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<div class="moz-cite-prefix">Hi Boaz,<br>
<br>
We're not aware of anything that changed on our end that would
stop Chimera from running. Try renaming or deleting your Chimera
preferences file, on Windows that is in C:\Documents and
Settings\USERNAME\Application Data\.chimera\preferences, and then
restart Chimera.<br>
<br>
HTH,<br>
<br>
Greg<br>
<br>
On 03/12/2014 02:11 PM, Boaz Shaanan wrote:<br>
</div>
<blockquote
cite="mid:4B2A491F685D1E4FBBF985E193095AAF9943C10E@hawk3.auth.ad.bgu.ac.il"
type="cite">
<pre wrap="">Hi,
For some reason, I couldn't get Chimera (1.8.1 and the 12/3 daily build) to work today on my laptop running XP (32bit). It gets stuck in 'initializing graphics'. See attached screen shot of run with --debug. Chimera worked for years on this machine. Other programs work fine (spdbv, Coot, etc.). I can't imagine it has to do with the imminent downfall of XP support, or maybe it does?
Please advise.
Thanks,
Boaz
Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben-Gurion University of the Negev
Beer-Sheva 84105
Israel
E-mail: <a class="moz-txt-link-abbreviated" href="mailto:bshaanan@bgu.ac.il">bshaanan@bgu.ac.il</a>
Phone: 972-8-647-2220 Skype: boaz.shaanan
Fax: 972-8-647-2992 or 972-8-646-1710
________________________________________
From: <a class="moz-txt-link-abbreviated" href="mailto:chimera-users-bounces@cgl.ucsf.edu">chimera-users-bounces@cgl.ucsf.edu</a> [<a class="moz-txt-link-abbreviated" href="mailto:chimera-users-bounces@cgl.ucsf.edu">chimera-users-bounces@cgl.ucsf.edu</a>] on behalf of <a class="moz-txt-link-abbreviated" href="mailto:chimera-users-request@cgl.ucsf.edu">chimera-users-request@cgl.ucsf.edu</a> [<a class="moz-txt-link-abbreviated" href="mailto:chimera-users-request@cgl.ucsf.edu">chimera-users-request@cgl.ucsf.edu</a>]
Sent: Wednesday, March 12, 2014 9:00 PM
To: <a class="moz-txt-link-abbreviated" href="mailto:chimera-users@cgl.ucsf.edu">chimera-users@cgl.ucsf.edu</a>
Subject: Chimera-users Digest, Vol 131, Issue 13
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Today's Topics:
1. match-align using just selected protein areas ? (Marek Maly)
2. Re: match-align using just selected protein areas ? (Elaine Meng)
3. Re: surface failures (Elaine Meng)
4. Re: match-align using just selected protein areas ? (Marek Maly)
----------------------------------------------------------------------
Message: 1
Date: Wed, 12 Mar 2014 02:53:47 +0100
From: "Marek Maly" <a class="moz-txt-link-rfc2396E" href="mailto:marek.maly@ujep.cz"><marek.maly@ujep.cz></a>
To: <a class="moz-txt-link-rfc2396E" href="mailto:chimera-users@cgl.ucsf.edu">"chimera-users@cgl.ucsf.edu"</a> <a class="moz-txt-link-rfc2396E" href="mailto:chimera-users@cgl.ucsf.edu"><chimera-users@cgl.ucsf.edu></a>
Subject: [Chimera-users] match-align using just selected protein areas
?
Message-ID: <a class="moz-txt-link-rfc2396E" href="mailto:op.xck57xhvlc8gdf@pocitadlon.ujep.cz"><op.xck57xhvlc8gdf@pocitadlon.ujep.cz></a>
Content-Type: text/plain; charset=iso-8859-2; format=flowed; delsp=yes
Hello,
I would like to know if it is possible in Chimera
align two proteins let say protein A and protein B,
but just using selected subsequences A_sel, B_sel
(i.e. just the selected subsequences are going to be
optimally matched and the rest of both proteins is not involved
in the matching process/calculation) ?
Thank you in advance !
