[Chimera-users] Chimera-users Digest, Vol 147, Issue 4

Thu Jul 2 12:05:26 PDT 2015

Thanks Greg!

To clarify, I wasn't actually intending these for use with a viewer of any
sort - just to provide in a paper for use as a stereo pair, viewed by
either diverging or crossing one's eyes to superimpose the two halves of
the pair.

Some people can easily view wall-eyed pairs, while others (myself included)
can only view cross-eyed pairs, so it would be nice to have the option of
generating either.

Cheers,
Oliver.

On Thu, Jul 2, 2015 at 3:00 PM, <chimera-users-request at cgl.ucsf.edu> wrote:

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> Today's Topics:
>
>    1. Re: on beta strand assignmet by chimera (Elaine Meng)
>    2. Cross eyed stereo pair generated by default (Oliver Clarke)
>    3. Re: Cross eyed stereo pair generated by default (Greg Couch)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 2 Jul 2015 09:55:55 -0700
> From: Elaine Meng <meng at cgl.ucsf.edu>
> To: Smith Liu <smith_liu123 at 163.com>
> Cc: chimera-users at cgl.ucsf.edu
> Subject: Re: [Chimera-users] on beta strand assignmet by chimera
> Message-ID: <E1E1B5D3-B0A5-4849-88D2-237944AFFA48 at cgl.ucsf.edu>
> Content-Type: text/plain; charset=utf-8
>
> Dear Smith,
> If the PDB files came from the Protein Data Bank repository, generally the
> proteins already have secondary structure assigned in HELIX and SHEET
> records.  If so, Chimera just uses those assignments.
> <
> http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/pdbintro.html#secondary
> >
>
> If the PDB file of a peptide/protein doesn?t have HELIX and SHEET records
> in it, then it runs a method ?ksdssp? described here:
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/ksdssp.html>
>
> If you don?t like the results for some reason, you could try re-running
> the ?ksdssp? command (or the ?compute SS? function in the Model Panel) with
> different (nondefault) parameters, or just manually assign residues as
> helix or strand however you like with the ?setattr? command, as shown in
> the lower part of this previous post:
> <
> http://plato.cgl.ucsf.edu/pipermail/chimera-users/2014-January/009574.html
> >
>
> 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 Jul 2, 2015, at 6:09 AM, Smith Liu <smith_liu123 at 163.com> wrote:
> >
> > Dear All,
> >
> > I have a protein, which contains fragment aa 239-251. The protein has
> been fitted its map with 2 different (minor difference) resolution, and
> thus I have 2 PDB. For PDB 1 (the first resolution), the H-bonds inside aa
> 239-251 include:
> > #2 Gly 245.A N-Asn 242.A O 2.708A
> > #2 Asn 242.A N-Tyr 246.A O 3.120 A
> > #2 Val 248.A N-Val 240.A O 3.120 A
> > #2 GLN 251.A N-Ser 238.A 0 3.033 A
> >
> > For PDB 2 (the second resolution), the H-bonds inside aa 239-251 include:
> > #0 Gly 245.A N-Asn 242.A O 2.715A
> > #0 Asn 242.A N-Tyr 246.A O 3.1206 A
> > #o Val 248.A N-Val 240.A O 2.858 A
> > #0 GLN 251.A N-Ser 238.A 0 3.074 A
> >
> > Naked eye check found the H-bonds in PDB 1 were almost the same H-bonds
> in PDB 2.
> >
> > However for PDB 2, aa23-242 and aa 247-251 form 2 strands, but for PDB
> 1, it was a un-disconnected loop for aa 239-251.
> >
> > Will you please explain how chimer assign beta strand?
> >
> > Best regards.
> >
> > Smith
> >
>
>
>
> ------------------------------
>
> Message: 2
> Date: Thu, 2 Jul 2015 14:20:01 -0400
> From: Oliver Clarke <olibclarke at gmail.com>
> To: Mailing List <chimera-users at cgl.ucsf.edu>
> Subject: [Chimera-users] Cross eyed stereo pair generated by default
> Message-ID: <B5D941AF-2692-4E71-8D5A-2A9C8D1610E2 at gmail.com>
> Content-Type: text/plain; charset=utf-8
>
> Hi all,
>
> I?ve noticed that when I save a stereo pair (using File/Save Image/Image
> Type/stereo pair), the resultant stereo pair is suitable for cross-eyed
> viewing.
>
> This is great for me, as I can?t do wall eyed stereo, but the default for
> many journals is to provide a wall-eyed stereo pair.
>
> Of course it is easy enough to convert by swapping the two halves of the
> pair, but for the sake of convenience, would it be possible to list stereo
> pair (cross eye) and stereo pair (wall eye) as two separate options in this
> dialogue?
>
> Cheers,
> Oliver.
>
>
> ------------------------------
>
> Message: 3
> Date: Thu, 02 Jul 2015 11:39:26 -0700
> From: Greg Couch <gregc at cgl.ucsf.edu>
> To: chimera-users at cgl.ucsf.edu
> Subject: Re: [Chimera-users] Cross eyed stereo pair generated by
>         default
> Message-ID: <5595855E.4020903 at cgl.ucsf.edu>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
> I'll look into it.
>
> FYI, cross-eyed stereo is the standard for stereo PNG and stereo JPEG
> files.  There is a buglet in stereo image saving -- the .png files
> should be renamed to have a .pns suffix, and the stereo JPEG images
> should have a .jps suffix.  However there aren't many viewers other than
> the one that comes with NVIDIA's 3D Vision setup.
>
>      -- Greg
>
> On 07/02/2015 11:20 AM, Oliver Clarke wrote:
> > Hi all,
> >
> > I?ve noticed that when I save a stereo pair (using File/Save Image/Image
> Type/stereo pair), the resultant stereo pair is suitable for cross-eyed
> viewing.
> >
> > This is great for me, as I can?t do wall eyed stereo, but the default
> for many journals is to provide a wall-eyed stereo pair.
> >
> > Of course it is easy enough to convert by swapping the two halves of the
> pair, but for the sake of convenience, would it be possible to list stereo
> pair (cross eye) and stereo pair (wall eye) as two separate options in this
> dialogue?
> >
> > Cheers,
> > Oliver.
> > _______________________________________________
> > Chimera-users mailing list
> > Chimera-users at cgl.ucsf.edu
> > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
> >
>
>
>
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> End of Chimera-users Digest, Vol 147, Issue 4
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