,ca,c,o #1:442 at n,ca,c,o
>
> HOWEVER: from your description it sounds like you do not really want to
> match (put 422 on top of 442), but instead you want to join the two
> peptides (add peptide bond between 422 and 442).  In that case you should
> use the Build Structure tool (in menu under Tools... Structure Editing),
> Join Models section.
>
> <
> http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html
> >
> <
> http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html#join
> >
>
> First select the two atoms you want to bond, maybe something like this:
>
> select #0:422 at c #1:442 at n
>
> ... and then use the C-N peptide bond option in Join Models.
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
> On Jan 25, 2013, at 6:57 AM, mahad iou muddei addò wrote:
>
> > Hi, i'm working with chimera for the first time. I need to patch 2
> structures that i have the PDBs. I've already read the user guide and try
> to follow the instructions for making a controlled superimposition of the
> two structures.
> > These are my two sequence:
> >
> >
> 1)RKYVYSLYWSTLTLTTIGETPPPVRDSEYFFVVADFLIGVLIFATIVGNIGSMISNMNAARAEFQARIDAIKQYMHFR
> >
> >
> 2)DSSRRQYQEKYKQVEQYMSFHKLPADFRQKIHDYYEHRYQG-KMFDEDSILGELNGPLREKIVNFNCRKLVASMPLFANADPNFVTAMLTKLKFEVFQP
> >
> GDYIIREGTIGKKMYFIQHGVVSVLTK-NKEM--KLSDGSYFGEICLLT------RGRRTASVRADTYCRLYSLSVDN
> > FNEVLEEYPMMRRAFETVAIDRLDR/
> >
> > I need to create a structure like this:
> >
> >
> RKYVYSLYWSTLTLTTIGETPPPVRDSEYFFVVADFLIGVLIFATIVGNIGSMISNMNAARAEFQARIDAIKQYMHFRDSSRRQYQEKYKQVEQYMSFH
> >
> KLPADFRQKIHDYYEHRYQG-KMFDEDSILGELNGPLREKIVNFNCRKLVASMPLFANADPNFVTAMLTKLKFEVFQP
> >
> GDYIIREGTIGKKMYFIQHGVVSVLTK-NKEM--KLSDGSYFGEICLLT------RGRRTASVRADTYCRLYSLSVDN
> > FNEVLEEYPMMRRAFETVAIDRLDR/
> >
> > I know the position of the aa involved but after i launch the command
> trough command line it gives me errors like
> >
> > match #0:422 #1:442
> > Unequal numbers of atoms chosen for evalutation
> >
> > What am i doing wrong?
> > Thanks, sincererly
> >
> > Mahad
>
>
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