Re: [ccp4bb] off topic: ITC or Biacore

[DUMAS Philippe (UDS)]

Le Jeudi 9 Août 2012 09:55 CEST, rashmi panigrahi 
 a écrit:

Hello Rashi
There is no problem with ITC at "low temperature", apart for a likely slower 
binding and, hence, lower heat power signal.
Do not conclude that there is no binding if deltaH is close to 0 around 20-25 
°C. You may well have DeltaH = 0 at a given temperature, and yet the affinity 
constant is maximum at that temperature (by the Van't Hoff equation).
However, if you have no signal (DeltaH = 0) at several temperatures, this  
means that this peptide does not bind. It is very well established that DeltaCp 
= dDeltaH/dT is often large, which means that a 15°C variation is sufficient to 
get a significant change in deltaH.
Conclusion: do ITC at low temperature and try to increase as much as possible 
the concentrations of the protein and of the peptide.
Also, if the peptide is too hydrophobic, you can put it in the cell and the 
protein in the syringe.
Finally, you may also try to repeat CD in presence of various amounts of 
peptide and see if this results in Tm increase.
Philippe Dumas



> Hi All,
> I am working on a protein that has a Tm of 30 degrees, and by CD I have
> observed that the secondary structure is intact at 10 degrees and slowly
> starts unfolding at 20 degrees.
> Literature suggest that it binds to a 5 residue peptide. I tried doing ITC
> @ 25 and 20 degrees , there was no binding observed.
>
> Does any one have the experience of doing ITC or Biacore(SPR) at 10 or 15
> degrees?
> wondering that temperature is a problem as suggested by CD.
> thanks for your suggestions
>
>
> --
> rashmi

Re: [ccp4bb] loading maps in coot using EDS

[Paul Emsley]

On 09/08/12 02:40, Shya Biswas wrote:

Thanks, I think the problem is with the EDS server ...


Err, yeah, that's what I thought I said (with somewhat different words).

Hence the alternative path using the PDBe server.

On 09/08/12 06:39, Edward A. Berry wrote:


Maybe we need to take up a collection and buy the folks at BMC a faster
server and network upgrade.


My understanding is that the EDS is a volunteer/"spare time" project - 
that may not be their first priority.


FWIW, and all other things being equal, I'd rather rely on PDBe than EDS.

Paul.

[ccp4bb] calculation of cavities within crystal protein

[Danilo Belviso]

Dear all,

I am Dr. Danilo Belviso and I am working on a platinum-based inhibitor 
for matrix-metallo proteasis.


I have obtained the crystal structure of the adduct Pt/protein and, for 
me, would be very interesting to know the cavities of the protein within 
the crystal, namely by considering symmetry-related protein molecules 
around the asymmetric unit.


Do you know a software (or server) that carries out this calculation?

Best regards

Dr. Danilo Belviso

Re: [ccp4bb] Pisa application

[Edwin Pozharski]

On 08/08/2012 09:00 AM, Jose Duarte wrote:

To my knowledge PISA by itself is not able to do interface prediction


To my understanding PISA is not *intended* to do interface prediction

Re: [ccp4bb] off topic: ITC or Biacore

[Edwin Pozharski]

On 08/09/2012 03:55 AM, rashmi panigrahi wrote:
Does any one have the experience of doing ITC or Biacore(SPR) at 10 or 
15 degrees?


You can do ITC at any temperature your instrument allows, certainly no 
problems at 4oC.  To share a trick, at least on a MIcrocal instrument 
cooling down is very slow, and I found it useful to wash the cell with 
ice cold water to quickly get down to 4 degrees.

[ccp4bb] Various OSes and Crystallography

[Jacob Keller]

Dear List,

I guess this is somewhat of a perennial issue, but I am faced with choosing
an OS for a new computer, and am curious about benefits and drawbacks with
regard to crystallography. So far, I have been using windows, and have
found no limitations whatsoever, but then again, maybe I don't know what I
am missing. But, since so many folks out there use Macs, I am open to using
one. Are there any really reasonable arguments for preferring Mac over
windows (or linux) with regard to crystallography? What can Mac/Linux do
that windows cannot (especially considering that there is Cygwin)? What
wonderful features am I missing?

Jacob

-- 
***
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
email: j-kell...@northwestern.edu
***

Re: [ccp4bb] calculation of cavities within crystal protein

[Dr. Lorenzo Finci]

Danilo, 
The protein cavity can be analyzed utilizing the program Voidoo ( Kleywegt GJ, 
1994). This program uses an atomic-flattening algorithm based on a 
3-dimensional grid to locate and delineate different cavities. A Van Der Waals 
cavity can further be generated with a probe radius with a computed cavity grid 
using the highest number of grid points, and a contact and accessible surface 
can further be evaluated...
Relevant 
Resources:http://pelican.rsvs.ulaval.ca/mediawiki/index.php/Analysing_protein_cavities_using_VOIDOOhttp://binf.gmu.edu/ttaylor/DELAUNAY_PAPERS/chakravarty1.pdf
I hope this helps!lorenzo

Lorenzo Ihsan FInci, Ph.D.Postdoctoral Scientist, Wang LaboratoryHarvard 
Medical SchoolDana-Farber Cancer InstituteBoston, MA Peking UniversityThe 
College of Life SciencesBeijing, China


> Date: Thu, 9 Aug 2012 13:53:09 +0200
> From: danilo.belv...@ic.cnr.it
> Subject: [ccp4bb] calculation of cavities within crystal protein
> To: CCP4BB@JISCMAIL.AC.UK
> 
>  Dear all,
> 
>  I am Dr. Danilo Belviso and I am working on a platinum-based inhibitor 
>  for matrix-metallo proteasis.
> 
>  I have obtained the crystal structure of the adduct Pt/protein and, for 
>  me, would be very interesting to know the cavities of the protein within 
>  the crystal, namely by considering symmetry-related protein molecules 
>  around the asymmetric unit.
> 
>  Do you know a software (or server) that carries out this calculation?
> 
>  Best regards
> 
>  Dr. Danilo Belviso
  

Re: [ccp4bb] Various OSes and Crystallography

[Graeme Winter]

Dear Jacob,

I would anticipate more than one response to this. Here's one: it depends
on the context. For a laptop machine I would consider a macbook pro a
no-brainer (i.e. OS X), as you can get a lot of horsepower in a decent size
box which works very well. For a box sat on a desk, I would probably use
Linux (essentially down to cost.)

I have found linux with wireless networking etc. to be patchy, though more
recent experience with openSuSE was good. Crystallography software wise
there is little to choose between them, though of course with OS X there's
no messing around with e.g. Nvidia drivers.

I have to say though, I use XDS a lot, which removes the use of Windows /
cygwin from bring a runner. At every conference I attend there are a lot of
macs to be seen, so you will be able to expect decent support software
wise.

I wonder how many pro-windows responses you get. I don't expect many :o)

Cheerio,

Graeme

On 9 August 2012 14:55, Jacob Keller  wrote:

> Dear List,
>
> I guess this is somewhat of a perennial issue, but I am faced with
> choosing an OS for a new computer, and am curious about benefits and
> drawbacks with regard to crystallography. So far, I have been using
> windows, and have found no limitations whatsoever, but then again, maybe I
> don't know what I am missing. But, since so many folks out there use Macs,
> I am open to using one. Are there any really reasonable arguments for
> preferring Mac over windows (or linux) with regard to crystallography? What
> can Mac/Linux do that windows cannot (especially considering that there is
> Cygwin)? What wonderful features am I missing?
>
> Jacob
>
> --
> ***
> Jacob Pearson Keller
> Northwestern University
> Medical Scientist Training Program
> email: j-kell...@northwestern.edu
> ***
>

Re: [ccp4bb] Various OSes and Crystallography

[Nat Echols]

On Thu, Aug 9, 2012 at 6:55 AM, Jacob Keller
 wrote:
> one. Are there any really reasonable arguments for preferring Mac over
> windows (or linux) with regard to crystallography? What can Mac/Linux do
> that windows cannot (especially considering that there is Cygwin)? What
> wonderful features am I missing?

