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
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 collec
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 s
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
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
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 kn
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 co
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 probab
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
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 n
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 la
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
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/
-
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
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 Resea
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 Ei
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-
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
Karolinsk
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.
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 st
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
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 p
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.
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
re
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
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 hav
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
Rockvil
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@JISCMAI
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 lap
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, i
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 ans
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 s
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
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
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
> rega
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
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
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