[Chimera-users] Chimera-users Digest, Vol 87, Issue 13
Jean Didier Pie Marechal
JeanDidier.Marechal at uab.cat
Sat Jul 17 08:28:19 PDT 2010
Hi again,
I'd like to do a mmaker for a region of space leading to something like this:
mmaker #(ref-model and part of the selection) #(flex-model and part of the selection)
So far I haven't found the correct syntax to do so but I am pretty sure we can do that.
any help?
Cheers
JD
Dr. Jean-Didier Maréchal
Lecturer
The Computational Biotechnological Chemistry Team
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
www: http://asklipio.qf.uab.es
----- Missatge original -----
De: chimera-users-request at cgl.ucsf.edu
Data: Divendres, Juliol 16, 2010 7:33 pm
Assumpte: Chimera-users Digest, Vol 87, Issue 13
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> Today's Topics:
>
> 1. Re: alignment + missing residues (Gesa Volkers)
> 2. Re: alignment + missing residues (Gesa Volkers)
> 3. Re: alignment + missing residues (Eric Pettersen)
>
>
> --------------------------------------------------------------------
> --
>
> Message: 1
> Date: Fri, 16 Jul 2010 11:58:48 +0200
> From: Gesa Volkers <gesa.volkers at uni-greifswald.de>
> Subject: Re: [Chimera-users] alignment + missing residues
> To: Eric Pettersen <pett at cgl.ucsf.edu>
> Cc: chimera-dev at cgl.ucsf.edu, chimera-users at cgl.ucsf.edu
> Message-ID: <4C402D58.7090906 at uni-greifswald.de>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Dear Eric,
>
> thanks for your suggestions. Unfortunately removing the SEQRES
> record
> did not help. I also downloaded and installed the new chimera-
> version
> today. The false numbering in the alignment still occurs. Also when
> I
> remove the SEQRES record and try with the new chimera version the
> false
> numbering appears. Quite annoying... The pdb-file is not in the
> protein
> data bank yet.
>
> Any more suggestions? Could I add "dummy atoms" in the structure?
>
> Thanks,
> Gesa
>
>
>
> Eric Pettersen schrieb:
> > On Jul 14, 2010, at 6:53 AM, Gesa Volkers wrote:
> >
> >> Dear All,
> >>
> >> I observed an issue with the alignment function of Chimera.
> >> I loaded a crystal structure where in between a loop is not
> modelled
> >> due to low electron density- so these residues are missing in
> the
> >> structure and the numbering also has this gap. When I align this
> >> structure with others, the missing residues are not recognized
> and
> >> chimera just overrides the numbering so after this loop all the
> >> numbers in the alignment do not fit anymore to the residues they
> >> should belong to although the structure and numberings are shown
> in
> >> the right way in the graphics window. How can I overcome this
> issue?
> >> Should I change the pdb-file? In which way?
> >>
> >> Thanks for all responses!
> >
> > Hi Gesa,
> > I had a similar problem reported with 1JFF 12 days ago and
> haven't yet
> > worked on fixing it. It seems to only happen for a small subset
> of
> > structures. 1JFF has a missing loop and also exactly one missing
> > residue at the N terminus. Is your structure like that? Is it a
> > standard PDB entry (if so, what's the ID code)? I'll add you to
> the
> > recipient list for the ticket we have open in our bug database
> for
> > this (#8585) so you will be notified when it gets fixed. It'll
> > probably be fairly soon.
> > Until then the only workaround that occurs to me is for you to
> remove
> > the SEQRES records from the PDB file before you open it. Then
> the
> > Sequence viewer will depict only the residues physically present
> in
> > the structure -- no gaps (incorrect or otherwise) will be depicted.
> >
> > --Eric
> >
> > Eric Pettersen
> >
> > UCSF Computer Graphics Lab
> >
> > http://www.cgl.ucsf.edu
> >
> >
> >
>
>
> --
> Gesa Volkers
> Institut f?r Biochemie, Molekulare Strukturbiologie
> Felix-Hausdorff-Stra?e 4
> 17489 Greifswald
> Germany
> +49 (3834)-864392
>
>
>
>
> ------------------------------
>
> Message: 2
> Date: Fri, 16 Jul 2010 12:06:56 +0200
> From: Gesa Volkers <gesa.volkers at uni-greifswald.de>
> Subject: Re: [Chimera-users] alignment + missing residues
> To: Eric Pettersen <pett at cgl.ucsf.edu>
> Cc: chimera-dev at cgl.ucsf.edu, chimera-users at cgl.ucsf.edu
> Message-ID: <4C402F40.2010604 at uni-greifswald.de>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Additionally I downloaded 1JFF and did an alignment with another
> tubulin-structure. And still the numbering does not recognize this
> gap
> between 34 and 61.