Mac vs. Linux: mostly a matter of personal preference, but I agree
with Graeme.  Most programs run equally well on either - with Coot a
partial exception, apparently due to problems with the X11
implementation (but once you get used to these, it's not a big deal).

Windows, on the other hand, simply doesn't support the full range of
modern crystallography software.  And in my experience, it has
crippling flaws that mean some programs will always work better on
Mac/Linux.  I wouldn't ever endorse trying to use Windows for serious
scientific computing unless you need to run an application that won't
work on any other OS, and as far as I know there isn't a single
(macromolecular) crystallography program that falls into this
category.

-Nat

Re: [ccp4bb] Various OSes and Crystallography

[Bosch, Juergen]

OS X is a triple OS
OS X, Unix, and Windows (via VM Ware Fusion or Parallels, or if you which 
directly booting into Windows)

@original poster,
you might regret the step to Mac - noticing what you have missed all the time 
on the other platform :-)
I don't think Windows has a Beachball, that's a nifty feature of OS X - you've 
been missing that one for sure.

Jürgen

P.S. I'm running Fusion as there is one piece of software only for Windows, not 
even for Linux called Scrubber

On Aug 9, 2012, at 10:58 AM, Nat Echols wrote:

On Thu, Aug 9, 2012 at 6:55 AM, Jacob Keller
mailto:j-kell...@fsm.northwestern.edu>> wrote:
one. Are there any really reasonable arguments for preferring Mac over
windows (or linux) with regard to crystallography? What can Mac/Linux do
that windows cannot (especially considering that there is Cygwin)? What
wonderful features am I missing?

Mac vs. Linux: mostly a matter of personal preference, but I agree
with Graeme.  Most programs run equally well on either - with Coot a
partial exception, apparently due to problems with the X11
implementation (but once you get used to these, it's not a big deal).

Windows, on the other hand, simply doesn't support the full range of
modern crystallography software.  And in my experience, it has
crippling flaws that mean some programs will always work better on
Mac/Linux.  I wouldn't ever endorse trying to use Windows for serious
scientific computing unless you need to run an application that won't
work on any other OS, and as far as I know there isn't a single
(macromolecular) crystallography program that falls into this
category.

-Nat

..
Jürgen Bosch
Johns Hopkins University
Bloomberg School of Public Health
Department of Biochemistry & Molecular Biology
Johns Hopkins Malaria Research Institute
615 North Wolfe Street, W8708
Baltimore, MD 21205
Office: +1-410-614-4742
Lab:  +1-410-614-4894
Fax:  +1-410-955-2926
http://lupo.jhsph.edu

Re: [ccp4bb] Various OSes and Crystallography

[Andreas Förster]

Mac OSX because of Time Machine, Illustrator and crystallographic 
software in one happy box.  XP on a Virtual Box for emergencies (SAXS, 
AUC and ITC programs).


Though with Microsoft and Apple both pushing towards gestures, fingertip 
interaction and tablets, Linux will be the only option for laptops in 
two/three years' time.


Mind that if you buy a MacBook, there's only one (hefty 15") model 
without a mirror-coated screen.



Andreas



On 09/08/2012 3:58, Nat Echols wrote:

On Thu, Aug 9, 2012 at 6:55 AM, Jacob Keller
 wrote:

one. Are there any really reasonable arguments for preferring Mac over
windows (or linux) with regard to crystallography? What can Mac/Linux do
that windows cannot (especially considering that there is Cygwin)? What
wonderful features am I missing?


Mac vs. Linux: mostly a matter of personal preference, but I agree
with Graeme.  Most programs run equally well on either - with Coot a
partial exception, apparently due to problems with the X11
implementation (but once you get used to these, it's not a big deal).

Windows, on the other hand, simply doesn't support the full range of
modern crystallography software.  And in my experience, it has
crippling flaws that mean some programs will always work better on
Mac/Linux.  I wouldn't ever endorse trying to use Windows for serious
scientific computing unless you need to run an application that won't
work on any other OS, and as far as I know there isn't a single
(macromolecular) crystallography program that falls into this
category.

-Nat

Re: [ccp4bb] Various OSes and Crystallography

[Quentin Delettre]

Le 09/08/2012 16:58, Nat Echols a écrit :

On Thu, Aug 9, 2012 at 6:55 AM, Jacob Keller
 wrote:

one. Are there any really reasonable arguments for preferring Mac over
windows (or linux) with regard to crystallography? What can Mac/Linux do
that windows cannot (especially considering that there is Cygwin)? What
wonderful features am I missing?

Mac vs. Linux: mostly a matter of personal preference, but I agree
with Graeme.  Most programs run equally well on either - with Coot a
partial exception, apparently due to problems with the X11
implementation (but once you get used to these, it's not a big deal).

Windows, on the other hand, simply doesn't support the full range of
modern crystallography software.  And in my experience, it has
crippling flaws that mean some programs will always work better on
Mac/Linux.  I wouldn't ever endorse trying to use Windows for serious
scientific computing unless you need to run an application that won't
work on any other OS, and as far as I know there isn't a single
(macromolecular) crystallography program that falls into this
category.

-Nat




I have seen that in the last Mac Os, X11 have been removed... But can 
still be used with some package installation.

Re: [ccp4bb] Various OSes and Crystallography

[Nat Echols]

On Thu, Aug 9, 2012 at 8:14 AM, Quentin Delettre  wrote:
> I have seen that in the last Mac Os, X11 have been removed... But can still
> be used with some package installation.

I guess it isn't distributed with the OS any more - but it is still available:

http://xquartz.macosforge.org/landing/

-Nat

Re: [ccp4bb] Various OSes and Crystallography

[Jacob Keller]

Are there no closet windows-users on this list to respond? Shall we have a
coming-out day?

Question--do macs have multiple-button mice? Last I checked they had only
one button, which seemed almost criminal.

JPK

On Thu, Aug 9, 2012 at 10:14 AM, Quentin Delettre  wrote:

> Le 09/08/2012 16:58, Nat Echols a écrit :
>
>  On Thu, Aug 9, 2012 at 6:55 AM, Jacob Keller
>> >
>> wrote:
>>
>>> one. Are there any really reasonable arguments for preferring Mac over
>>> windows (or linux) with regard to crystallography? What can Mac/Linux do
>>> that windows cannot (especially considering that there is Cygwin)? What
>>> wonderful features am I missing?
>>>
>> Mac vs. Linux: mostly a matter of personal preference, but I agree
>> with Graeme.  Most programs run equally well on either - with Coot a
>> partial exception, apparently due to problems with the X11
>> implementation (but once you get used to these, it's not a big deal).
>>
>> Windows, on the other hand, simply doesn't support the full range of
>> modern crystallography software.  And in my experience, it has
>> crippling flaws that mean some programs will always work better on
>> Mac/Linux.  I wouldn't ever endorse trying to use Windows for serious
>> scientific computing unless you need to run an application that won't
>> work on any other OS, and as far as I know there isn't a single
>> (macromolecular) crystallography program that falls into this
>> category.
>>
>> -Nat
>>
>>
>>
> I have seen that in the last Mac Os, X11 have been removed... But can
> still be used with some package installation.
>



-- 
***
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
email: j-kell...@northwestern.edu
***

Re: [ccp4bb] Various OSes and Crystallography

[Antony Oliver]

Mountain Lion does not come with X11 preinstalled.  However, as Nat
states, you can very easily install Xquartz
Thus far, all of the crystallography programs that were working under Snow
Leopard and Lion are still working on my laptop with Mountain Lion.

