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Dear all,
I am surprised by the discussion about chiraliy of an utterly
centrosymmetric molecule. Shouldn't the four Oxygen atoms be at least
from a QM point-of-view to indistinguishable? What reason is there to
maintain a certain 'order' in the
Dear All,
I'm with Dale on this one. It's better to have a standard and roll with it,
than allow for ambiguity. The discussion just happened to start with a
rather silly example as Tim pointed out. The ligand 1N1
(http://ligand-expo.rcsb.org/reports/1/1N1/1N1_D3L1.gif) is a better
example:
The
Dear Robbie and ccp4bb,
Is 1N1 not a different type of problem though, where a chirality
restraint is valid and so the atom labelling is important?
Are you saying that we should always use the cif dictionary, even when
there are errors? Surely in the SO4 case, as Ian said, it is better to
The Bujnicki laboratory at the International Institute of Molecular and
Cell Biology (IIMCB) in Warsaw, Poland (http://iimcb.gov.pl) offers a
position for a PhD student with background in experimental structural
biology and/or biochemistry.
The project aims at structural characterization of
Dear Peter,
This noise could be due to the presence of some air in the pump. Before call
any service, try to flux about 100 ml of 100% methanol (or ethanol if you don’t
like to use methanol) at 10 ml/min and 5 ml/min (50:50).
This should be remove any bubble. If the noise persist, the pump
Hi Andrew,
Indeed, provided the atom labeling is correct the chiral volume restraint
actually says whether the groups on the ring a axial or equatorial. The cif
files do not define that any other way, so without the restraint the
description of the molecule is ambiguous. Note that the chirality
Hi Anna,
Actually I just tried lithium sulfate: I made a cryo with 1M KCl, 1.3M Lithium
sulfate to replace the ammonia sulfate totally at pH7. it is not freezing
clear. I guess I should try to increase the amount of LiSO4. But from all the
warm responses here, I found sometimes people don't
Dear all,
I want align a couple or protein structures by secondary structure matching to
one target and want get a kind of aminoacid alignment file e.g. what residue
fit
the other, without adjustments due to sequence based alignments.
I tried Strap, but as far as I understood it, it takes
Hi,
SSM (via PDBefold) (http://www.ebi.ac.uk/msd-srv/ssm/cgi-bin/ssmserver)
will do a structure based alignment and outputs a table of rmsd but will
not give you a alignment file as such.
-Sujata
On Fri, Jul 13, 2012 at 10:30 AM, Christian Roth
christian.r...@bbz.uni-leipzig.de wrote:
Dear
On 13/07/12 15:30, Christian Roth wrote:
Dear all,
I want align a couple or protein structures by secondary structure matching to
one target and want get a kind of aminoacid alignment file e.g. what residue fit
the other, without adjustments due to sequence based alignments.
I tried Strap, but
Hi Robbie,
Interesting! In the article you referred to there isn't a single mention of the
word chiral or its derivatives. They talk more about strained ligands, a
problem which is addressed by the Grade operation and similar tools, and wrong
geometry altogether, which we all agree should be
Dear Christian,
PDBefold superimposes the structures and generates the sequence
alignment in fasta(??) format. You can then read this file in Multialign
for example to get the sequence alignment and then add the secondary
structures to the sequence alignment using ESPript for example.
David
On
Dear all,
I want to refine a model of the complex that consists of rigid subunits
using an electron microscopy electron density map.
I've tried to use phenix for this purpose. Thus I have to back-FT the
electron density map to a mtz reflection file.
I've experienced problem using sfall for this
Dear Wojtek,
you can try something of this type to get the EM map converted into an hkl list
and mtz file with I's and some sigma I's estimated to 1/10 of the I's (the
latter is required for running fittings/refinements etc.).
Best,
Bruno
/usr/local/rave/rave_linux/lx_mapman EOF
re m2
If its old and out of warrenty, see if you have a local shop that can do it.
We found the guys in physics here are great with such things (and a lot cheaper
than official company repair guys).
=
Phoebe A. Rice
Dept. of Biochemistry Molecular Biology
The
Dear Wojtek,
sounds like an mtz format issue.
Can you read it in with coot?
Maybe Pavel or others have an idea?
