[Chimera-users] Command Patch problem

[mahad iou muddei addò]

Everytime i'm getting closer to what i need and it's all thanks to you! i
used the "Adjust Bonds" command (after i manually put the 2 proteins in the
position i wanted and combine them in a single structure) because it
maintains the structure of my two protein and only adds the bond. Instead
using "Join Models" every chain was bonded indipendently and this results
in a conformation that is non useful for my work because the various chains
moved following the bond but non according to each other (sorry for my bad
explanation). Now i'm searching a way to rename every residue of the new
model in a sequential way (Example: sequence residues number before 300-351
aa renamed in 1-51 aa) but i don't  have the solution right now. There is a
function with chimera? And if i use the function "Minimize Structure" it
will change the bonds added and make them better?

Regards

Mahad

2013/1/29 Elaine Meng <meng at cgl.ucsf.edu>

> Not sure I understand the question.  You could just repeat the process as
> many times as you need to.  If you meant that you want to join multiple
> chains from one structure to multiple chains in another structure (for
> example, A from first structure to A in second structure, B from the same
> first structure to B in the same second structure, ...) I think you would
> have to first split the second structure to make each of its chains a
> separate model.
>
> For example, if the second structure is open as model 1, you could split
> it with the command:
>
> split #1
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/split.html>
>
> Then, you could use Join Models several times to combine the chains of the
> second structure (which are now separate models) with the chains of the
> first structure.  After each join, you would need to select one atom from
> the new combined model and then one atom from the next chain of the second
> structure.
>
> Another way to add bonds is with the Adjust Bonds section of the same
> tool, but that only works on atoms that are already within the same model.
> <
> http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html
> >
>
> Elaine
>
> On Jan 28, 2013, at 10:15 AM, mahad iou muddei addò wrote:
>
> > 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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>
>
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