>
> Gesa Volkers schrieb:
> > Dear Eric,
> >
> > thanks for your suggestions. Unfortunately removing the SEQRES
> record
> > did not help. I also downloaded and installed the new chimera-
> version
> > today. The false numbering in the alignment still occurs. Also
> when I
> > remove the SEQRES record and try with the new chimera version the
> > false numbering appears. Quite annoying... The pdb-file is not in
> the
> > protein data bank yet.
> >
> > Any more suggestions? Could I add "dummy atoms" in the structure?
> >
> > Thanks,
> > Gesa
> >
> >
> >
> > Eric Pettersen schrieb:
> >> On Jul 14, 2010, at 6:53 AM, Gesa Volkers wrote:
> >>
> >>> Dear All,
> >>>
> >>> I observed an issue with the alignment function of Chimera.
> >>> I loaded a crystal structure where in between a loop is not
> modelled
> >>> due to low electron density- so these residues are missing in
> the
> >>> structure and the numbering also has this gap. When I align
> this
> >>> structure with others, the missing residues are not recognized
> and
> >>> chimera just overrides the numbering so after this loop all the
> >>> numbers in the alignment do not fit anymore to the residues
> they
> >>> should belong to although the structure and numberings are
> shown in
> >>> the right way in the graphics window. How can I overcome this
> issue?
> >>> Should I change the pdb-file? In which way?
> >>>
> >>> Thanks for all responses!
> >>
> >> Hi Gesa,
> >> I had a similar problem reported with 1JFF 12 days ago and
> haven't
> >> yet worked on fixing it. It seems to only happen for a small
> subset
> >> of structures. 1JFF has a missing loop and also exactly one
> missing
> >> residue at the N terminus. Is your structure like that? Is it
> a
> >> standard PDB entry (if so, what's the ID code)? I'll add you to
> the
> >> recipient list for the ticket we have open in our bug database
> for
> >> this (#8585) so you will be notified when it gets fixed. It'll
> >> probably be fairly soon.
> >> Until then the only workaround that occurs to me is for you to
> remove
> >> the SEQRES records from the PDB file before you open it. Then
> the
> >> Sequence viewer will depict only the residues physically present
> in
> >> the structure -- no gaps (incorrect or otherwise) will be depicted.
> >>
> >> --Eric
> >>
> >> Eric Pettersen
> >>
> >> UCSF Computer Graphics Lab
> >>
> >> http://www.cgl.ucsf.edu
> >>
> >>
> >>
> >
> >
>
>
> --
> Gesa Volkers
> Institut f?r Biochemie, Molekulare Strukturbiologie
> Felix-Hausdorff-Stra?e 4
> 17489 Greifswald
> Germany
> +49 (3834)-864392
>
>
>
>
> ------------------------------
>
> Message: 3
> Date: Fri, 16 Jul 2010 10:32:39 -0700
> From: Eric Pettersen <pett at cgl.ucsf.edu>
> Subject: Re: [Chimera-users] alignment + missing residues
> To: Gesa Volkers <gesa.volkers at uni-greifswald.de>
> Cc: chimera-dev at cgl.ucsf.edu, chimera-users at cgl.ucsf.edu
> Message-ID: <CF134751-B951-403B-B9E3-E441DB44644D at cgl.ucsf.edu>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Dear Gesa,
> I suspect you are using a Mac, since the daily builds failed last
> night for the Mac platforms. You need to get a daily build dated
> July
> 16 or later. I tried opening the sequence view for 1JFF in one of
> the
> successful daily builds and it was correct, e.g.:
>
>
>
> You can see that the interior gap is correctly recognized now.
> Hopefully the daily builds on the Mac platforms will work tonight.
