[Chimera-users] Command Patch problem

[mahad iou muddei addò]

Perfect! now it worked! but if i want to make 4 bonds for for chains how am
i suppose to do?

Thank you so much anyway

2013/1/28 Elaine Meng <meng at cgl.ucsf.edu>

> Hi Mahad,
> I can't tell what exactly is the problem, but make sure that you have only
> two atoms selected (not the whole residues), the C at the end of one
> peptide and the N at the start of the other.   Then you should be able to
> choose the "C-N peptide bond" option, and then apply.  You do not need to
> position the structures before joining them.
>
> Something like the example "select" command I gave in the earlier message
> should select only two atoms.  Or, if you prefer to use the mouse to select
> from the screen, you would first need to show the atoms... for example:
>
> preset apply int 2
>
> ... use Ctrl-click to select the carbonyl C at the end of the first
> peptide, then Shift-Ctrl-click to select the amino N at the start of the
> second peptide.   Then choose "C-N peptide bond" in the Join Models part of
> Build Structure, then click Apply.
>
> 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 26, 2013, at 4:06 AM, mahad iou muddei addò wrote:
>
> > 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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