[Chimera-users] Chimera and XP?

Greg Couch gregc at cgl.ucsf.edu
Thu Mar 13 16:22:13 PDT 2014


Hi Boaz,

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.

     HTH,

     Greg

On 03/12/2014 02:11 PM, Boaz Shaanan wrote:
> 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]
> Sent: Wednesday, March 12, 2014 9:00 PM
> To: chimera-users at cgl.ucsf.edu
> 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
>>
>> __________ Informace od ESET NOD32 Antivirus, verze databaze 9532
>> (20140312) __________
>>
>> Tuto zpravu proveril ESET NOD32 Antivirus.
>>
>> http://www.eset.cz
>>
>>
>>
>
> --
> Tato zpr?va byla vytvo?ena p?evratn?m po?tovn?m klientem Opery:
> http://www.opera.com/mail/
>
>
> ------------------------------
>
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