[Chimera-users] box size limit

Franken, L.E. l.e.franken at rug.nl
Mon Jun 6 15:08:37 PDT 2016


Dear chimera users,
I am running into troubles displaying a map of a 650x650x650 volume and I
was wondering if there is a box size limit to chimera or what else could be
the problem. The way it displays the 3D .mrc file is as a single slice
rather than a volume. It will also go straight to solid display rather than
surface, did anyone encounter such a problem before? I can open the map in
coot and relion (slices), so I do not think that the map is corrupt. Thank
you for your time.

Best wishes,
Linda

On Mon, Jun 6, 2016 at 11:14 PM, <chimera-users-request at cgl.ucsf.edu> wrote:

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> Today's Topics:
>
>    1. Re: coloring by RMSD (conformational variability) (Elaine Meng)
>    2. Re: Chimera-win10-install (Greg Couch)
>    3. Re: coloring by RMSD (conformational variability) (George Tzotzos)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 6 Jun 2016 12:55:52 -0700
> From: Elaine Meng <meng at cgl.ucsf.edu>
> To: George Tzotzos <gtzotzos at me.com>
> Cc: "chimera-users at cgl.ucsf.edu BB" <chimera-users at cgl.ucsf.edu>
> Subject: Re: [Chimera-users] coloring by RMSD (conformational
>         variability)
> Message-ID: <5242FA3C-E185-453E-93DD-BEF75F495BBC at cgl.ucsf.edu>
> Content-Type: text/plain; charset=utf-8
>
> Hi George,
> I?m not really sure how you got those flat ribbons, but I think you can
> just use the transparency command.  It takes a percentage transparency, so
> for 75% transparent, a command something like:
>
>  transp 75,r  :1-10,124-125
>
> ? where the ?,r? part does NOT have any space before it, and ?r? stands
> for ribbons.
>
> 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 Jun 6, 2016, at 11:36 AM, George Tzotzos <gtzotzos at me.com> wrote:
> >
> > Following PC analysis, I have obtained pseudo trajectories for each of
> the first 3 principal components. I used Chimera to colour the regions
> exhibiting the largest structural variations as per instructions of Elain
> Meng, which I attach for easy reference.
> >
> > I have placed side by side, say the 1st PC, of two independent pseudo
> trajectories (see attached image). As the structure is disordered between
> residues 1-10 and 124-125, I?d like to render these ranges of residues
> semitransparent. I?ve tried to do this with the transparency command but
> this applies to ribbons only (I think).
> >
> > I?d appreciate any suggestions as to how this can be done.
> >
> > Thank you in advance
> >
> > George
> >
> > <dimer_deet2015_6MH2016.tif>
> > From: Elaine Meng <meng at cgl.ucsf.edu>
> > Subject: coloring by RMSD (conformational variability)
> > Date: 25 March 2014 at 19:32:47 GMT+1
> > To: George Tzotzos <gtzotzos at me.com>
> > Cc: chimera List <chimera-users at cgl.ucsf.edu>
> > Reply-To: "chimera-users at cgl.ucsf.edu BB" <chimera-users at cgl.ucsf.edu>
> >
> > Hi George,
> > Sure, you can do it by having Chimera calculate the CA-RMSD at each
> position and then mapping that value to color.  The file is a little
> strange in that it has only CA atoms and all the residues are ALA, but it
> will still work:
> >
> > (1) show the sequence (menu: Favorites? Sequence).  Just choose any one
> of the 34 -- it doesn't matter which one, since they all have the same
> sequence.
> >
> > (2) associate all 34 copies of the structure with the one sequence: in
> the sequence window menu, choose Structure? Associations. In that dialog,
> change all the "none" to the same sequence, then click OK.  This is
> somewhat tedious, but I just did it, so you can too! Now, all of the
> structures will be connected to that one sequence.
> >
> > (3) tell Chimera to calculate the RMSD at each position: in the sequence
> window menu, choose Headers? RMSD.  Now the sequence window will have an
> RMSD histogram above the sequence.  It may almost look like a line because
> most of the bars in the histogram (the RMSD values) are very low.
> >
> > (4) color the structures by the RMSD values with Render by Attribute (in
> main Chimera menu under Tools? Depiction).  In that tool, choose attributes
> of "residues" and attribute name "mavRMSD" (the "mav" part stands for
> Multalign Viewer, which is showing the sequence).  It will show a histogram
> of the values with some vertical colored bars.  You use those bars to
> define how the values are mapped to color.  The bars can be dragged left
> and right, and you can delete bars or add more bars with Ctrl-click.  You
> can change the color of each bar by clicking it and then clicking the
> "Color" square below the histogram and using the Color Editor, or you can
> just use one of the Palette options below that.  You can keep clicking
> Apply and then adjusting the coloring until it is how you like it.  For
> example, I show coloring by RMSD from blue->red->yellow  (and then menu:
> Presets? Publication 1) in the attached image.
> >
> > I hope this helps,
> > Elaine
> > _______________________________________________
> > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> > Manage subscription:
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>
>
>
>
> ------------------------------
>
> Message: 2
> Date: Mon, 6 Jun 2016 14:01:18 -0700
> From: Greg Couch <gregc at cgl.ucsf.edu>
> To: Mitja Ogrizek <ogrizek.mitja at gmail.com>,
>         chimera-users at cgl.ucsf.edu
> Subject: Re: [Chimera-users] Chimera-win10-install
> Message-ID: <5755E49E.7070006 at cgl.ucsf.edu>
> Content-Type: text/plain; charset="windows-1252"; Format="flowed"
>
> Hello Mitja,
>
> I was able to get the Windows installer to fail in one situation -- I
> hope this is the same problem you're having.
>