Best wishes,
Marek
--
Tato zpr?va byla vytvo?ena p?evratn?m po?tovn?m klientem Opery:
<a class="moz-txt-link-freetext" href="http://www.opera.com/mail/">http://www.opera.com/mail/</a>
------------------------------
Message: 2
Date: Wed, 12 Mar 2014 09:35:39 -0700
From: Elaine Meng <a class="moz-txt-link-rfc2396E" href="mailto:meng@cgl.ucsf.edu"><meng@cgl.ucsf.edu></a>
To: "Marek Maly" <a class="moz-txt-link-rfc2396E" href="mailto:marek.maly@ujep.cz"><marek.maly@ujep.cz></a>
Cc: <a class="moz-txt-link-rfc2396E" href="mailto:chimera-users@cgl.ucsf.edu">"chimera-users@cgl.ucsf.edu"</a> <a class="moz-txt-link-rfc2396E" href="mailto:chimera-users@cgl.ucsf.edu"><chimera-users@cgl.ucsf.edu></a>
Subject: Re: [Chimera-users] match-align using just selected protein
areas ?
Message-ID: <a class="moz-txt-link-rfc2396E" href="mailto:67EFA59C-7032-4F2A-8517-6D32E11C4F2D@cgl.ucsf.edu"><67EFA59C-7032-4F2A-8517-6D32E11C4F2D@cgl.ucsf.edu></a>
Content-Type: text/plain; charset=us-ascii
Hi Marek,
Yes, if you mean MatchMaker (Match->Align does not align the structures, it just makes a sequence alignment from a structural alignment you already made).
In the MatchMaker GUI, there is a "Further restrict matching to current selection" setting:
<a class="moz-txt-link-rfc2396E" href="http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/matchmaker/matchmaker.html"><http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/matchmaker/matchmaker.html></a>
In the matchmaker (mmaker) command,
<a class="moz-txt-link-rfc2396E" href="http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/mmaker.html"><http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/mmaker.html></a>
... it is similar but you instead specify the residues directly instead of selecting them:
<a class="moz-txt-link-rfc2396E" href="http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/mmaker.html#restrict"><http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/mmaker.html#restrict></a>
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 Mar 11, 2014, at 6:53 PM, Marek Maly wrote:
</pre>
<blockquote type="cite">
<pre wrap="">Hello,
I would like to know if it is possible in Chimera
align two proteins let say protein A and protein B,
but just using selected subsequences A_sel, B_sel
(i.e. just the selected subsequences are going to be
optimally matched and the rest of both proteins is not involved
in the matching process/calculation) ?
Thank you in advance !
Best wishes,
Marek
</pre>
</blockquote>
<pre wrap="">
------------------------------
Message: 3
Date: Wed, 12 Mar 2014 09:51:04 -0700
From: Elaine Meng <a class="moz-txt-link-rfc2396E" href="mailto:meng@cgl.ucsf.edu"><meng@cgl.ucsf.edu></a>
To: Julian Marzi <a class="moz-txt-link-rfc2396E" href="mailto:julian.marzi@googlemail.com"><julian.marzi@googlemail.com></a>
Cc: <a class="moz-txt-link-rfc2396E" href="mailto:chimera-users@cgl.ucsf.eduBB">"chimera-users@cgl.ucsf.edu BB"</a> <a class="moz-txt-link-rfc2396E" href="mailto:chimera-users@cgl.ucsf.edu"><chimera-users@cgl.ucsf.edu></a>
Subject: Re: [Chimera-users] surface failures
Message-ID: <a class="moz-txt-link-rfc2396E" href="mailto:91C53A76-7F10-4123-9752-0AE5F5C58689@cgl.ucsf.edu"><91C53A76-7F10-4123-9752-0AE5F5C58689@cgl.ucsf.edu></a>
Content-Type: text/plain; charset=us-ascii
On Mar 12, 2014, at 6:46 AM, Julian Marzi wrote:
</pre>
<blockquote type="cite">
<pre wrap="">Dear Eric,
I tryed the command surfcat c1 and surfcat c1 :.1 & ~:ohx, but this will also not work on my mac... The mac show for short time an activity, but nothing happens. The comand from Elaine molmap :.1&~:ohx 5 worked and it looks great! Is there also a possibility to select a part of the sequence in the "surface" (molmap) presentation to show it in an other color? I select one part on the 25S-rRNa in green, but the molmap view covers it in grey and if I make a higher transparency, the selected part will be seen. But it would be better, if the selected part is colored in the molmap view. This would allow the marked spot directly recognize without transparency. If there is an answer for my question, please let it me know. If not, is not bad, you two have helped me incredibly much.
