Hi David,
We have had success with the ASUS VG248QE connected with DisplayPort, on an HP
Z620 running RHEL 6.4.
We like to have dual stereo displays on Linux, and Nvidia is discontinuing many
of the cheaper multi-DVI-port cards. We had no success trying to take two Acer
DVI monitors and conn
It seem the LINK line I provided eariler was chopped by the email system.
Here it is again:
LINKRC1**MAN*C***1*OG**SER*B*912MAN-SER
Simply replace each * with a space and change the residue IDs.
Also to clarify the procedure of using refmac to generate the
Hi Dmitry,
COOT does have the MAN-SER linkage record in its monomer lib, but it won't
detect the bond for you. It also haven't provided an interface for the user
to specify the bond type yet.
The COOT procedure you described is perfectly fine for generating a generic
covalent bond record for a
Hi Engin,
Thanks for the information! I didn't realize that O-glycans can also be
specified as specific linkages like N-glycans. Those two extra angle
restraints should be helpful.
Zhijie
-Original Message-
From: Engin Özkan
Sent: Thursday, November 21, 2013 1:00 PM
To: Zhijie Li
Thank you all for helpful suggestions.
My question was how to properly connect a mannose to a serine and real-space
refine the result. My apologies for not being clear enough.
Coot can't find MAN-SER or SER-MAN in it's library (Coot 0.7.1, mon_lib 5.41)
It does not automatically make the bond be
On 11/21/13 07:50, mesters wrote:
...(both handle the dual link DVI-D standard)...
Are there any monitors on the market yet which can produce stereo 3D
from a Displayport 1.2 input? With or without a built-in emitter.
--
==
Hi,
one could indeed get much better phases with the correct positions of
the HA cluster. If there is sufficient anomalous signal one could use
the cluster as search model for Molecular replacement using the
anomalous data as described in Dahms et al. to get the exact position
of the cluste
Dear Lisa,
You are not saying how far your data extends in resolution.
In my experience, finding the cluster(s) can work better if you limit your data
used in the
search ~5A, as scattering goes down beyond this due to interference between
atoms of the clusters.
It does come back at higher scat
If you set the atom type to "TX", phaser will use the built-in scattering
factors for the tantalum bromide cluster. This will be represented as a point
scatterer rather than the actual cluster - if you have very good data you may
be able to actually position the tantalum atoms in the cluster an
Sorry, I have to correct a wrong
statement in my previous email..
I own a CLUB 3D mini displayport to active dvi dual link adaptor
330 mhz stereo 3d gaming cable (the 270 mhz model is the wrong
model so do not buy the 270 mhz one!!!)
- J. -
I second everything Jeroen said except the need for a €450 graphics
card. We have a Quadro 600, which was only £105 or something like that.
The slightly cheaper Quadro 400 would have worked as well. There are
now successors to these cards. Unless something has changed in their
specification
What is the solution to this?
Hi Meisam,
you have it, it is just three molecules in the asu. Look at the overall crystal
lattice packing and see if you have contacts supporting each molecule. Generate
a large representation of your symmetry mates, I suspect you have a channel in
your crystal lat
The quadro 600 or k600 works fine, been using it for more than a year with
that Asus with the built in emitter. In fact the absolute oldest and
cheapest option which works is the quadro 370, but you'll want the 600 at
least.
On Thu, Nov 21, 2013 at 9:19 AM, mesters wrote:
> Hi Andreas,
>
> the
Here's an easy experiment to try:
What happens when you flash-cool your reservoir solution in Liquid Nitrogen?
Does it remains "glass-clear" at 100 K or lower?
Jim
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of abhimanyu singh
[abhising
Dear all,
Recently I got couple of crystallization hits in conditions containing
30-40% sokalan cp 42 provided in MIDAS commercial screen from
molecular dimensions. I tried to look up for information regarding its
probable cryo protection activity but failed to find anything. Could
someone have an
Dear Abhimanyu,
Sokalan CP42 is a modified polycarboxylate with 'medium' molecular
weight. In terms of cryoprotective properties it is likely to behave
similar to PEG 2. Try adding 25-35% glycerol as a starting point.