>
> >> thanks for your suggestions. Unfortunately removing the SEQRES
> >> record did not help. I also downloaded and installed the new
> >> chimera-version today. The false numbering in the alignment
> still
> >> occurs. Also when I remove the SEQRES record and try with the
> new
> >> chimera version the false numbering appears. Quite annoying...
> The
> >> pdb-file is not in the protein data bank yet.
>
> Ah, the "remove SEQRES records" hack will only work for the single-
> sequence viewer, not an alignment. I tested that in the 1.4.1
> release
> and it indeed worked as I expected:
>
>
>
> The whole sequence is smushed together with no gaps, but the
> correspondences are correct. You could then align additional
> sequences to the smushed sequence and the correspondences would
> remain
> correct. Nonetheless it's probably simply better to wait for a
> daily
> build to succeed than to use the hack now. So make sure you check
> the
> date in the download table. If you still have problems with a
> release
> later than July 16, let me know.
>
> --Eric
>
> Eric Pettersen
> UCSF Computer Graphics Lab
> http://www.cgl.ucsf.edu
>
> On Jul 16, 2010, at 3:06 AM, Gesa Volkers wrote:
>
> > Additionally I downloaded 1JFF and did an alignment with another
> > tubulin-structure. And still the numbering does not recognize
> this
> > gap between 34 and 61.
> >
> > Gesa Volkers schrieb:
> >> Dear Eric,
> >>
> >> thanks for your suggestions. Unfortunately removing the SEQRES
> >> record did not help. I also downloaded and installed the new
> >> chimera-version today. The false numbering in the alignment
> still
> >> occurs. Also when I remove the SEQRES record and try with the
> new
> >> chimera version the false numbering appears. Quite annoying...
> The
> >> pdb-file is not in the protein data bank yet.
> >>
> >> Any more suggestions? Could I add "dummy atoms" in the structure?
> >>
> >> Thanks,
> >> Gesa
> >>
> >>
> >>
> >> Eric Pettersen schrieb:
> >>> On Jul 14, 2010, at 6:53 AM, Gesa Volkers wrote:
> >>>
> >>>> Dear All,
> >>>>
> >>>> I observed an issue with the alignment function of Chimera.
> >>>> I loaded a crystal structure where in between a loop is not
> >>>> modelled due to low electron density- so these residues are
> >>>> missing in the structure and the numbering also has this gap.
> >>>> When I align this structure with others, the missing residues
> are
> >>>> not recognized and chimera just overrides the numbering so
> after
> >>>> this loop all the numbers in the alignment do not fit anymore
> to
> >>>> the residues they should belong to although the structure and
> >>>> numberings are shown in the right way in the graphics window.
> How
> >>>> can I overcome this issue? Should I change the pdb-file? In
> which
> >>>> way?
> >>>>
> >>>> Thanks for all responses!
> >>>
> >>> Hi Gesa,
> >>> I had a similar problem reported with 1JFF 12 days ago and
> haven't
> >>> yet worked on fixing it. It seems to only happen for a small
> >>> subset of structures. 1JFF has a missing loop and also exactly
>
> >>> one missing residue at the N terminus. Is your structure like
> >>> that? Is it a standard PDB entry (if so, what's the ID code)?
> >>> I'll add you to the recipient list for the ticket we have open
> in
> >>> our bug database for this (#8585) so you will be notified when
> it
> >>> gets fixed. It'll probably be fairly soon.
> >>> Until then the only workaround that occurs to me is for you to
> >>> remove the SEQRES records from the PDB file before you open it.
>
> >>> Then the Sequence viewer will depict only the residues
> physically
> >>> present in the structure -- no gaps (incorrect or otherwise)
> will
> >>> be depicted.
> >>>
> >>> --Eric
> >>>
> >>> Eric Pettersen
> >>>
> >>> UCSF Computer Graphics Lab
> >>>
> >>> http://www.cgl.ucsf.edu
> >>>
> >>>
> >>>
> >>
> >>
> >
> >
> > --
> > Gesa Volkers
> > Institut f?r Biochemie, Molekulare Strukturbiologie
> > Felix-Hausdorff-Stra?e 4
> > 17489 Greifswald
> > Germany
> > +49 (3834)-864392
> >
> >
>
>
>
>
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