Thank you so much
Regards
Julian
</pre>
</blockquote>
<pre wrap="">
Hi Julian,
The "molmap" surface can be colored to match atoms with the Color Zone tool. The atoms can be hidden, it is just a step to the surface coloring that you want. After you color some atoms (for example, some part of the RNA that you selected) you can also color the part of the surface that is near the currently selected atoms with Color Zone (in menu under Tools... Depiction).
Color Zone is mentioned along with molmap in #3 in the surface workarounds page:
<a class="moz-txt-link-rfc2396E" href="http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/surfprobs.html"><http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/surfprobs.html></a>
<a class="moz-txt-link-rfc2396E" href="http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/colorzone/colorzone.html"><http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/colorzone/colorzone.html></a>
Also, you could color the molmap surface any overall color you want first, it doesn't have to be the default grayish color. You could just click the color square on the Volume Viewer tool (that appears when you create the molmap surface) and then use the Color Editor, or you can select the surface directly in the main window and use the Actions... Color menu.
I hope this helps!
P.S. please send chimera questions to the chimera-users address instead of our individual addresses (to allow others to see the Q & A) - thanks!
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
------------------------------
Message: 4
Date: Wed, 12 Mar 2014 19:44:27 +0100
From: "Marek Maly" <a class="moz-txt-link-rfc2396E" href="mailto:marek.maly@ujep.cz"><marek.maly@ujep.cz></a>
To: <a class="moz-txt-link-rfc2396E" href="mailto:chimera-users@cgl.ucsf.eduBB">"chimera-users@cgl.ucsf.edu BB"</a> <a class="moz-txt-link-rfc2396E" href="mailto:chimera-users@cgl.ucsf.edu"><chimera-users@cgl.ucsf.edu></a>
Subject: Re: [Chimera-users] match-align using just selected protein
areas ?
Message-ID: <a class="moz-txt-link-rfc2396E" href="mailto:op.xcmg0dxylc8gdf@pocitadlon.ujep.cz"><op.xcmg0dxylc8gdf@pocitadlon.ujep.cz></a>
Content-Type: text/plain; charset=iso-8859-2; format=flowed; delsp=yes
Dear Elaine,
thank you very much for your help !
Best wishes,
Marek
Dne Wed, 12 Mar 2014 17:35:39 +0100 Elaine Meng <a class="moz-txt-link-rfc2396E" href="mailto:meng@cgl.ucsf.edu"><meng@cgl.ucsf.edu></a>
napsal/-a:
</pre>
<blockquote type="cite">
<pre wrap="">Hi Marek,
Yes, if you mean MatchMaker (Match->Align does not align the structures,
it just makes a sequence alignment from a structural alignment you
already made).
In the MatchMaker GUI, there is a "Further restrict matching to current
selection" setting:
<a class="moz-txt-link-rfc2396E" href="http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/matchmaker/matchmaker.html"><http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/matchmaker/matchmaker.html></a>
In the matchmaker (mmaker) command,
<a class="moz-txt-link-rfc2396E" href="http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/mmaker.html"><http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/mmaker.html></a>
... it is similar but you instead specify the residues directly instead
of selecting them:
<a class="moz-txt-link-rfc2396E" href="http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/mmaker.html#restrict"><http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/mmaker.html#restrict></a>
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 Mar 11, 2014, at 6:53 PM, Marek Maly wrote:
</pre>
<blockquote type="cite">
<pre wrap="">Hello,
I would like to know if it is possible in Chimera
align two proteins let say protein A and protein B,
but just using selected subsequences A_sel, B_sel
(i.e. just the selected subsequences are going to be
optimally matched and the rest of both proteins is not involved
in the matching process/calculation) ?
Thank you in advance !
Best wishes,
Marek
</pre>
</blockquote>
<pre wrap="">
__________ Informace od ESET NOD32 Antivirus, verze databaze 9532
(20140312) __________
Tuto zpravu proveril ESET NOD32 Antivirus.
<a class="moz-txt-link-freetext" href="http://www.eset.cz">http://www.eset.cz</a>
</pre>
</blockquote>
<pre wrap="">
--
Tato zpr?va byla vytvo?ena p?evratn?m po?tovn?m klientem Opery:
<a class="moz-txt-link-freetext" href="http://www.opera.com/mail/">http://www.opera.com/mail/</a>
------------------------------
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End of Chimera-users Digest, Vol 131, Issue 13
**********************************************
</pre>
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</pre>
</blockquote>
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