Best,
Clemens
Zitat von abhimanyu singh :
Dear all,
Recently I g
* Open molecular replacement solution in Coot
* Display crystal packing (Draw>Cell & Symmetry), perhaps as Calphas only
* Find the symmetry-related instance of copyB that is in the correct
position relative to copyA according to your preferences
* Use File>Save Symmetry Coordinates to write the s
Hi,
On 11/20/13, 4:17 PM, Zhijie Li wrote:
If you need to refine the structure with phenix.refine then you need
to make an edit file to specify that the mannose C1 is linked to the
ser OG by a covalent bond.
I am not sure if this is what was meant, but you don't need to define
bonds explicitl
Dear All,
I think i have not explained my problem precisely. This
may be weird one but let me elaborate more. I have have a protein
moleculeA, having N-term, and C-term end. Structurally, it is dimer
with anti-parallel arrangement i.e N-terminal of one copyA of molecule
form dimer in
half-seriously...old-school method:
- apart from the excellent suggestions by Juergen and Phil, you could
experimentally determine the density of the crystals and calculate their
protein content from that. This looks like a fun method to try:
http://journals.iucr.org/j/issues/1999/05/00/wb0070/wb
Dear All,
I seek your valuable suggestion on a MR problem. I am
asking phaser to search for two molecules in ASU, first molecules
phaser searched right but when placing the second molecule, it
orientation has got flipped by 180 deegree. Is there any way to tell
phaser to fix the ori
Meisam:
Probabilities are just that: many of us have had structures with large
solvent contents that are statistically unlikely.
Pedantic quibble: "It scales in P21 Space group with 7% linear
Rfactor." really means that it scales in primitive monoclinic with a
reasonable Rsymm, and I hope y
Dear Dmitry,
I only work with N-glycosylated proteins and here the people from coot and
refmac have done a wonderful job in creating all necessary dictionaries. I
would be very surprised if this would not be true for O-glycosidic bonds.
Instead of reinventing the wheel myself, I would first try
Dear all,
We are looking into ordering a stereo monitor. I am aware that this
question comes up every so often on this BB (and I read the post by Alice),
but maybe someone has any comments or recent experience with passive vs.
active monitors?
And: Which graphics card can you recommended? The mon
Oxford Cryosystems 600 series Cryostream Cooler
We would like to offer an Oxford Cryosystems 600 series Cryostream Cooler free
of charge. The recipient will have to arrange the shipping.
Please contact Marty Rajaratnam (Randall division of Cell and Molecular
Biophysics, King's College London) e
Dear Lisa,
[there is a SHARP discussion list at
http://www.globalphasing.com/mailman/listinfo/sharp-discuss]
On Thu, Nov 21, 2013 at 02:29:23PM +0800, LISA wrote:
> Dear All,
>
> I am running autosharp with a single wavelength data soked with Ta6Br12.
> This data collected at the wavelength of 1
Dear Lisa,
You could try using SHELXD (e.g. via hkl2map) to find the heavy atoms,
it doesn't need f' and f". However you should take into account that
many soaks have not absorbed the intended heavy atoms or clusters, and
that if a tantalum bromide cluster has actually been incorporated it
will pr
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Dear Lisa,
the wavelength indicates you collected the data at a synchrotron. Do
you have a fluorescence scan of your crystal? That should tell you f'
and f''.
Other than that you can use Ethan Merritt's excellent server at
http://skuld.bmsc.washingto
Dear Dr. Matthias Zebisch,
how to do the specific cluster search in phaser sad pipline? Thank you.
Lisa
On Thu, Nov 21, 2013 at 3:37 PM, Matthias Zebisch <
matthias.zebi...@bbz.uni-leipzig.de> wrote:
> Dear Lisa,
>
> if you have proper anomalous data I rather recommend using the Phaser SAD
> p
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