[Chimera-users] Chimera and XP?

Boaz Shaanan bshaanan at bgu.ac.il
Wed Mar 12 14:11:28 PDT 2014


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: bshaanan at bgu.ac.il
Phone: 972-8-647-2220  Skype: boaz.shaanan
Fax:   972-8-647-2992 or 972-8-646-1710





________________________________________
From: chimera-users-bounces at cgl.ucsf.edu [chimera-users-bounces at cgl.ucsf.edu] on behalf of chimera-users-request at cgl.ucsf.edu [chimera-users-request at cgl.ucsf.edu]
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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" <marek.maly at ujep.cz>
To: "chimera-users at cgl.ucsf.edu" <chimera-users at cgl.ucsf.edu>
Subject: [Chimera-users] match-align using just selected protein areas
        ?
Message-ID: <op.xck57xhvlc8gdf at pocitadlon.ujep.cz>
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:
http://www.opera.com/mail/


------------------------------

Message: 2
Date: Wed, 12 Mar 2014 09:35:39 -0700
From: Elaine Meng <meng at cgl.ucsf.edu>
To: "Marek Maly" <marek.maly at ujep.cz>
Cc: "chimera-users at cgl.ucsf.edu" <chimera-users at cgl.ucsf.edu>
Subject: Re: [Chimera-users] match-align using just selected protein
        areas ?
Message-ID: <67EFA59C-7032-4F2A-8517-6D32E11C4F2D at cgl.ucsf.edu>
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:
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/matchmaker/matchmaker.html>

In the matchmaker (mmaker) command,
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/mmaker.html>
... it is similar but you instead specify the residues directly instead of selecting them:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/mmaker.html#restrict>

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:

> 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




------------------------------

Message: 3
Date: Wed, 12 Mar 2014 09:51:04 -0700
From: Elaine Meng <meng at cgl.ucsf.edu>
To: Julian Marzi <julian.marzi at googlemail.com>
Cc: "chimera-users at cgl.ucsf.edu BB" <chimera-users at cgl.ucsf.edu>
Subject: Re: [Chimera-users] surface failures
Message-ID: <91C53A76-7F10-4123-9752-0AE5F5C58689 at cgl.ucsf.edu>
Content-Type: text/plain; charset=us-ascii

On Mar 12, 2014, at 6:46 AM, Julian Marzi wrote:

> 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

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:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/surfprobs.html>
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/colorzone/colorzone.html>

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" <marek.maly at ujep.cz>
To: "chimera-users at cgl.ucsf.edu BB" <chimera-users at cgl.ucsf.edu>
Subject: Re: [Chimera-users] match-align using just selected protein
        areas ?
Message-ID: <op.xcmg0dxylc8gdf at pocitadlon.ujep.cz>
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 <meng at cgl.ucsf.edu>
napsal/-a:

> 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:
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/matchmaker/matchmaker.html>
>
> In the matchmaker (mmaker) command,
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/mmaker.html>
> ... it is similar but you instead specify the residues directly instead
> of selecting them:
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/mmaker.html#restrict>
>
> 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:
>
>> 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
>
>
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> (20140312) __________
>
> Tuto zpravu proveril ESET NOD32 Antivirus.
>
> http://www.eset.cz
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>
>


--
Tato zpr?va byla vytvo?ena p?evratn?m po?tovn?m klientem Opery:
http://www.opera.com/mail/


------------------------------

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