-Tony

---
Dr Antony W Oliver

Senior Research Fellow
CR-UK DNA Repair Enzymes Group
Genome Damage and Stability Centre
Science Park Road
University of Sussex
Falmer, Brighton, BN1 9RQ

email: antony.oli...@sussex.ac.uk
tel (office): +44 (0)1273 678349
tel (lab): +44 (0)1273 677512






On 8/9/12 4:25 PM, "Nat Echols"  wrote:

>On Thu, Aug 9, 2012 at 8:14 AM, Quentin Delettre  wrote:
>> I have seen that in the last Mac Os, X11 have been removed... But can
>>still
>> be used with some package installation.
>
>I guess it isn't distributed with the OS any more - but it is still
>available:
>
>http://xquartz.macosforge.org/landing/
>
>-Nat

Re: [ccp4bb] Various OSes and Crystallography

[Ben Eisenbraun]

On Thu, Aug 09, 2012 at 10:29:10AM -0500, Jacob Keller wrote:
> Question--do macs have multiple-button mice? Last I checked they had only
> one button, which seemed almost criminal.

You're about 7 years behind the times on that one:

http://en.wikipedia.org/wiki/Apple_Mighty_Mouse

-b

--
| Ben Eisenbraun
| SBGrid Consortium  | http://sbgrid.org   |
| Harvard Medical School | http://hms.harvard.edu  |

Re: [ccp4bb] Various OSes and Crystallography

[Bosch, Juergen]

you can use your favourite 24 button mice from windows on a Mac as long as it 
has USB.
And I highly recommend Bill Scott's Crystallography on OS X website.

Jürgen

On Aug 9, 2012, at 11:29 AM, Jacob Keller wrote:

Are there no closet windows-users on this list to respond? Shall we have a 
coming-out day?

Question--do macs have multiple-button mice? Last I checked they had only one 
button, which seemed almost criminal.

JPK

On Thu, Aug 9, 2012 at 10:14 AM, Quentin Delettre 
mailto:q...@hotmail.fr>> wrote:
Le 09/08/2012 16:58, Nat Echols a écrit :

On Thu, Aug 9, 2012 at 6:55 AM, Jacob Keller
mailto:j-kell...@fsm.northwestern.edu>> wrote:
one. Are there any really reasonable arguments for preferring Mac over
windows (or linux) with regard to crystallography? What can Mac/Linux do
that windows cannot (especially considering that there is Cygwin)? What
wonderful features am I missing?
Mac vs. Linux: mostly a matter of personal preference, but I agree
with Graeme.  Most programs run equally well on either - with Coot a
partial exception, apparently due to problems with the X11
implementation (but once you get used to these, it's not a big deal).

Windows, on the other hand, simply doesn't support the full range of
modern crystallography software.  And in my experience, it has
crippling flaws that mean some programs will always work better on
Mac/Linux.  I wouldn't ever endorse trying to use Windows for serious
scientific computing unless you need to run an application that won't
work on any other OS, and as far as I know there isn't a single
(macromolecular) crystallography program that falls into this
category.

-Nat



I have seen that in the last Mac Os, X11 have been removed... But can still be 
used with some package installation.



--
***
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
email: j-kell...@northwestern.edu
***

..
Jürgen Bosch
Johns Hopkins University
Bloomberg School of Public Health
Department of Biochemistry & Molecular Biology
Johns Hopkins Malaria Research Institute
615 North Wolfe Street, W8708
Baltimore, MD 21205
Office: +1-410-614-4742
Lab:  +1-410-614-4894
Fax:  +1-410-955-2926
http://lupo.jhsph.edu

Re: [ccp4bb] Various OSes and Crystallography

[Luca Jovine]

Yes, you can define 3 buttons on a MagicMouse with this free software:

http://magicprefs.com/

or simply attach a mouse with 3 real buttons...

-Luca


Luca Jovine, Ph.D.
Assistant Professor & EMBO Young Investigator
Karolinska Institutet
Department of Biosciences and Nutrition & Center for Biosciences
Hälsovägen 7, SE-141 83 Huddinge, Sweden
Voice: +46.(0)8.524-81136  FAX: +46.(0)8.6081-501
E-mail: luca.jov...@ki.se
W3: http://jovinelab.org


On Aug 9, 2012, at 17:29 , Jacob Keller wrote:

> Are there no closet windows-users on this list to respond? Shall we have a 
> coming-out day?
> 
> Question--do macs have multiple-button mice? Last I checked they had only one 
> button, which seemed almost criminal.
> 
> JPK
> 
> On Thu, Aug 9, 2012 at 10:14 AM, Quentin Delettre  wrote:
> Le 09/08/2012 16:58, Nat Echols a écrit :
> 
> On Thu, Aug 9, 2012 at 6:55 AM, Jacob Keller
>  wrote:
> one. Are there any really reasonable arguments for preferring Mac over
> windows (or linux) with regard to crystallography? What can Mac/Linux do
> that windows cannot (especially considering that there is Cygwin)? What
> wonderful features am I missing?
> Mac vs. Linux: mostly a matter of personal preference, but I agree
> with Graeme.  Most programs run equally well on either - with Coot a
> partial exception, apparently due to problems with the X11
> implementation (but once you get used to these, it's not a big deal).
> 
> Windows, on the other hand, simply doesn't support the full range of
> modern crystallography software.  And in my experience, it has
> crippling flaws that mean some programs will always work better on
> Mac/Linux.  I wouldn't ever endorse trying to use Windows for serious
> scientific computing unless you need to run an application that won't
> work on any other OS, and as far as I know there isn't a single
> (macromolecular) crystallography program that falls into this
> category.
> 
> -Nat
> 
> 
> 
> I have seen that in the last Mac Os, X11 have been removed... But can still 
> be used with some package installation.
> 
> 
> 
> -- 
> ***
> Jacob Pearson Keller
> Northwestern University
> Medical Scientist Training Program
> email: j-kell...@northwestern.edu
> ***

Re: [ccp4bb] Various OSes and Crystallography

[Colbert, Christopher]

How critical is stereo visualization for you?  Macs are great with Zalman, but 
have fallen behind (again) with active stereo (ie. shutter glasses).

I will disclaim that I haven't revisited stereo visualization in about 1 year 
so my info is dated.

HTH,

Chris


From: Jacob Keller 
mailto:j-kell...@fsm.northwestern.edu>>
Reply-To: Jacob Keller 
mailto:j-kell...@fsm.northwestern.edu>>
Date: Thursday, August 9, 2012 10:29 AM
To: "CCP4BB@JISCMAIL.AC.UK" 
mailto:CCP4BB@JISCMAIL.AC.UK>>
Subject: Re: [ccp4bb] Various OSes and Crystallography

Are there no closet windows-users on this list to respond? Shall we have a 
coming-out day?

Question--do macs have multiple-button mice? Last I checked they had only one 
button, which seemed almost criminal.

