[Chimera-users] successive minimizations: can we use a unique protein setup?
Jean Didier Pie Marechal
JeanDidier.Marechal at uab.cat
Thu Nov 6 01:13:49 PST 2008
Hi everyone,
I want to do the following:
1. minimize a region of a structure
2. change some part of the region by hand (like swap a residue)
3. minimize once more.
and this 2 or three times.
However, each time I want to minimize I have to pass through the all setup of the protein (add H, hist protonation, and so one).
Couldn't we keep the information of the first setup and directly fo through the minimization?
All the best,
JD
Dr. Jean-Didier Maréchal
Lecturer
Computational Bioorganic and Bioionorganic Chemistry @ Transmet
Unitat de Química Física
Departament de Química
Universitat Autònoma de Barcelona
Edifici C.n.
08193 Cerdanyola (Barcelona)
Tel: +34.935814936
e-mail: JeanDidier.Marechal at uab.es
----- Missatge original -----
De: chimera-users-request at cgl.ucsf.edu
Data: Dimecres, Novembre 5, 2008 2:00 am
Assumpte: Chimera-users Digest, Vol 67, Issue 4
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> Today's Topics:
>
> 1. Using match (Omar Davulcu)
> 2. Re: Using match (Eric Pettersen)
> 3. Re: Models or chain (Eric Pettersen)
> 4. removing side chains (Matthew Dougherty)
> 5. Re: removing side chains (Eric Pettersen)
> 6. Re: Using match (Elaine Meng)
>
>
> --------------------------------------------------------------------
> --
>
> Message: 1
> Date: Mon, 3 Nov 2008 14:53:19 -0800
> From: "Omar Davulcu" <davulcuo at ohsu.edu>
> Subject: [Chimera-users] Using match
> To: chimera-users at cgl.ucsf.edu
> Message-ID: <001301c93e06$f7394020$e5abc060$@edu>
> Content-Type: text/plain; charset="us-ascii"
>
> Hi,
>
>
>
> I'm using the match command with a cutoff to align specific regions of
> related enzymes. It appears to work fine and remove residue pairs
> above the
> cutoff, but is there a way to list those residue pairs which were
> (or were
> not) removed?
>
>
>
> Thanks for any help!
>
> Omar Davulcu
>
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> ------------------------------
>
> Message: 2
> Date: Tue, 4 Nov 2008 15:12:48 -0800
> From: Eric Pettersen <pett at cgl.ucsf.edu>
> Subject: Re: [Chimera-users] Using match
> To: "Omar Davulcu" <davulcuo at ohsu.edu>
> Cc: chimera-users at cgl.ucsf.edu
> Message-ID: <DF8D8087-95EB-466A-A0C8-EB522C716E27 at cgl.ucsf.edu>
> Content-Type: text/plain; charset="windows-1252"
>
> Hi Omar,
> If you are using the match command, then there is no way to get
> that
> information without using Chimera's Python interface. If, however,
>
> you use the MatchMaker tool or the mmaker command, you can get a
> sequence alignment of the structures. That alignment will have a
> highlighted region of the residues used in the final match
> interation. Clicking on the region will select the residues. You
> can
> then use Actions->Write List... to write a list of the selected/
> unselected residues to a file.
> I can provide guidance on the Python interface if you need to go
> that
> route instead.
>
> --Eric
>
> Eric Pettersen
> UCSF Computer Graphics Lab
> http://www.cgl.ucsf.edu
>
>
> On Nov 3, 2008, at 2:53 PM, Omar Davulcu wrote:
>
> > Hi,
> >
> > I?m using the match command with a cutoff to align specific
> regions
> > of related enzymes. It appears to work fine and remove residue
> > pairs above the cutoff, but is there a way to list those residue
> > pairs which were (or were not) removed?
> >
> > Thanks for any help!
> > Omar Davulcu
> > _______________________________________________
> > Chimera-users mailing list
> > Chimera-users at cgl.ucsf.edu
> > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
>
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> ------------------------------
>
> Message: 3
> Date: Tue, 4 Nov 2008 16:10:31 -0800
> From: Eric Pettersen <pett at cgl.ucsf.edu>
> Subject: Re: [Chimera-users] Models or chain
> To: "chimera-users at cgl.ucsf.edu users" <chimera-users at cgl.ucsf.edu>
> Message-ID: <E6EB19D3-59F3-4DC5-8544-28A195FA444C at cgl.ucsf.edu>
> Content-Type: text/plain; charset="us-ascii"
>
> Hernando Sosa wrote:
> > Hi Elaine,
> >
> > The problem I have is actually not with chimera itself. I can
> > display all the models etc nicely within it. However, I want to
> make> now a PDB file of a multi-protein complex in a format that
> can be
> > deposited in the PDB database. Then I run into problems if the
> models> are separated by Model ENDMDL lines or have chains with the
> same
> > letter
> > identifier. I was hoping to be able to generate a multi-protein
> PDB> file from my chimera fitting without having to manually edit
> a lot of
> > lines in the multimodel PDB file. Any suggestions on how to best
> do
> > this
> > would be appreciated.
> >
> Hi Hernando,
> Elaine kind of mentioned this in passing in another posting, but
> you
> can now do what you wanted to do above with the new "combine"
> command
> (also available as the Combine button of the Model Panel). It's in
>
> the current daily build and upcoming release candidate/production
> release.
>
> --Eric
>
>
> Eric Pettersen
> UCSF Computer Graphics Lab
> http://www.cgl.ucsf.edu
>
>
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> ------------------------------
>
> Message: 4
> Date: Tue, 4 Nov 2008 18:13:53 -0600
> From: Matthew Dougherty <matthewd at bcm.edu>
> Subject: [Chimera-users] removing side chains
> To: chimera-users at cgl.ucsf.edu
> Message-ID: <7062BA65-C3B7-4470-A3E8-6C64558B4738 at bcm.edu>
> Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes
>
> I have a session that someone has given me. It consists of 24
> monomers in two states, each monomer colored differently.