> If you download the installer as a non-administrative user and then try
> to run it, it fails because it can't install Chimera in the default
> location even though you've typed in an administrative password.  My
> workaround was to use the file browser to locate the installer on the
> disk, do a right-mouse click on the installer, and then "Run as
> Administrator".  I expect that it would also work if you installed
> Chimera to a non-system directory.
>
>    HTH,
>
>    Greg
>
> On 06/04/2016 05:46 AM, Mitja Ogrizek wrote:
> > Dear all,
> >
> > I tried to install a new version of chimera on my laptop with win10,
> > but it doesn't want to load and start the setup.
> > Has anybody else reported or had the same troubles?
> >
> > Kind regards,
> > Mitja Ogrizek
> >
> >
> > _______________________________________________
> > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> > Manage subscription:
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>
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> ------------------------------
>
> Message: 3
> Date: Mon, 06 Jun 2016 22:13:15 +0200
> From: George Tzotzos <gtzotzos at me.com>
> To: "chimera-users at cgl.ucsf.edu BB" <chimera-users at cgl.ucsf.edu>
> Subject: Re: [Chimera-users] coloring by RMSD (conformational
>         variability)
> Message-ID: <E8E115FF-478E-4C4A-AD42-C1084C536E3F at me.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hi Elaine,
>
> Grateful for the prompt and useful response.
>
> The flat ribbons come for a cluster of pdb files sampled from the first
> eigenvector of PCA. I?m attaching such a file.
>
> Once again, many thanks
>
> George
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>
>
> > On 6 Jun 2016, at 21:55, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> >
> > Hi George,
> > I?m not really sure how you got those flat ribbons, but I think you can
> just use the transparency command.  It takes a percentage transparency, so
> for 75% transparent, a command something like:
> >
> > transp 75,r  :1-10,124-125
> >
> > ? where the ?,r? part does NOT have any space before it, and ?r? stands
> for ribbons.
> >
> > 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 Jun 6, 2016, at 11:36 AM, George Tzotzos <gtzotzos at me.com> wrote:
> >>
> >> Following PC analysis, I have obtained pseudo trajectories for each of
> the first 3 principal components. I used Chimera to colour the regions
> exhibiting the largest structural variations as per instructions of Elain
> Meng, which I attach for easy reference.
> >>
> >> I have placed side by side, say the 1st PC, of two independent pseudo
> trajectories (see attached image). As the structure is disordered between
> residues 1-10 and 124-125, I?d like to render these ranges of residues
> semitransparent. I?ve tried to do this with the transparency command but
> this applies to ribbons only (I think).
> >>
> >> I?d appreciate any suggestions as to how this can be done.
> >>
> >> Thank you in advance
> >>
> >> George
> >>
> >> <dimer_deet2015_6MH2016.tif>
> >> From: Elaine Meng <meng at cgl.ucsf.edu>
> >> Subject: coloring by RMSD (conformational variability)
> >> Date: 25 March 2014 at 19:32:47 GMT+1
> >> To: George Tzotzos <gtzotzos at me.com>
> >> Cc: chimera List <chimera-users at cgl.ucsf.edu>
> >> Reply-To: "chimera-users at cgl.ucsf.edu BB" <chimera-users at cgl.ucsf.edu>
> >>
> >> Hi George,
> >> Sure, you can do it by having Chimera calculate the CA-RMSD at each
> position and then mapping that value to color.  The file is a little
> strange in that it has only CA atoms and all the residues are ALA, but it
> will still work:
> >>
> >> (1) show the sequence (menu: Favorites? Sequence).  Just choose any one
> of the 34 -- it doesn't matter which one, since they all have the same
> sequence.
> >>
> >> (2) associate all 34 copies of the structure with the one sequence: in
> the sequence window menu, choose Structure? Associations. In that dialog,
> change all the "none" to the same sequence, then click OK.  This is
> somewhat tedious, but I just did it, so you can too! Now, all of the
> structures will be connected to that one sequence.
> >>
> >> (3) tell Chimera to calculate the RMSD at each position: in the
> sequence window menu, choose Headers? RMSD.  Now the sequence window will
> have an RMSD histogram above the sequence.  It may almost look like a line
> because most of the bars in the histogram (the RMSD values) are very low.
> >>
> >> (4) color the structures by the RMSD values with Render by Attribute
> (in main Chimera menu under Tools? Depiction).  In that tool, choose
> attributes of "residues" and attribute name "mavRMSD" (the "mav" part
> stands for Multalign Viewer, which is showing the sequence).  It will show
> a histogram of the values with some vertical colored bars.  You use those
> bars to define how the values are mapped to color.  The bars can be dragged
> left and right, and you can delete bars or add more bars with Ctrl-click.
> You can change the color of each bar by clicking it and then clicking the
> "Color" square below the histogram and using the Color Editor, or you can
> just use one of the Palette options below that.  You can keep clicking
> Apply and then adjusting the coloring until it is how you like it.  For
> example, I show coloring by RMSD from blue->red->yellow  (and then menu:
> Presets? Publication 1) in the attached image.
> >>
> >> I hope this helps,
> >> Elaine
> >> _______________________________________________
> >> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> >> Manage subscription:
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
> >
>
>
> ------------------------------
>
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