JPK

On Thu, Aug 9, 2012 at 10:14 AM, Quentin Delettre 
mailto:q...@hotmail.fr>> wrote:
Le 09/08/2012 16:58, Nat Echols a écrit :

On Thu, Aug 9, 2012 at 6:55 AM, Jacob Keller
mailto:j-kell...@fsm.northwestern.edu>> wrote:
one. Are there any really reasonable arguments for preferring Mac over
windows (or linux) with regard to crystallography? What can Mac/Linux do
that windows cannot (especially considering that there is Cygwin)? What
wonderful features am I missing?
Mac vs. Linux: mostly a matter of personal preference, but I agree
with Graeme.  Most programs run equally well on either - with Coot a
partial exception, apparently due to problems with the X11
implementation (but once you get used to these, it's not a big deal).

Windows, on the other hand, simply doesn't support the full range of
modern crystallography software.  And in my experience, it has
crippling flaws that mean some programs will always work better on
Mac/Linux.  I wouldn't ever endorse trying to use Windows for serious
scientific computing unless you need to run an application that won't
work on any other OS, and as far as I know there isn't a single
(macromolecular) crystallography program that falls into this
category.

-Nat



I have seen that in the last Mac Os, X11 have been removed... But can still be 
used with some package installation.



--
***
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
email: j-kell...@northwestern.edu
***

Re: [ccp4bb] Various OSes and Crystallography

[Bosch, Juergen]

Can you explain to me what the difference in stereo is ?
I like my Zalman's and the visual stereo effect is pretty impressive. I have no 
idea if active stereo would improve the perception of the 3D effect or not.

Jürgen

On Aug 9, 2012, at 11:47 AM, Colbert, Christopher wrote:

How critical is stereo visualization for you?  Macs are great with Zalman, but 
have fallen behind (again) with active stereo (ie. shutter glasses).

I will disclaim that I haven't revisited stereo visualization in about 1 year 
so my info is dated.

HTH,

Chris


From: Jacob Keller 
mailto:j-kell...@fsm.northwestern.edu>>
Reply-To: Jacob Keller 
mailto:j-kell...@fsm.northwestern.edu>>
Date: Thursday, August 9, 2012 10:29 AM
To: "CCP4BB@JISCMAIL.AC.UK" 
mailto:CCP4BB@JISCMAIL.AC.UK>>
Subject: Re: [ccp4bb] Various OSes and Crystallography

Are there no closet windows-users on this list to respond? Shall we have a 
coming-out day?

Question--do macs have multiple-button mice? Last I checked they had only one 
button, which seemed almost criminal.

JPK

On Thu, Aug 9, 2012 at 10:14 AM, Quentin Delettre 
mailto:q...@hotmail.fr>> wrote:
Le 09/08/2012 16:58, Nat Echols a écrit :

On Thu, Aug 9, 2012 at 6:55 AM, Jacob Keller
mailto:j-kell...@fsm.northwestern.edu>> wrote:
one. Are there any really reasonable arguments for preferring Mac over
windows (or linux) with regard to crystallography? What can Mac/Linux do
that windows cannot (especially considering that there is Cygwin)? What
wonderful features am I missing?
Mac vs. Linux: mostly a matter of personal preference, but I agree
with Graeme.  Most programs run equally well on either - with Coot a
partial exception, apparently due to problems with the X11
implementation (but once you get used to these, it's not a big deal).

Windows, on the other hand, simply doesn't support the full range of
modern crystallography software.  And in my experience, it has
crippling flaws that mean some programs will always work better on
Mac/Linux.  I wouldn't ever endorse trying to use Windows for serious
scientific computing unless you need to run an application that won't
work on any other OS, and as far as I know there isn't a single
(macromolecular) crystallography program that falls into this
category.

-Nat



I have seen that in the last Mac Os, X11 have been removed... But can still be 
used with some package installation.



--
***
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
email: j-kell...@northwestern.edu
***

..
Jürgen Bosch
Johns Hopkins University
Bloomberg School of Public Health
Department of Biochemistry & Molecular Biology
Johns Hopkins Malaria Research Institute
615 North Wolfe Street, W8708
Baltimore, MD 21205
Office: +1-410-614-4742
Lab:  +1-410-614-4894
Fax:  +1-410-955-2926
http://lupo.jhsph.edu

Re: [ccp4bb] Various OSes and Crystallography

[Colbert, Christopher]

Hi Jurgen,

I am using the term active stereo to refer to shutter glass stereo.  This was 
originally implemented with CRT monitors and more recently with LCD monitors 
and Nvidia 3D vision.  It is usually implemented using OpenGL.

The advantage of active stereo over Zalman stereo is that the text in the 
window or on the screen is not half resolution when viewing through the stereo 
glasses.  Some may argue about the stereoscopic effect, but I find them both to 
be quite useful.

Chris


From: , Juergen mailto:jubo...@jhsph.edu>>
Date: Thursday, August 9, 2012 10:51 AM
To: Christopher Colbert 
mailto:christopher.colb...@ndsu.edu>>
Cc: "CCP4BB@JISCMAIL.AC.UK" 
mailto:CCP4BB@JISCMAIL.AC.UK>>
Subject: Re: [ccp4bb] Various OSes and Crystallography

Can you explain to me what the difference in stereo is ?
I like my Zalman's and the visual stereo effect is pretty impressive. I have no 
idea if active stereo would improve the perception of the 3D effect or not.

Jürgen

On Aug 9, 2012, at 11:47 AM, Colbert, Christopher wrote:

How critical is stereo visualization for you?  Macs are great with Zalman, but 
have fallen behind (again) with active stereo (ie. shutter glasses).

I will disclaim that I haven't revisited stereo visualization in about 1 year 
so my info is dated.

HTH,

Chris


From: Jacob Keller 
mailto:j-kell...@fsm.northwestern.edu>>
Reply-To: Jacob Keller 
mailto:j-kell...@fsm.northwestern.edu>>
Date: Thursday, August 9, 2012 10:29 AM
To: "CCP4BB@JISCMAIL.AC.UK" 
mailto:CCP4BB@JISCMAIL.AC.UK>>
Subject: Re: [ccp4bb] Various OSes and Crystallography

Are there no closet windows-users on this list to respond? Shall we have a 
coming-out day?

Question--do macs have multiple-button mice? Last I checked they had only one 
button, which seemed almost criminal.

JPK

On Thu, Aug 9, 2012 at 10:14 AM, Quentin Delettre 
mailto:q...@hotmail.fr>> wrote:
Le 09/08/2012 16:58, Nat Echols a écrit :

On Thu, Aug 9, 2012 at 6:55 AM, Jacob Keller
mailto:j-kell...@fsm.northwestern.edu>> wrote:
one. Are there any really reasonable arguments for preferring Mac over
windows (or linux) with regard to crystallography? What can Mac/Linux do
that windows cannot (especially considering that there is Cygwin)? What
wonderful features am I missing?
Mac vs. Linux: mostly a matter of personal preference, but I agree
with Graeme.  Most programs run equally well on either - with Coot a
partial exception, apparently due to problems with the X11
implementation (but once you get used to these, it's not a big deal).

Windows, on the other hand, simply doesn't support the full range of
modern crystallography software.  And in my experience, it has
crippling flaws that mean some programs will always work better on
Mac/Linux.  I wouldn't ever endorse trying to use Windows for serious
scientific computing unless you need to run an application that won't
work on any other OS, and as far as I know there isn't a single
(macromolecular) crystallography program that falls into this
category.

-Nat



I have seen that in the last Mac Os, X11 have been removed... But can still be 
used with some package installation.



