Re: [ccp4bb] 3-D Coot Capable Computer Monitor/Glasses for Mac Laptop?

[nathanielclar5 .]

I misstated something earlier, and I would like to correct the record:

Magic Eye books instruct you on using wall-eyed stereo (with excellent
instructions, highly recommended!).  Currently (with computer monitors) I
find cross-eyed much easier (and I think more people should try it).
Thanks,
Nat



On Fri, Mar 2, 2018 at 1:41 PM, nathanielclar5 . 
wrote:

> To learn how to cross eyes, just hold you index fingers strait up, ~12-18
> inches from your eyes, and cross your eyes until the two fingers overlap to
> form a third finger in the middle.  Then practice holding your eyes there.
> You can also practice with ceiling tiles, floor tiles, anything that
> repeats,  Just cross your eyes until adjacent things overlap, and that's
> it.
>
> It's best to start with a small image, like a small (4"x6") Coot window
> with a simple object like a sulfate ion displayed.  Once you get the hang
> if it, you can use larger windows.  It's totally worth learning to see in
> cross-eye stereo if you look at structures.
>
> I learned to see cross-eye as a kid from the 'Magic Eye' books.  I'm sure
> there are great tutorials and examples on the web.
> Nat
>
> On Fri, Mar 2, 2018 at 11:39 AM, Xiao Lei  wrote:
>
>> I never learn how to "cross eye", I may need to check if some video
>> instruction online...
>>
>>
> On Fri, Mar 2, 2018 at 11:28 AM, nathanielclar5 . <
> nathanielcl...@gmail.com> wrote:
>
>> You already have stereo built in, just turn on 'cross eyed stereo' and
>> learn to cross your eyes!  It's brighter than any 3d monitor, requires no
>> hardware, and no, it won't hurt your eyes (even for hours at a time)
>>
>> Nat
>>
>> On Fri, Mar 2, 2018 at 11:01 AM, Jim Fairman 
>> wrote:
>>
>>> Daniel,
>>>
>>> To best of my knowledge, options for 3d stereo on Mac are limited to
>>> Zalman:  https://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php
>>> /Zalman_Stereo
>>>
>>> If you're willing to go to Linux or Windows, you can do an Nvidia Quadro
>>> Card with a 120 or 144Hz monitor with a 3D Vision glasses kit.
>>>
>>> Cheers, Jim
>>>
>>> -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
>>> Jim Fairman
>>> Principal Scientist II
>>> Roche Sequencing Solutions
>>> 2841 Scott Blvd
>>> <https://maps.google.com/?q=2841+Scott+Blvd+Santa+Clara,+CA+95050&entry=gmail&source=g>
>>> Santa Clara, CA 95050
>>> <https://maps.google.com/?q=2841+Scott+Blvd+Santa+Clara,+CA+95050&entry=gmail&source=g>
>>> fairman@gmail.com jim.fair...@roche.com
>>>
>>>
>>>
>>>
>>> 
>>> --
>>> Jim Fairman
>>> C: 1-240-479-6575 <(240)%20479-6575>
>>>
>>> On Fri, Mar 2, 2018 at 8:24 AM, Daniel M. Himmel, Ph. D. <
>>> danielmhim...@gmail.com> wrote:
>>>
>>>> I'm looking for some computer hardware advice.
>>>> I have a MacBook Pro with a "Retina" screen and
>>>> an Intel HD Graphics 4000 1536 MB graphics card,
>>>> running OS X 10.11.16 ("El Capitan"), and I would
>>>> like to view structures in 3-D in Coot.
>>>>
>>>> Which computer monitors and which 3-D glasses brands
>>>> would allow me to view 3-D graphics in Coot?  Should I
>>>> be going for dynamic 3-D glasses?
>>>>
>>>> -Daniel
>>>>
>>>>
>>>
>>
>

Re: [ccp4bb] 3-D Coot Capable Computer Monitor/Glasses for Mac Laptop?

[nathanielclar5 .]

