<div dir="ltr"><div><div>Thanks Greg! <br><br>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. <br><br>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.<br><br></div>Cheers,<br></div>Oliver.<br></div><div class="gmail_extra"><br><div class="gmail_quote">On Thu, Jul 2, 2015 at 3:00 PM, <span dir="ltr"><<a href="mailto:chimera-users-request@cgl.ucsf.edu" target="_blank">chimera-users-request@cgl.ucsf.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Send Chimera-users mailing list submissions to<br>
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Today's Topics:<br>
<br>
1. Re: on beta strand assignmet by chimera (Elaine Meng)<br>
2. Cross eyed stereo pair generated by default (Oliver Clarke)<br>
3. Re: Cross eyed stereo pair generated by default (Greg Couch)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Thu, 2 Jul 2015 09:55:55 -0700<br>
From: Elaine Meng <<a href="mailto:meng@cgl.ucsf.edu">meng@cgl.ucsf.edu</a>><br>
To: Smith Liu <<a href="mailto:smith_liu123@163.com">smith_liu123@163.com</a>><br>
Cc: <a href="mailto:chimera-users@cgl.ucsf.edu">chimera-users@cgl.ucsf.edu</a><br>
Subject: Re: [Chimera-users] on beta strand assignmet by chimera<br>
Message-ID: <<a href="mailto:E1E1B5D3-B0A5-4849-88D2-237944AFFA48@cgl.ucsf.edu">E1E1B5D3-B0A5-4849-88D2-237944AFFA48@cgl.ucsf.edu</a>><br>
Content-Type: text/plain; charset=utf-8<br>
<br>
Dear Smith,<br>
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.<br>
<<a href="http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/pdbintro.html#secondary" rel="noreferrer" target="_blank">http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/pdbintro.html#secondary</a>><br>
<br>
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:<br>
<<a href="http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/ksdssp.html" rel="noreferrer" target="_blank">http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/ksdssp.html</a>><br>
<br>
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:<br>
<<a href="http://plato.cgl.ucsf.edu/pipermail/chimera-users/2014-January/009574.html" rel="noreferrer" target="_blank">http://plato.cgl.ucsf.edu/pipermail/chimera-users/2014-January/009574.html</a>><br>
<br>
I hope this helps,<br>
Elaine<br>
----------<br>
Elaine C. Meng, Ph.D.<br>
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab<br>
Department of Pharmaceutical Chemistry<br>
University of California, San Francisco<br>
<br>
> On Jul 2, 2015, at 6:09 AM, Smith Liu <<a href="mailto:smith_liu123@163.com">smith_liu123@163.com</a>> wrote:<br>
><br>
> Dear All,<br>
><br>
> 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:<br>
> #2 Gly 245.A N-Asn 242.A O 2.708A<br>
> #2 Asn 242.A N-Tyr 246.A O 3.120 A<br>
> #2 Val 248.A N-Val 240.A O 3.120 A<br>
> #2 GLN 251.A N-Ser 238.A 0 3.033 A<br>
><br>
> For PDB 2 (the second resolution), the H-bonds inside aa 239-251 include:<br>
> #0 Gly 245.A N-Asn 242.A O 2.715A<br>
> #0 Asn 242.A N-Tyr 246.A O 3.1206 A<br>
> #o Val 248.A N-Val 240.A O 2.858 A<br>
> #0 GLN 251.A N-Ser 238.A 0 3.074 A<br>
><br>
> Naked eye check found the H-bonds in PDB 1 were almost the same H-bonds in PDB 2.<br>
><br>
> 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.<br>
><br>
> Will you please explain how chimer assign beta strand?<br>
><br>
> Best regards.<br>
><br>
> Smith<br>
><br>
<br>
<br>
<br>
------------------------------<br>
<br>
Message: 2<br>
Date: Thu, 2 Jul 2015 14:20:01 -0400<br>
From: Oliver Clarke <<a href="mailto:olibclarke@gmail.com">olibclarke@gmail.com</a>><br>
To: Mailing List <<a href="mailto:chimera-users@cgl.ucsf.edu">chimera-users@cgl.ucsf.edu</a>><br>
Subject: [Chimera-users] Cross eyed stereo pair generated by default<br>
Message-ID: <<a href="mailto:B5D941AF-2692-4E71-8D5A-2A9C8D1610E2@gmail.com">B5D941AF-2692-4E71-8D5A-2A9C8D1610E2@gmail.com</a>><br>
Content-Type: text/plain; charset=utf-8<br>
<br>
Hi all,<br>
<br>
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.<br>
<br>
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.<br>
<br>
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?<br>
<br>
Cheers,<br>
Oliver.<br>
<br>
<br>
------------------------------<br>
<br>
Message: 3<br>
Date: Thu, 02 Jul 2015 11:39:26 -0700<br>
From: Greg Couch <<a href="mailto:gregc@cgl.ucsf.edu">gregc@cgl.ucsf.edu</a>><br>
To: <a href="mailto:chimera-users@cgl.ucsf.edu">chimera-users@cgl.ucsf.edu</a><br>
Subject: Re: [Chimera-users] Cross eyed stereo pair generated by<br>
default<br>
Message-ID: <<a href="mailto:5595855E.4020903@cgl.ucsf.edu">5595855E.4020903@cgl.ucsf.edu</a>><br>
Content-Type: text/plain; charset=utf-8; format=flowed<br>
<br>
I'll look into it.<br>
<br>
FYI, cross-eyed stereo is the standard for stereo PNG and stereo JPEG<br>
files. There is a buglet in stereo image saving -- the .png files<br>
should be renamed to have a .pns suffix, and the stereo JPEG images<br>
should have a .jps suffix. However there aren't many viewers other than<br>
the one that comes with NVIDIA's 3D Vision setup.<br>
<br>
-- Greg<br>
<br>
On 07/02/2015 11:20 AM, Oliver Clarke wrote:<br>
> Hi all,<br>
><br>
> 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.<br>
><br>
> 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.<br>
><br>
> 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?<br>
><br>
> Cheers,<br>
> Oliver.<br>
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</blockquote></div><br></div>