--
***
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
email: j-kell...@northwestern.edu
***

..
Jürgen Bosch
Johns Hopkins University
Bloomberg School of Public Health
Department of Biochemistry & Molecular Biology
Johns Hopkins Malaria Research Institute
615 North Wolfe Street, W8708
Baltimore, MD 21205
Office: +1-410-614-4742
Lab:  +1-410-614-4894
Fax:  +1-410-955-2926
http://lupo.jhsph.edu

Re: [ccp4bb] Various OSes and Crystallography

[Bosch, Juergen]

Thanks Chris,

I really prefer the 30g Zalman glasses versus 400 g shutter glasses that have 
troubles (at least the old ones) when people are sitting next to each other in 
terms of interference of the signal.

Half resolution ? 1600 x 1040 on a Zalman I think is full but I have not 
counted the pixels when looking at them and I might be wrong.

Dr. Coot might know more about that what happens when turning on stereo on 
Zalmans.

Jürgen

On Aug 9, 2012, at 12:10 PM, Colbert, Christopher wrote:

Hi Jurgen,

I am using the term active stereo to refer to shutter glass stereo.  This was 
originally implemented with CRT monitors and more recently with LCD monitors 
and Nvidia 3D vision.  It is usually implemented using OpenGL.

The advantage of active stereo over Zalman stereo is that the text in the 
window or on the screen is not half resolution when viewing through the stereo 
glasses.  Some may argue about the stereoscopic effect, but I find them both to 
be quite useful.

Chris


From: , Juergen mailto:jubo...@jhsph.edu>>
Date: Thursday, August 9, 2012 10:51 AM
To: Christopher Colbert 
mailto:christopher.colb...@ndsu.edu>>
Cc: "CCP4BB@JISCMAIL.AC.UK" 
mailto:CCP4BB@JISCMAIL.AC.UK>>
Subject: Re: [ccp4bb] Various OSes and Crystallography

Can you explain to me what the difference in stereo is ?
I like my Zalman's and the visual stereo effect is pretty impressive. I have no 
idea if active stereo would improve the perception of the 3D effect or not.

Jürgen

On Aug 9, 2012, at 11:47 AM, Colbert, Christopher wrote:

How critical is stereo visualization for you?  Macs are great with Zalman, but 
have fallen behind (again) with active stereo (ie. shutter glasses).

I will disclaim that I haven't revisited stereo visualization in about 1 year 
so my info is dated.

HTH,

Chris


From: Jacob Keller 
mailto:j-kell...@fsm.northwestern.edu>>
Reply-To: Jacob Keller 
mailto:j-kell...@fsm.northwestern.edu>>
Date: Thursday, August 9, 2012 10:29 AM
To: "CCP4BB@JISCMAIL.AC.UK" 
mailto:CCP4BB@JISCMAIL.AC.UK>>
Subject: Re: [ccp4bb] Various OSes and Crystallography

Are there no closet windows-users on this list to respond? Shall we have a 
coming-out day?

Question--do macs have multiple-button mice? Last I checked they had only one 
button, which seemed almost criminal.

JPK

On Thu, Aug 9, 2012 at 10:14 AM, Quentin Delettre 
mailto:q...@hotmail.fr>> wrote:
Le 09/08/2012 16:58, Nat Echols a écrit :

On Thu, Aug 9, 2012 at 6:55 AM, Jacob Keller
mailto:j-kell...@fsm.northwestern.edu>> wrote:
one. Are there any really reasonable arguments for preferring Mac over
windows (or linux) with regard to crystallography? What can Mac/Linux do
that windows cannot (especially considering that there is Cygwin)? What
wonderful features am I missing?
Mac vs. Linux: mostly a matter of personal preference, but I agree
with Graeme.  Most programs run equally well on either - with Coot a
partial exception, apparently due to problems with the X11
implementation (but once you get used to these, it's not a big deal).

Windows, on the other hand, simply doesn't support the full range of
modern crystallography software.  And in my experience, it has
crippling flaws that mean some programs will always work better on
Mac/Linux.  I wouldn't ever endorse trying to use Windows for serious
scientific computing unless you need to run an application that won't
work on any other OS, and as far as I know there isn't a single
(macromolecular) crystallography program that falls into this
category.

-Nat



I have seen that in the last Mac Os, X11 have been removed... But can still be 
used with some package installation.



--
***
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
email: j-kell...@northwestern.edu
***

..
Jürgen Bosch
Johns Hopkins University
Bloomberg School of Public Health
Department of Biochemistry & Molecular Biology
Johns Hopkins Malaria Research Institute
615 North Wolfe Street, W8708
Baltimore, MD 21205
Office: +1-410-614-4742
Lab:  +1-410-614-4894
Fax:  +1-410-955-2926
http://lupo.jhsph.edu





..
Jürgen Bosch
Johns Hopkins University
Bloomberg School of Public Health
Department of Biochemistry & Molecular Biology
Johns Hopkins Malaria Research Institute
615 North Wolfe Street, W8708
Baltimore, MD 21205
Office: +1-410-614-4742
Lab:  +1-410-614-4894
Fax:  +1-410-955-2926
http://lupo.jhsph.edu

Re: [ccp4bb] Various OSes and Crystallography

[Fred. Vellieux]

Hi,

To make it short:

If you want a computer you wish to bring home so that you can do plenty of
things (i.e. not crystallography-related in addition to crystallography):
Windows because you can edit videos easily, or play games, or (I don't)
because there is plenty of (free) software available. But Windows is 'the'
target for (personal computer) malware as well because there are many such
computers around. I.e. a good target for the malware developers.

If you wish to have all crystallographic software running, then Unices are
more adequate. Some people prefer Linux (on Intel or AMD...), some people
prefer OSX (BSD-based Unix), i.e. Apple (Intel as well). The latter is
more expensive than the former.

So if you wish to have fun at home as well as work, go for Windows. If you
want to have all crystallographic software running then one of the 2
unices, if your budget is limited then you'll want to have a PC running
Linux.

F.

> Dear List,
>
> I guess this is somewhat of a perennial issue, but I am faced with
> choosing
> an OS for a new computer, and am curious about benefits and drawbacks with
> regard to crystallography. So far, I have been using windows, and have
> found no limitations whatsoever, but then again, maybe I don't know what I
> am missing. But, since so many folks out there use Macs, I am open to
> using
> one. Are there any really reasonable arguments for preferring Mac over
> windows (or linux) with regard to crystallography? What can Mac/Linux do
> that windows cannot (especially considering that there is Cygwin)? What
> wonderful features am I missing?
>
> Jacob
>
> --
> ***
> Jacob Pearson Keller
> Northwestern University
> Medical Scientist Training Program
> email: j-kell...@northwestern.edu
> ***
>


-- 
F.M.D. Vellieux (B.Sc., Ph.D., hdr)
IBS / ELMA
41 rue Jules Horowitz
38027 Grenoble Cedex 01
France
Tel: +33 438789605
Fax: +33 438785494

[ccp4bb] Problem in REFMAC TLS refinement with CCP4 6.3.0

[Huiying Li]

We have installed the new version of CCP4 6.3.0 (REFMAC 5.7.0029) lately. 
I noticed that the "TLS & restrained refinement" in the new version somehow 
messed up the B factor calculation, many atoms with the residual B factor 
down to the minimum (2.0) value in the output PDB file, and both the 
resulting R (Rfree) and RMS were high. However, the identical refinement 
using the older version CCP4 (6.2.0, REFMAC 5.6.0117) ran okay with nice 
geometries and low R (Rfree).