To learn how to cross eyes, just hold you index fingers strait up, ~12-18
inches from your eyes, and cross your eyes until the two fingers overlap to
form a third finger in the middle.  Then practice holding your eyes there.
You can also practice with ceiling tiles, floor tiles, anything that
repeats,  Just cross your eyes until adjacent things overlap, and that's
it.

It's best to start with a small image, like a small (4"x6") Coot window
with a simple object like a sulfate ion displayed.  Once you get the hang
if it, you can use larger windows.  It's totally worth learning to see in
cross-eye stereo if you look at structures.

I learned to see cross-eye as a kid from the 'Magic Eye' books.  I'm sure
there are great tutorials and examples on the web.
Nat

On Fri, Mar 2, 2018 at 11:39 AM, Xiao Lei  wrote:

> I never learn how to "cross eye", I may need to check if some video
> instruction online...
>
>
On Fri, Mar 2, 2018 at 11:28 AM, nathanielclar5 . 
wrote:

> You already have stereo built in, just turn on 'cross eyed stereo' and
> learn to cross your eyes!  It's brighter than any 3d monitor, requires no
> hardware, and no, it won't hurt your eyes (even for hours at a time)
>
> Nat
>
> On Fri, Mar 2, 2018 at 11:01 AM, Jim Fairman 
> wrote:
>
>> Daniel,
>>
>> To best of my knowledge, options for 3d stereo on Mac are limited to
>> Zalman:  https://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php
>> /Zalman_Stereo
>>
>> If you're willing to go to Linux or Windows, you can do an Nvidia Quadro
>> Card with a 120 or 144Hz monitor with a 3D Vision glasses kit.
>>
>> Cheers, Jim
>>
>> -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
>> Jim Fairman
>> Principal Scientist II
>> Roche Sequencing Solutions
>> 2841 Scott Blvd
>> <https://maps.google.com/?q=2841+Scott+Blvd+Santa+Clara,+CA+95050&entry=gmail&source=g>
>> Santa Clara, CA 95050
>> <https://maps.google.com/?q=2841+Scott+Blvd+Santa+Clara,+CA+95050&entry=gmail&source=g>
>> fairman@gmail.com jim.fair...@roche.com
>>
>>
>>
>>
>> 
>> --
>> Jim Fairman
>> C: 1-240-479-6575 <(240)%20479-6575>
>>
>> On Fri, Mar 2, 2018 at 8:24 AM, Daniel M. Himmel, Ph. D. <
>> danielmhim...@gmail.com> wrote:
>>
>>> I'm looking for some computer hardware advice.
>>> I have a MacBook Pro with a "Retina" screen and
>>> an Intel HD Graphics 4000 1536 MB graphics card,
>>> running OS X 10.11.16 ("El Capitan"), and I would
>>> like to view structures in 3-D in Coot.
>>>
>>> Which computer monitors and which 3-D glasses brands
>>> would allow me to view 3-D graphics in Coot?  Should I
>>> be going for dynamic 3-D glasses?
>>>
>>> -Daniel
>>>
>>>
>>
>

Re: [ccp4bb] 3-D Coot Capable Computer Monitor/Glasses for Mac Laptop?

[nathanielclar5 .]

You already have stereo built in, just turn on 'cross eyed stereo' and
learn to cross your eyes!  It's brighter than any 3d monitor, requires no
hardware, and no, it won't hurt your eyes (even for hours at a time)

Nat

On Fri, Mar 2, 2018 at 11:01 AM, Jim Fairman  wrote:

> Daniel,
>
> To best of my knowledge, options for 3d stereo on Mac are limited to
> Zalman:  https://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.
> php/Zalman_Stereo
>
> If you're willing to go to Linux or Windows, you can do an Nvidia Quadro
> Card with a 120 or 144Hz monitor with a 3D Vision glasses kit.
>
> Cheers, Jim
>
> -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
> Jim Fairman
> Principal Scientist II
> Roche Sequencing Solutions
> 2841 Scott Blvd
> 
> Santa Clara, CA 95050
> 
> fairman@gmail.com jim.fair...@roche.com
>
>
>
>
> --
> Jim Fairman
> C: 1-240-479-6575 <(240)%20479-6575>
>
> On Fri, Mar 2, 2018 at 8:24 AM, Daniel M. Himmel, Ph. D. <
> danielmhim...@gmail.com> wrote:
>
>> I'm looking for some computer hardware advice.
>> I have a MacBook Pro with a "Retina" screen and
>> an Intel HD Graphics 4000 1536 MB graphics card,
>> running OS X 10.11.16 ("El Capitan"), and I would
>> like to view structures in 3-D in Coot.
>>
>> Which computer monitors and which 3-D glasses brands
>> would allow me to view 3-D graphics in Coot?  Should I
>> be going for dynamic 3-D glasses?
>>
>> -Daniel
>>
>>
>

Re: [ccp4bb] metal chelation

[nathanielclar5 .]

Are you treating all your buffers with metal chelating resin?  Are you
washing all plasticware with EDTA and metal-free buffer prior to use?  How
are you quantifying your metal content, and what metal ions are
contaminating your sample?  You might be pulling out the metal ions, but
they get right back in as soon as you remove the chelators.  Metal ions are
present at trace levels in all water and chemicals (Zn is particularly
common).  You might need to 'soften up' the protein a little bit, we use a
pH 3.8 stripping protocol.  Denaturants may be required.  Time is also a
factor, extending your chelating step might help.  It's not trivial to make
app-enzymes, in my experience,
Nat



On Mon, May 19, 2014 at 12:20 PM, SUBSCRIBE CCP4BB Adam Brummett <
adam-brumm...@uiowa.edu> wrote:

> Hello All,
>
>   I apologize for the non-crystal related question. I am trying to get a
> fully metal-free apo enzyme. The 6x His construct is consistently purified
> with some metal (20-30%). I have attempted chelating away the metal with up
> to 30 mM EDTA and DFO and then dialyzing it away, but this has shown little
> to no effect. Any thoughts or recommendations would be greatly appreciated.
> Thanks.
>
> Adam
>

Re: [ccp4bb] Insect cell SF9 expression

[nathanielclar5 .]

Dhananjay,
Hopefully you are using the 'Bac to Bac' system, not the older version
'Bac-N-Blue'.  I'd recommend getting a high-titer virus to use as a
positive control for infection.  Baculovirus is challenging because before
you can check for protein expression, you need to do virology experiments.
 If you don't have a high-titer virus stock, you can't conclude anything
about your expression level.  Using a positive control virus will help you
learn to recognize the signs of infection.  Then you can judge if you
problem is related to virus amplification, or expression optimization.  If
I had to make a wild guess, I would say you probably don't have a
high-titer stock yet, as a result you don't see protein expression, and you
conclude that it is 'not working'.  Consider using the pIB vectors for
transient expression alongside with baculovirus, the transient experiments
are less complicated and offer a quicker readout.
Good luck,

Nat

PS:  One useful trick:  If you are struggling to boost the titer of a early
virus stock (ie. P0, P1), take a t25 flask of Sf9 cells (50-70% confluent),
remove the media, place 1 ml of your low-titer virus stock on the cells,
rock for 1 hr, remove virus and replace with fresh media.  Let that go for
3-5 days and hope you see signs of infection.  If not you probably don't
have any virus and need to repeat the transfection and/or miniprep.


On Fri, Dec 6, 2013 at 6:32 PM, dhananjay kulkarni <
dhananjay...@rediffmail.com> wrote:

> Dear all,
> Does any one has protocols for expression and making stable virus for SF-9
> Cell, I was trying
> with Invitrogen manual but somehow it is not working, any alternative
> protocols which works
> quickly? I am new to thins insect cell expression.
> your suggestion and protocols are really helpful
> Thanking in advance
>
>
>
> Dhananjay.K
> Post Doctoral Research Associate
> Department of Biochemistry
> Indian Institute of Science
> Bangalore
> India
>
> 
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