> In the model panel I see only two IDs.
>
> I need to do a morph showing just the ribbons.
>
> Because the overall number of atoms is quite large, I want to strip
>
> off the side chains in order to reduce the computation.
>
> Is there an easy way to do this?
> Or do I have to go back to individual monomers, strip off the side
> chains, recolor, and recombine them, before morphing?
>
> thanks, Matt
>
>
> ------------------------------
>
> Message: 5
> Date: Tue, 4 Nov 2008 16:24:35 -0800
> From: Eric Pettersen <pett at cgl.ucsf.edu>
> Subject: Re: [Chimera-users] removing side chains
> To: Matthew Dougherty <matthewd at bcm.edu>
> Cc: chimera-users at cgl.ucsf.edu
> Message-ID: <DECC60E9-C941-4107-A054-0858207BCEEA at cgl.ucsf.edu>
> Content-Type: text/plain; charset="us-ascii"
>
> Unless I'm misunderstanding something, isn't it just:
>
> Select->Structure->side chain/base->without CA/C1'
> Actions->Atoms/Bonds->delete
>
> or, as a command:
>
> del without CA/C1'
>
> --Eric
>
> Eric Pettersen
> UCSF Computer Graphics Lab
> http://www.cgl.ucsf.edu
>
>
> On Nov 4, 2008, at 4:13 PM, Matthew Dougherty wrote:
>
> > I have a session that someone has given me. It consists of 24
> > monomers in two states, each monomer colored differently.
> > In the model panel I see only two IDs.
> >
> > I need to do a morph showing just the ribbons.
> >
> > Because the overall number of atoms is quite large, I want to strip
> > off the side chains in order to reduce the computation.
> >
> > Is there an easy way to do this?
> > Or do I have to go back to individual monomers, strip off the side
> > chains, recolor, and recombine them, before morphing?
> >
> > thanks, Matt
> > _______________________________________________
> > Chimera-users mailing list
> > Chimera-users at cgl.ucsf.edu
> > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
>
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> ------------------------------
>
> Message: 6
> Date: Tue, 4 Nov 2008 17:00:14 -0800
> From: Elaine Meng <meng at cgl.ucsf.edu>
> Subject: Re: [Chimera-users] Using match
> To: Omar Davulcu <davulcuo at ohsu.edu>
> Cc: chimera users <chimera-users at cgl.ucsf.edu>
> Message-ID: <31183B9E-1035-4FE9-AF71-7B8AB5A48B15 at cgl.ucsf.edu>
> Content-Type: text/plain; charset=WINDOWS-1252; format=flowed;
> delsp=yes
>
> Hi Omar,
> Just wanted to add a little more discussion on the matching methods
>
> (possibly more information than you wanted!):
>
> - Matchmaker only uses one atom per residue (CA for amino acids),
> whereas match can use whatever atoms you specify, as long as there
> are
> equal numbers of atoms from the two structures
>
> - however, if the main reason you were using match instead of
> matchmaker was to include only parts of the enzymes instead of
> their
> full sequences, you can also do that with Matchmaker and Multalign
> Viewer:
>
> (a) Perform an initial round of matching just to get the
> sequence
> alignment: use Matchmaker with iteration/pruning turned off and
> showing the sequence alignment turned on (GUI and command both have
>
> these options). This displays the pairwise sequence alignment and
> uses all aligned pairs to superimpose the structures. Keep this
> alignment open.
> Example commands:
> open 2mnr
> open 4enl
> preset apply int 1
> mmaker #0 #1 iterate false show true
>
> (b) In the alignment, draw box(es) for the segments you want to
> consider in the match: If it is a single contiguous region, you
> can
> simply drag to create that box. If there are disjoint parts, you
> would need to use Shift-drag so that the separate boxes would still
>
> belong to the same region. The corresponding parts of the
> structures
> will become selected in the main Chimera window.
> Example:
> I only want to use the N-terminal domains of these enzymes, approx
> up
> to 2mnr residue 127, so I drag a box from the beginning of the
> sequence alignment to position 150.
>
> (c) Perform another match with iteration considering only the
> boxed
> segment(s): In the Multalign Viewer (sequence alignment) window,
> choose "Structure... Match" - in the resulting dialog, turn on
> "Match
> active region only", "Iterate..." with the desired cutoff, and
> "Create
> region showing matched residues". After OK/Apply, there will be
> light
> orange boxes that you can click on and proceed as described by Eric.
>
> Elaine
>
> On Nov 4, 2008, at 3:12 PM, Eric Pettersen wrote:
>
> > Hi Omar,
> > If you are using the match command, then there is no way to get
> > that information without using Chimera's Python interface. If,
> > however, you use the MatchMaker tool or the mmaker command, you
> can
> > get a sequence alignment of the structures. That alignment will
> > have a highlighted region of the residues used in the final match
>
> > interation. Clicking on the region will select the residues.
> You
> > can then use Actions->Write List... to write a list of the
> selected/
> > unselected residues to a file.
> > I can provide guidance on the Python interface if you need to go
>
> > that route instead.
> > --Eric
> >
> > On Nov 3, 2008, at 2:53 PM, Omar Davulcu wrote:
> >
> >> Hi,
> >> I?m using the match command with a cutoff to align specific
> regions
> >> of related enzymes. It appears to work fine and remove residue
> >> pairs above the cutoff, but is there a way to list those residue
>
> >> pairs which were (or were not) removed?
> >> Thanks for any help!
> >> Omar Davulcu
> >>
>
>
> ------------------------------
>
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
>
>
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