I am not sure if this problem is due to our installation (configuration) 
or more generic with the new version. Please advice.


Best,
Huiying

--
Huiying Li, Ph. D
Department of Molecular Biology and Biochemistry
Natural Sciences I, Rm 2443
University of California at Irvine
Irvine, CA 92697, USA
Tel: 949-824-4322(or -1953);  Fax: 949-824-3280
email: h...@uci.edu

[ccp4bb] molecular models

[Sickmier, Allen]

I was wondering if anyone knows where to get the Labquip/Nicholson molecular 
models.  The Labquip website was last updated in 2001 and no one is answering 
the emails.  We have another brand models but would prefer the 
Labquip/Nicholson molecular models.



Allen Sickmier,  Ph.D.
Senior Scientist
Amgen Inc
1 Amgen Center Dr.
Thousand Oaks, CA 91320-1789

Re: [ccp4bb] Question on stereo monitor: LG D2342P-PN

[Zhijie Li]

Hello,

We have received our LG D2342P-PN monitor yesterday and did a little test. 
Simply put, it works perfectly for stereo display on COOT and Chimera. We 
didn't test pymol, as the 0.99 version doesn't have support for the Zalman 
mode. But the educational version of the new pymol seems to have the Zalman 
mode.


Here I list some observations:
1. We had a Zalman ZM-M215W monitor shortly before this one. The two models 
are quite comparable to each other.
2. Both the Zalman and the LG D2342P emit circular polarized light. So 
simple linear polarization films won't be able to separate the light from 
the odd and even lines. But the 3D stereo cinemas are of the same type. My 
3D stereo glasses from a cinema is about 45 degrees counter-clockwise off 
the LG glasses' axes, but the left and right images are not switched. So it 
can work OK with the LG monitors, with only a little ghost image, and if I 
tilt my head to the left then it is as clean as the LG glasses. On the other 
hand, except for the two pairs of glasses came with the monitor, I haven't 
figured out where to buy extra glasses yet.
3. Both Zalman and LG D2342P have wide horizontal viewing angles, but 
limited vertical viewing angle (maybe 20-40 degrees) for the stereo display 
(2D display is not limited). This is probably due to that there is a 
distance between the polarizer layer and the pixel layer so that if viewed 
from an angle above or below, some light from one row of pixels would have 
to travel through the line of polarizer one row above or below and then the 
polarization is mixed - just my guess.
4. Both Zalman and LG D2342P can work on any computer with a VGA or DVI 
output and have nothing to do with the operating systems. No special driver 
is needed. We tested them on our desktops and laptops, in Linux, real and VM 
Windows. They worked just fine in all cases.


Regards,

Zhijie

--
From: "William G. Scott" 
Sent: Tuesday, July 24, 2012 10:52 AM
To: 
Subject: Re: [ccp4bb] Question on stereo monitor: LG D2342P-PN


Dear Zhijie:

I saw this for under $300 at Amazon's Showroom and wondered the same 
thing.  I can verify that the LG TV will work with coot, etc., as long as 
you turn OFF all stereographic processing and allow the software to do the 
work.  There is an extremely detailed review of this at 
http://www.amazon.com/LG-D2342P-PN-23-Inch-Widescreen-Passive/dp/B004WK3R4U/ref=cm_cr-mr-title 
by Bill Costa (he gives his email address at the end).  He seems to 
suggest that the 3D glasses for the LG TV are not compatible with this, 
which left me scratching my head.


Having said that, I'll bet it will work fine.  If you can get it from Best 
Buy for under $300 and return it within 30 days for a full refund, it 
might be worth it.


Either way, let us know.

Bill




William G. Scott
Professor
Department of Chemistry and Biochemistry
and The Center for the Molecular Biology of RNA
228 Sinsheimer Laboratories
University of California at Santa Cruz
Santa Cruz, California 95064
USA



On Jul 23, 2012, at 11:42 AM, Zhijie Li wrote:


Dear CCP4BBers:

Sorry to bring up this highly repeated topic again. After some internet 
research, we are about to make the commitment to buy an LG D2342P-PN for 
setting up a stereo system. I would like to have a final confirmation 
from someone with real life experience that this model does work with 
COOT and Chimera the same way as the Zalman monitors. Thanks in advance.


Zhijie 

Re: [ccp4bb] Question on stereo monitor: LG D2342P-PN

[Scott Thomas Walsh]

Hi Zhijie,

Is the LG D2342P-PN screen glossy or anti-glare surface?  The Zalman ZM-M240W I 
have is
glossy.

Thank you.

Scott


Scott T. R. Walsh, Ph.D.
Assistant Professor
University of Maryland
IBBR/CBMG
Rm 3127E CARB-2
9600 Gudelsky Drive
Rockville, MD 20850
email: swals...@umd.edu
phone: (240) 314-6478
fax: (240) 314-6255

On Aug 9, 2012, at 2:26 PM, Zhijie Li wrote:

Hello,

We have received our LG D2342P-PN monitor yesterday and did a little test.
Simply put, it works perfectly for stereo display on COOT and Chimera. We
didn't test pymol, as the 0.99 version doesn't have support for the Zalman
mode. But the educational version of the new pymol seems to have the Zalman
mode.

Here I list some observations:
1. We had a Zalman ZM-M215W monitor shortly before this one. The two models
are quite comparable to each other.
2. Both the Zalman and the LG D2342P emit circular polarized light. So
simple linear polarization films won't be able to separate the light from
the odd and even lines. But the 3D stereo cinemas are of the same type. My
3D stereo glasses from a cinema is about 45 degrees counter-clockwise off
the LG glasses' axes, but the left and right images are not switched. So it
can work OK with the LG monitors, with only a little ghost image, and if I
tilt my head to the left then it is as clean as the LG glasses. On the other
hand, except for the two pairs of glasses came with the monitor, I haven't
figured out where to buy extra glasses yet.
3. Both Zalman and LG D2342P have wide horizontal viewing angles, but
limited vertical viewing angle (maybe 20-40 degrees) for the stereo display
(2D display is not limited). This is probably due to that there is a
distance between the polarizer layer and the pixel layer so that if viewed
from an angle above or below, some light from one row of pixels would have
to travel through the line of polarizer one row above or below and then the
polarization is mixed - just my guess.
4. Both Zalman and LG D2342P can work on any computer with a VGA or DVI
output and have nothing to do with the operating systems. No special driver
is needed. We tested them on our desktops and laptops, in Linux, real and VM
Windows. They worked just fine in all cases.

Regards,

Zhijie

--
From: "William G. Scott" mailto:wgsc...@ucsc.edu>>
Sent: Tuesday, July 24, 2012 10:52 AM
To: mailto:CCP4BB@JISCMAIL.AC.UK>>
Subject: Re: [ccp4bb] Question on stereo monitor: LG D2342P-PN

Dear Zhijie:

I saw this for under $300 at Amazon's Showroom and wondered the same
thing.  I can verify that the LG TV will work with coot, etc., as long as
you turn OFF all stereographic processing and allow the software to do the
work.  There is an extremely detailed review of this at
http://www.amazon.com/LG-D2342P-PN-23-Inch-Widescreen-Passive/dp/B004WK3R4U/ref=cm_cr-mr-title
by Bill Costa (he gives his email address at the end).  He seems to
suggest that the 3D glasses for the LG TV are not compatible with this,
which left me scratching my head.

Having said that, I'll bet it will work fine.  If you can get it from Best
Buy for under $300 and return it within 30 days for a full refund, it
might be worth it.

Either way, let us know.

