[Chimera-users] Chimera-users Digest, Vol 75, Issue 17
Burkhard Heil
burkhard.heil at gmail.com
Wed Jul 15 14:30:11 PDT 2009
Liebste,
hab jetzt auch AB abgehört:-) und warte auf meine gesättigte oder
essende Sarah:-)
Knutschknutsch!
Küsse
Dein Burkhard
On 14.07.2009, at 21:00, chimera-users-request at cgl.ucsf.edu wrote:
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> Today's Topics:
>
> 1. suggestion/transform molecule coordinates (Dougherty, Matthew T.)
> 2. Re: suggestion/transform molecule coordinates (Thomas Goddard)
> 3. Re: sequence viewer (Eric Pettersen)
> 4. Re: sequence viewer (Elaine Meng)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 13 Jul 2009 15:30:21 -0500
> From: "Dougherty, Matthew T." <matthewd at bcm.tmc.edu>
> Subject: [Chimera-users] suggestion/transform molecule coordinates
> To: <chimera-users at cgl.ucsf.edu>
> Message-ID:
> <B5CA7C88183F884CB316B04DCD343849013465D6 at BCMEVS13.ad.bcm.edu>
> Content-Type: text/plain; charset="iso-8859-1"
>
> relating to the apply, close & help buttons
>
> 1)"reset" button
> The reset would remove prior transformations
>
> 2) "apply once" button.
> The apply once would function the same as a reset and apply in
> sequence.
>
> 3) display sum of current transformation (Euler & shift)
>
>
> Matthew Dougherty
> 713-433-3849
> National Center for Macromolecular Imaging
> Baylor College of Medicine/Houston Texas USA
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> Message: 2
> Date: Mon, 13 Jul 2009 16:38:18 -0700
> From: Thomas Goddard <goddard at cgl.ucsf.edu>
> Subject: Re: [Chimera-users] suggestion/transform molecule coordinates
> To: "Dougherty, Matthew T." <matthewd at bcm.tmc.edu>
> Cc: chimera-users at cgl.ucsf.edu
> Message-ID: <4A5BC56A.3030200 at cgl.ucsf.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Hi Matt,
>
> Ok I added Set and Reset buttons and cumulative transform output
> (Euler angles and shift) to the Transform Molecule Coordinates dialog
> (menu Tools / Movement). Will be in tonight's builds:
>
> http://www.cgl.ucsf.edu/chimera/alpha-downloads.html
>
> Tom
>
>
> -------- Original Message --------
> Subject: [Chimera-users] suggestion/transform molecule coordinates
> From: Dougherty, Matthew T.
> To: chimera-users at cgl.ucsf.edu
> Date: 7/13/09 1:30 PM
>
>> relating to the apply, close & help buttons
>>
>> 1)"reset" button
>> The reset would remove prior transformations
>>
>> 2) "apply once" button.
>> The apply once would function the same as a reset and apply in
>> sequence.
>>
>> 3) display sum of current transformation (Euler & shift)
>>
>>
>> Matthew Dougherty
>> 713-433-3849
>> National Center for Macromolecular Imaging
>> Baylor College of Medicine/Houston Texas USA
>> =
>> =
>> =
>> =
>> =====================================================================
>
>
>
> ------------------------------
>
> Message: 3
> Date: Mon, 13 Jul 2009 16:43:42 -0700
> From: Eric Pettersen <pett at cgl.ucsf.edu>
> Subject: Re: [Chimera-users] sequence viewer
> To: Chimera BB <chimera-users at cgl.ucsf.edu>
> Message-ID: <88DD2086-745E-4B43-BB61-392854D2929D at cgl.ucsf.edu>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi all,
> I have made my intended improvements to the single-sequence viewer
> now and the new version is in the daily build (which you can get by
> going to www.cgl.ucsf.edu/chimera and following the "Daily Builds"
> link). I encourage people who use the sequence viewer a lot to fetch
> the new version and let me know what you like and what you don't.
