The cooot method is easiest, as long as you have model coordinates. Then
coot works out the transformation between molecule 1, 2, etc and
averages any map requested to cover molecule 1.
However if you dont have a model it is very tricky to get a proper
transformation matrix.
If you have
Hi,
Anybody having problems with Zalmans and the newer macs? We can't get
the MACS to even _recognise_ the existence of the Zalman display using a
minidisplay port -DVI adapter and also using Thunderbolt out on a new iMAC
(minidisplay port) -- DVI adapter. This is a real problem if
I don't recall but the Zalman also has a VGA port right? Have you
tried minidisplay port to VGA? Have you tried your zalman with PC or
older mac hardware just to make sure it works?
On Thu, Sep 22, 2011 at 4:58 AM, Adrian Goldman
adrian.gold...@helsinki.fi wrote:
Hi,
Anybody having
(B494) Postdoctoral Training fellow - High Throughput X-ray
Crystallography/Structure-Based Drug Design
Cancer Research UK Cancer Therapeutics Unit and Division of Structural Biology,
The Institute of Cancer Research (Sutton, Surrey Chelsea, London)
The Institute of Cancer Research (a college
I got the same trouble and got it fixed:
Contact Zalman e.g. at j...@zalman.co.kr
I got this answer:
Dear Joachim,
I apologize for the delay in responding to your inquiry. I was away on
multiple business trips abroad, and was terribly occupied.
I can provide the fix – a custom DVI cable
On 09/21/11 16:28, Sean Seaver wrote:
Dear Rex,
1. What are the limits to data set completeness imposed by a Laue experiment
versus those of monochromatic data collection?
Laue allows for a greater number of Bragg reflections to be measured compared
to monochromatic data collection over a
Hi Peter
This idea was discussed at the recent RAMC meeting, and there is at least
one example where it has worked.
Generally, cross-seeding can work as long as you have homology. See e.g.
Obmolova et al. Acta Crystallogr. 2010, D66, 927–933. The same group has
reported seeding a complex with
Am 22.09.11 11:58, schrieb Adrian Goldman:
Hi,
Anybody having problems with Zalmans and the newer macs? We can't get
the MACS to even _recognise_ the existence of the Zalman display using a
minidisplay port -DVI adapter and also using Thunderbolt out on a new iMAC
(minidisplay
agree, any crystallisation idea is worth pursuing, given you have or can make
enough sample to try it with.
having said that, wouldn't you tend to select for the same crystals as the
seed, i.e. crystals of the component on its own?
have you tried limited proteolysis of your sample, incl. a bit
Hi all,
Looks like our ZM-M240W came in a few days ago and the researcher has
been using it fine with a standard minidisplay port to DVI adapter off
his newer imac. Zalman must have fixed the issue with pins 15 16
being switched. Unfortunately he got used to using the 3d vision setup
in our
Thanks to sabuj and all who replied. We do indeed have the older monitors and
clearly we will have to contact zalman for a miswired DVi adapter!
Adrian
Sent from my iPhone
On 22 Sep 2011, at 18:27, Sabuj Pattanayek sab...@gmail.com wrote:
Hi all,
Looks like our ZM-M240W came in a few
We have a few final slots open in this tutorial on using the Desmond
molecular dynamics software.
The SBGrid Consortium would like to invite you to a workshop to be held at
Harvard Medical School:
Desmond 3.0 Tutorial
Dr. Istvan Kolossváry,
D.E. Shaw Research
Wednesday, October 5, 2011
Wow, neutrons are pretty cool! No radiation damage--and time
resolution? I guess this is since they have much higher energy, and
are measurable individually? What are the numbers for fluxes
(neutrons/sec)? Are the neutrons all at one energy, or is there a
bandwidth?
JPK
With X-rays, Laue
Wow, neutrons are pretty cool! No radiation damage--and time
resolution?
Actually, as calculated by Richard Henderson in 1995, there is non-negligible
radiation damage from neutrons due to infrequent but energetic nuclear
reactions. The reason that radiation damage by neutrons is not observed
Yes, I have read that paper (a seminal one and the source of the
Henderson limit, no?), and saw that the best deal is electrons, I
think, but I was just delighted to learn that it doesn't happen in
practice. As I recall, x-rays are the worst deal?
JPK
On Thu, Sep 22, 2011 at 11:58 AM, Murray,
Hi all,
I emailed the guy at Zalman to let him know that the newer ZM-M240W
works out of the box with minidisplay/thunderbolt port cards. He let
me know that he no longer works at Zalman (not sure why his email
addr. still works) but that if anyone needs the re-wired DVI cable for
the ZM-M220W
I've noticed that people seem to be using or recommending secondary
structure restraints for low resolution refinement lately, but I'm
somewhat confused about the logic underlying their use.
Using ballpark figures from a system I'm familiar with: 3 atoms
(9 positional parameters),
Hi Pete,
the rationale is: at that low resolution the density map and traditional set
of restraints are not enough to preserve secondary structure elements during
refinement. For example, if you start with a model having good secondary
structure elements, they will be distorted after refinement
Its also a bit too simple to count secondary structure restraints as 2
restraints per residue, because if they're tight enough on, say, an alpha
helix, in combination with other geometry restraints (good bond angles, no
clashes, etc) you could probably turn the backbone of the entire helix into
On Thu, Sep 22, 2011 at 4:18 PM, Pete Meyer pame...@mcw.edu wrote:
In short, the effective observation to parameter ratio improves by ~4%.
This seems like a relatively small improvement, especially if the trade-off
is that Ramachandran statistics can't be used for validation anymore. It
Hi folks,
My love/hate relationship continues with linux. I have had to reinstall
everything and when I install CCP4 6.2.0 It seems to work fine but upon opening
a shell I get the error below and by typing ccp4 I simply get changed to the
ccp4 directory.
Dear all,
I am trying to refine a structure with two domains. The electron
density of one domain is reasonable, but that of the other domain is
poor. So, I am wondering whether the refinement by Phenix or Refmac
can be done locally with two parts, the first domain is refined with
normal
I've been having the same issues and appreciate the update in this thread about
pins 15/16 being swapped - likely explains why the DVI port seems dead when
connecting to a new Mac but works fine on older systems.
On the VGA side, I did get the MZ-M220W to work correctly with a
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