Bill




William G. Scott
Professor
Department of Chemistry and Biochemistry
and The Center for the Molecular Biology of RNA
228 Sinsheimer Laboratories
University of California at Santa Cruz
Santa Cruz, California 95064
USA



On Jul 23, 2012, at 11:42 AM, Zhijie Li wrote:

Dear CCP4BBers:

Sorry to bring up this highly repeated topic again. After some internet
research, we are about to make the commitment to buy an LG D2342P-PN for
setting up a stereo system. I would like to have a final confirmation
from someone with real life experience that this model does work with
COOT and Chimera the same way as the Zalman monitors. Thanks in advance.

Zhijie

Re: [ccp4bb] Question on stereo monitor: LG D2342P-PN

[Zhijie Li]

Hi Scott, 

The surface doesn't reflect a sharp-edged image so I guess that means it is not 
glossy. But I am not quite sure if it is anti-glare - it does reflect the 
person sitting before it. 

Regards,
Zhijie



From: Scott Thomas Walsh 
Sent: Thursday, August 09, 2012 2:48 PM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] Question on stereo monitor: LG D2342P-PN


Hi Zhijie, 


Is the LG D2342P-PN screen glossy or anti-glare surface?  The Zalman ZM-M240W I 
have is
glossy.


Thank you.


Scott



Scott T. R. Walsh, Ph.D.
Assistant Professor
University of Maryland
IBBR/CBMG
Rm 3127E CARB-2
9600 Gudelsky Drive
Rockville, MD 20850
email: swals...@umd.edu
phone: (240) 314-6478
fax: (240) 314-6255


On Aug 9, 2012, at 2:26 PM, Zhijie Li wrote:


  Hello,

  We have received our LG D2342P-PN monitor yesterday and did a little test. 
  Simply put, it works perfectly for stereo display on COOT and Chimera. We 
  didn't test pymol, as the 0.99 version doesn't have support for the Zalman 
  mode. But the educational version of the new pymol seems to have the Zalman 
  mode.

  Here I list some observations:
  1. We had a Zalman ZM-M215W monitor shortly before this one. The two models 
  are quite comparable to each other.
  2. Both the Zalman and the LG D2342P emit circular polarized light. So 
  simple linear polarization films won't be able to separate the light from 
  the odd and even lines. But the 3D stereo cinemas are of the same type. My 
  3D stereo glasses from a cinema is about 45 degrees counter-clockwise off 
  the LG glasses' axes, but the left and right images are not switched. So it 
  can work OK with the LG monitors, with only a little ghost image, and if I 
  tilt my head to the left then it is as clean as the LG glasses. On the other 
  hand, except for the two pairs of glasses came with the monitor, I haven't 
  figured out where to buy extra glasses yet.
  3. Both Zalman and LG D2342P have wide horizontal viewing angles, but 
  limited vertical viewing angle (maybe 20-40 degrees) for the stereo display 
  (2D display is not limited). This is probably due to that there is a 
  distance between the polarizer layer and the pixel layer so that if viewed 
  from an angle above or below, some light from one row of pixels would have 
  to travel through the line of polarizer one row above or below and then the 
  polarization is mixed - just my guess.
  4. Both Zalman and LG D2342P can work on any computer with a VGA or DVI 
  output and have nothing to do with the operating systems. No special driver 
  is needed. We tested them on our desktops and laptops, in Linux, real and VM 
  Windows. They worked just fine in all cases.

  Regards,

  Zhijie

  --
  From: "William G. Scott" 
  Sent: Tuesday, July 24, 2012 10:52 AM
  To: 
  Subject: Re: [ccp4bb] Question on stereo monitor: LG D2342P-PN


Dear Zhijie:



I saw this for under $300 at Amazon's Showroom and wondered the same 

thing.  I can verify that the LG TV will work with coot, etc., as long as 

you turn OFF all stereographic processing and allow the software to do the 

work.  There is an extremely detailed review of this at 


http://www.amazon.com/LG-D2342P-PN-23-Inch-Widescreen-Passive/dp/B004WK3R4U/ref=cm_cr-mr-title
 

by Bill Costa (he gives his email address at the end).  He seems to 

suggest that the 3D glasses for the LG TV are not compatible with this, 

which left me scratching my head.



Having said that, I'll bet it will work fine.  If you can get it from Best 

Buy for under $300 and return it within 30 days for a full refund, it 

might be worth it.



Either way, let us know.



Bill









William G. Scott

Professor

Department of Chemistry and Biochemistry

and The Center for the Molecular Biology of RNA

228 Sinsheimer Laboratories

University of California at Santa Cruz

Santa Cruz, California 95064

USA







On Jul 23, 2012, at 11:42 AM, Zhijie Li wrote:



  Dear CCP4BBers:



  Sorry to bring up this highly repeated topic again. After some internet 

  research, we are about to make the commitment to buy an LG D2342P-PN for 

  setting up a stereo system. I would like to have a final confirmation 

  from someone with real life experience that this model does work with 

  COOT and Chimera the same way as the Zalman monitors. Thanks in advance.



  Zhijie 

[ccp4bb] Mac or PC?

[Lee, Ting Wai]

Hi, everyone.

May I ask a very general question? I am going to buy a laptop. I am going
to do a lot of structural biology work on it using programs such as CCP4,
Phenix, Coot and Pymol. Mac or PC, which is better? I have never installed
this kind of programs and done structural biology work on laptops except
using Pymol. Will these programs cause any problems when they are run on
laptops? I mean, will they slow down very much or even freeze the
laptops? Can the programs finish the jobs at an OK speed? I mean, maybe not
as fast as desktops, but not taking too long like days or weeks.

Sorry if this question is stupid. I hope to have your advice. Thank you.

HS

Re: [ccp4bb] Mac or PC?

[Bosch, Juergen]

On Aug 9, 2012, at 3:52 PM, Lee, Ting Wai wrote:

I mean, maybe not as fast as desktops, but not taking too long like days or 
weeks.

Sorry that time is over when you could get a cup of coffee while refinement of 
a structure was running.
Any system will work as long as you have sufficient RAM, if you invest into SSD 
you'll get spoiled very quickly.
Modern laptops are as powerful as 3 year old Desktop machines (I'm comparing 
Macbook Air 2012 versus MacPro 2009, if you run Geekbench on them you get tears 
how slow the 16 Core cluster is compared to the 4 core MacBook Air.

Jürgen



Sorry if this question is stupid. I hope to have your advice. Thank you.

HS


..
Jürgen Bosch
Johns Hopkins University
Bloomberg School of Public Health
Department of Biochemistry & Molecular Biology
Johns Hopkins Malaria Research Institute
615 North Wolfe Street, W8708
Baltimore, MD 21205
Office: +1-410-614-4742
Lab:  +1-410-614-4894
Fax:  +1-410-955-2926
http://lupo.jhsph.edu

Re: [ccp4bb] Mac or PC?

[Nat Echols]

On Thu, Aug 9, 2012 at 12:52 PM, Lee, Ting Wai  wrote:
> May I ask a very general question? I am going to buy a laptop. I am going to
> do a lot of structural biology work on it using programs such as CCP4,
> Phenix, Coot and Pymol. Mac or PC, which is better?

See this morning's thread.  Short answer: either works, just avoid Windows.

> I have never installed
> this kind of programs and done structural biology work on laptops except
> using Pymol. Will these programs cause any problems when they are run on
> laptops? I mean, will they slow down very much or even freeze the laptops?
> Can the programs finish the jobs at an OK speed? I mean, maybe not as fast
> as desktops, but not taking too long like days or weeks.