>
> --Eric
>
> Eric Pettersen
> UCSF Computer Graphics Lab
> http://www.cgl.ucsf.edu
>
>
> On Dec 18, 2008, at 10:20 AM, Eric Pettersen wrote:
>
>> Hi Christos,
>> In previous releases, there were two tools that showed sequences:
>> the sequence viewer (single sequences) and Multalign Viewer (sequence
>> alignments). We plan to show additional information with sequences
>> (e.g. UniProt markups) and as a step in that direction we decided to
>> unify our presentation of sequence info by making MAV capable of
>> showing single sequences. That way, the work to show sequence
>> information in the user interface won't have to be duplicated each
>> time we add something.
>> So, rather than restore the old sequence viewer, what I would prefer
>> to do is make the MAV interface better for showing single sequences.
>> Would it help if single sequences were combined in a single dialog,
>> like in the previous sequence viewer? I don't think that's too hard
>> to do. As for color, I think you're right that for a single sequence
>> it makes more sense to show that columns as black, since there is no
>> conservation per se down the column. I can easily change that. You
>> can too, in fact, by choosing Preferences->Analysis in the MAV window
>> and changing "Residue letter coloring" to "black" (the preference
>> will
>> be carried over to future MAV dialogs).
>> So what other changes would make the MAV version of the sequence
>> version more usable? I guess this is actually a general question to
>> everybody...
>>
>> --Eric
>>
>> On Dec 17, 2008, at 5:05 PM, Gatsogiannis, Christos wrote:
>>
>>> Hi all,
>>>
>>> i ve just installed the latest daily build version and i?ve noticed
>>> that the sequence viewer has a new "look".
>>> However, i have difficulties to get used to it...
>>> Some examples:
>>> -when i want to view the sequence of a pdb file containing seven
>>> chains, i get seven different pop-up windows (...) showing the
>>> sequences corresponding to the seven different chain ID?s....
>>> -Moreover, it isn?t so "easy" anymore to select aminoacids directly
>>> in the sequence viewer (e.g. too many colors) and therefore now i?m
>>> selecting residues using only the command line..
>>> My colleagues also prefer the older version..
>>> is there a simple way to install the latest chimera version but keep
>>> the old version of the sequence viewer?
>>> Thanks!
>>
>> _______________________________________________
>> Chimera-users mailing list
>> Chimera-users at cgl.ucsf.edu
>> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
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> ------------------------------
>
> Message: 4
> Date: Mon, 13 Jul 2009 16:54:43 -0700
> From: Elaine Meng <meng at cgl.ucsf.edu>
> Subject: Re: [Chimera-users] sequence viewer
> To: Chimera BB <chimera-users at cgl.ucsf.edu>
> Message-ID: <36533581-E031-490E-B300-FA1C962B779F at cgl.ucsf.edu>
> Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes
>
> Just to chime in on Eric's announcement -- he didn't mention that the
> sequence window preferences have also been expanded and reorganized,
> so that you can save separate "Appearance" preferences for single
> sequences and multiple alignments. I thought that was important
> because if you *do* want to adjust the spacing or wrapping or font,
> etc. of the single sequence view, this can be saved as a preference
> and it won't affect the appearance of your sequence alignments.
>
> We just adjusted the default spacing of single sequences, so you might
> want to wait one more day to get the daily build to see what we chose
> for defaults. Otherwise, the many improvements mentioned by Eric are
> in there already.
>
> Best,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> http://www.cgl.ucsf.edu/home/meng/index.html
>
> On Jul 13, 2009, at 4:43 PM, Eric Pettersen wrote:
>
>> Hi all,
>> I have made my intended improvements to the single-sequence viewer
>> now and the new version is in the daily build (which you can get by
>> going to www.cgl.ucsf.edu/chimera and following the "Daily Builds"
>> link). I encourage people who use the sequence viewer a lot to
>> fetch the new version and let me know what you like and what you
>> don't.
>>
>> --Eric
>>
>> Eric Pettersen
>> UCSF Computer Graphics Lab
>> http://www.cgl.ucsf.edu
>>
>
>
>
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> End of Chimera-users Digest, Vol 75, Issue 17
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