Bruno
-Message d'origine-
De : CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] De la part de Wojtek
Potrzebowski
Envoyé : Friday, July 13, 2012 6:51 PM
À :
Hi Wojtek,
you need to convert your EM map into a reflection file (for example, cns or
mtz formatted, format doesn't matter). This reflection file should contain
Fobs - the amplitudes of Fourier map coefficients and phases
corresponding to your EM map. The phases should be presented as
Hello Wojtek,
a more straightforward approach is to use the rigid body refinement
implemented in Situs. http://situs.biomachina.org/fguide.html
After placing your pdb into the map via the colores program, you can refine
the positions of individual portions using collage, by splitting your pdb
Several have mentioned harvesting in the cold room to reduce
evaporation. I used to do this also as a postdoc, but I worried whether
I risked nitrogen gas poisoning from liquid N2 boil-off, since the cold
room did not seem very well-ventilated. I've also hesitated to
recommend it to trainees in
You probably already know this, but nitrogen is not at all poisonous--about
78% of the air is nitrogen. I guess you were probably worried about
asphyxiation?
JPK
On Fri, Jul 13, 2012 at 4:19 PM, Radisky, Evette S., Ph.D.
radisky.eve...@mayo.edu wrote:
Several have mentioned harvesting in
On Fri, Jul 13, 2012 at 2:19 PM, Radisky, Evette S., Ph.D.
radisky.eve...@mayo.edu wrote:
Several have mentioned harvesting in the cold room to reduce evaporation. I
used to do this also as a postdoc, but I worried whether I risked nitrogen
gas poisoning from liquid N2 boil-off, since the cold
On 07/13/12 17:29, Jacob Keller wrote:
You probably already know this, but nitrogen is not at all
poisonous--about 78% of the air is nitrogen. I guess you were probably
worried about asphyxiation?
We have oxygen sensors in our X-ray hutches for precisely that reason.
--
How frequently do the sensors go off?
JPK
On Fri, Jul 13, 2012 at 4:37 PM, David Schuller dj...@cornell.edu wrote:
On 07/13/12 17:29, Jacob Keller wrote:
You probably already know this, but nitrogen is not at all
poisonous--about 78% of the air is nitrogen. I guess you were probably
I've noticed that pretty much every time there is an autofill of the dewars in
the hutches of SSRL or APS, the oxygen sensors go off. but that is a small
space and many liters of liquid nitrogen. I've frozen routinely in a small cold
room with a liter or 2 of liquid nitrogen with no issue.
Thanks much. It helps a lot.
On Jul 13, 2012, at 5:31 PM, Henry Bellamy hbell...@lsu.edu wrote:
liquid N2 expands about 600 fold to RT gas. The minimum O2 concentration is
19% (per OSHA I think) so if the amount of vaporized N2 is greater than 2%
of the cold room volume you could have
How low does O2 have to get to be dangerous?
To reduce the oxygen concentration by a factor of two, you would have to mix
equal
volumes of air and nitrogen. Now since the nitrogen is coming off at about 70K,
assuming equal heat capacity for N2 and 80% N2, the temperature of that mixture
would
My cold room is also too small for comfort, but I think your method could work
in a pinch. Thanks!
Evette Radisky, PhD
Mayo Clinic Cancer Center
Griffin Cancer Research Building
4500 San Pablo Road
Jacksonville, FL 32224
tel: 904-953-6372
fax: 904-953-0277
On Jul 13, 2012, at 5:52 PM,
RE: [ccp4bb] harvesting in cold roomDensity of LN2=807g/L, that's roughly
807/28*22.4=645.6L gas at RT, 1 atm. At 4C the volume will be less:
645.6/298*277=600L. An empty 2x2x2m cold room=8000L, containing 8000x21%=1680L
oxygen.
We normally won't let the whole liter of LN2 to evaporate when
Hi Evette:
Technically:
The expansion ratio of liquid to gaseous nitrogen is approximately 1:700, that
is, 1 liter of liquid becomes 700 liters of gas (at room temperature). When you
are in a room that is 3 (~10ft) meters tall, 6 (~18ft) meters wide and 10
(~30ft) meters long and you assume
Quoting Jacob Keller j-kell...@fsm.northwestern.edu:
The expansion ratio of liquid to gaseous nitrogen is approximately 1:700,
that is, 1 liter of liquid becomes 700 liters of gas (at room temperature).
When you are in a room that is 3 (~10ft) meters tall, 6 (~18ft) meters wide
and 10 (~30ft)
FYI, I live at 5500 ft elevation and the oxygen content of air is 21.5% here.
The TOTAL amount of oxygen is less where I am than where you are because there
is less air (lower density). Therefore my body has to do more work to get the
same amount of oxygen to my cells.
OSHA has nothing to do
This is a very interesting topic I have to say.
But what I missed in this discussion is the pain you go through when freezing
in the cold room. As the name implies it's supposed to be cold (most of the
times). But that's not too much of an issue as you can dress up accordingly.
The problem I
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