It depends on how big the structures you work with are, and what
you're trying to run.  I have a MacBook Air and it is quite adequate
for crystallography, but I've only worked with small and/or
low-resolution structures where there's no danger of exceeding the 4GB
memory limit.  (Of course, one can buy far more powerful laptops, but
the price goes up steeply.)  The important thing is *not* to buy the
cheapest PC laptop you can find, because the really low-end hardware
probably won't work very well.

-Nat

Re: [ccp4bb] Mac or PC?

[HS]

Thank you for your information. Actually I'm using my friend's old email
account. I forgot to change the name. My name is HS.

HS



On Thu, Aug 9, 2012 at 3:52 PM, Lee, Ting Wai wrote:

> Hi, everyone.
>
> May I ask a very general question? I am going to buy a laptop. I am going
> to do a lot of structural biology work on it using programs such as CCP4,
> Phenix, Coot and Pymol. Mac or PC, which is better? I have never installed
> this kind of programs and done structural biology work on laptops except
> using Pymol. Will these programs cause any problems when they are run on
> laptops? I mean, will they slow down very much or even freeze the
> laptops? Can the programs finish the jobs at an OK speed? I mean, maybe not
> as fast as desktops, but not taking too long like days or weeks.
>
> Sorry if this question is stupid. I hope to have your advice. Thank you.
>
> HS
>
>

Re: [ccp4bb] Problem with Coot on Mountain Lion

[Jeremiah Farelli]

I have had success with the standalone Coot, found here: 

http://scottlab.ucsc.edu/~wgscott/xtal/wiki/index.php/Stand-Alone_Coot

It doesn't use the Fink package, which seems to be part of your problem.  Try 
completely uninstalling your version and reinstalling this one.  I've had no 
problems at all, though it did take Coot a minute or two to start once I 
upgraded to Mountain Lion.

Re: [ccp4bb] Various OSes and Crystallography

[Roger Rowlett]

For me, Windows would be my last choice for crystallographic software. Most
of the popular packages are developed for *nix in the first place, so you
know you will be able to run it. Not everything is compiled for Windows.
Programs will run faster and with less hardware in *nix than in Windows,
and backups and file shares are both easier to set up and more secure in
*nix than in Windows. And scripting (yes, it's still necessary on occasion)
is less clumsy in *nix than Windows. The command shell in Windows is a pale
imitation of tcsh or bash, and the freely available editors leave something
to be desired. (Textpad is awesome, though.)  For the random Windows-only
stuff (CrysalisPro still runs only in Windows) there is Wine or a virtual
box.

The choice for me is really Mac or Linux. Linux is much less expensive,
especially if you build your own boxes. I've not experienced driver hell
since the early versions of Fedora. In Ubuntu 12.04 Nvidia drivers install
seamlessly, and I've had no trouble with wireless or Bluetooth, audio
hardware, etc. Just don't buy bleeding edge hardware.

Roger Rowlett
On Aug 9, 2012 9:55 AM, "Jacob Keller" 
wrote:

> Dear List,
>
> I guess this is somewhat of a perennial issue, but I am faced with
> choosing an OS for a new computer, and am curious about benefits and
> drawbacks with regard to crystallography. So far, I have been using
> windows, and have found no limitations whatsoever, but then again, maybe I
> don't know what I am missing. But, since so many folks out there use Macs,
> I am open to using one. Are there any really reasonable arguments for
> preferring Mac over windows (or linux) with regard to crystallography? What
> can Mac/Linux do that windows cannot (especially considering that there is
> Cygwin)? What wonderful features am I missing?
>
> Jacob
>
> --
> ***
> Jacob Pearson Keller
> Northwestern University
> Medical Scientist Training Program
> email: j-kell...@northwestern.edu
> ***
>

Re: [ccp4bb] Various OSes and Crystallography

[James Stroud]

You should choose an OS that interfaces well with your phone.

James


On Aug 9, 2012, at 7:55 AM, Jacob Keller wrote:

> Dear List,
> 
> I guess this is somewhat of a perennial issue, but I am faced with choosing 
> an OS for a new computer, and am curious about benefits and drawbacks with 
> regard to crystallography. So far, I have been using windows, and have found 
> no limitations whatsoever, but then again, maybe I don't know what I am 
> missing. But, since so many folks out there use Macs, I am open to using one. 
> Are there any really reasonable arguments for preferring Mac over windows (or 
> linux) with regard to crystallography? What can Mac/Linux do that windows 
> cannot (especially considering that there is Cygwin)? What wonderful features 
> am I missing?
> 
> Jacob
> 
> -- 
> ***
> Jacob Pearson Keller
> Northwestern University
> Medical Scientist Training Program
> email: j-kell...@northwestern.edu
> ***

Re: [ccp4bb] off topic: ITC or Biacore

[rashmi panigrahi]

Thank you all for your suggestions. In the same way can Biacore work be
done at lower temperature??
I want to do both ITC and Biacore  for my protein and peptide
regards
Rashmi

On Thu, Aug 9, 2012 at 9:19 PM, Edwin Pozharski wrote:

>
> On 08/09/2012 03:55 AM, rashmi panigrahi wrote:
>
>> Does any one have the experience of doing ITC or Biacore(SPR) at 10 or 15
>> degrees?
>>
>
> You can do ITC at any temperature your instrument allows, certainly no
> problems at 4oC.  To share a trick, at least on a MIcrocal instrument
> cooling down is very slow, and I found it useful to wash the cell with ice
> cold water to quickly get down to 4 degrees.
>



-- 
rashmi

Re: [ccp4bb] Various OSes and Crystallography

[Harry]

Hi

My two ha'porth.

For  a laptop, this is the clincher for me - if you want to use your  
laptop anywhere that has reasonable light levels (e.g. demonstrating  
to anyone in an exhibition hall), you may well find that the beautiful  
shiny mirror that Apple put on the front of their screens on most of  
their laptops makes your investment almost useless in reasonable  
levels of ambient light. Unless I could buy a Macbook with a matt  
screen I doubt I'd want to buy another one.


Sometimes I wonder if my Macbook was "designed in California in a  
cave" to paraphrase what it says on the sticker on the back...


It runs all the software I want it to without problems, though,  
including WIndows stuff via wine or VMWare. And I do *really* like OSX  
as an interface.


On 9 Aug 2012, at 16:18, Andreas Förster wrote:


Mind that if you buy a MacBook, there's only one (hefty 15") model  
without a mirror-coated screen.



Andreas



On 09/08/2012 3:58, Nat Echols wrote:

On Thu, Aug 9, 2012 at 6:55 AM, Jacob Keller
 wrote:
one. Are there any really reasonable arguments for preferring Mac  
over
windows (or linux) with regard to crystallography? What can Mac/ 
Linux do
that windows cannot (especially considering that there is Cygwin)?  
What

wonderful features am I missing?


Mac vs. Linux: mostly a matter of personal preference, but I agree
with Graeme.  Most programs run equally well on either - with Coot a
partial exception, apparently due to problems with the X11
implementation (but once you get used to these, it's not a big deal).

Windows, on the other hand, simply doesn't support the full range of
modern crystallography software.  And in my experience, it has
crippling flaws that mean some programs will always work better on
Mac/Linux.  I wouldn't ever endorse trying to use Windows for serious
scientific computing unless you need to run an application that won't
work on any other OS, and as far as I know there isn't a single
(macromolecular) crystallography program that falls into this
category.

-Nat



Harry
--
Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre,  
Hills Road, Cambridge, CB2 0QH