Dear colleagues,
I am now trying to purify a strange protein. The known function of the
protein was little, and it was speculated that the protein linked on the
surface of cell membrane.
It was expressed with a Trx-tag at very low level of solubility.
Furthermore, the protein polymerized
A new version of the Protein Geometry Database (PGD) has just been released.
This version includes
- The ability to compose queries and analyze the behavior of side chain
chi angles.
- Structures released in the wwPDB up to April 8, 2010 consisting of
roughly 18,000 nonredundant protein c
You haven't given much detail to work with so I can only
guess about your problem. A Wilson B of 20 for a 4 A data set
is ridiculous, but the uncertainty in the Wilson B calculation
at 4 A is enormous, so what might be a more reasonable statement
would be to say your Wilson B calculates to 20 +
For large amount of media, it's actually cheaper to buy liquid media in bags
when factor in the cost of labor and water. MilliQ water may not be low
endotoxin. --Chun
-Original Message-
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of
Nathaniel Clark
Sent: Monday, Jun
since the ligands bare being soaked into a known solved structure, why
is MR necessary? Why not just start out with some rigid body refinement
of the native structure to account for possible slight differences in
the cell dimensions?
--
Dear colleagues,
We are now trying to soak some ligands into a protein, which is about
60kd in size and the structure has been solved
before. But the molecular replacement cannot give a right solution. Below
is some contrast of the data:
Native 2A P212121 monomer
Soaked4A F2
Dear Tim,
Thanks for your advice.
I am refining my structure anisotropically.
If, as you suggested, I did something wrong converting
files to use in SHELXL I would expect that the whole
structure to have problems or am I wrong?
And how can I assign a free variable to the whole ligand?
I'v
Dear Fatima,
just a couple of things you may consider:
- you can let shelxl refine the occupancy by assigning a free variable to the
whole ligand
- did you refine the structure anisotropically? At this resolution you certainly
should.
- maybe you made a mistake converting the files from refmac
I mentioned to to Chris already, but we use nothing but HyClone
SFX-Insect powder. We make 20-30 L batches, sterilize with a large
peristaltic pump and a disposable Millipak filter from Millipore. We
never have contamination problems that are due to preparing our own
media from powder. We buy 10
Most of what Kevin says applies equally well to Phenix - refinement is a
relatively complex series of calculations, much less inherently parallel
than what VMD is using GPUs for. There are many other things we could do to
speed up calculations that would probably be more useful and more effective.
Dear all,
I solved the structure of an enzyme at resolution of 1.1A with a bound
substrate using Refmac5 and Coot for refinement/building. I have a very nice
density for my ligand and a very good structure, as judged by Molprobity
analysis.
Now I'm using SHELXL to finish refinement but most of
Dear Simon,
mosflm does indeed estimate the intensity of
overloaded reflections, and these are rejected by default in SCALA,
but you can choose to include them using the appropriate keywords
(ACCEPT OVERLOADS). The number of overloads in the MTZ file, and the
number a
Rashmi,
You can try 1%DMSO and also acetonitrile but the former is preferable.
Gauri
On Mon, Jun 7, 2010 at 3:04 AM, rashmi panigrahi <
rashmi.panigrah...@gmail.com> wrote:
> Hello everybody,
> I have a 16 mer peptide which is predicted to be positively charged alpha
> helix and has 50% of its s
Hi, well, actually this is availalbe as powder (HYClone), as it says
on the page.. (we have it made in our media kitchen on a regular
basis, but
not for huge scale... so i dont know about the prices..)
https://www.thermoscientific.com/wps/portal/ts/products/detail?navigationId=LA11074__10347&
We have happily made a transition last year from using Invitrogen's
SFM medium and cellfectin to Insect-Xpress (Lonza) and
polyethyleneimine for transfection. We are moving several protein
targets to large-scale cultures and would consider cost-cutting
alternatives. For example, Invitrogen and The
I looked at it and concluded that our FFTs are on the whole too short
for it to be worthwhile, and a lot of calculations aren't FFT bound
anyway. An awful lot of our stuff is simply not very slow.
Also, GPU computing at the moment is crippled for many problems by the
bandwidth bottleneck and m
Mosflm integrates them (profile-fitted overloads) but flags them. Pointless
uses them for systematic absence tests. Scala by default ignores them, but you
can include them if you want: this is not normally recommended since they are
pretty inaccurate (look in the "Excluded data" tab of ccp4i/Sca
Dear Colleagues,
I would like to draw your attention to the upcoming Pcube-user meeting
(September 8-9, 2010 in Grenoble). You are probably aware that the
EU-founded Pcube project provides open access to several supportive
technologies for macromolecular crystallography, ranging from fragment
Hi All,
I am wondering anyone is looking into GPU computing on structural refinement? I
see VMD supports GPU computing already, how about other programs such as CCP4
and Phenix
Thanks,
Tongqing
Tongqing Zhou, Ph.D.
Staff Scientist
Structural Biology Section
Vaccine Research Center, NIAID
Hello Simon,
if I remember correctly, mosflm only estimates overloads if you explicitly ask
for it - which you should NOT do especially since you do have a low resolution
pass.
(from the documentation at
http://www.mrc-lmb.cam.ac.uk/harry/mosflm/mosflm_user_guide.html :
"Note that you MUST includ
Dear CCP4bb,
I was wondering if someone could tell me how mosflm and scala deal
with overloaded reflections. From my understanding mosflm extrapolates
the overloaded peaks but then scala throws them out completely - is
this right?
If so am I right to not worry about "contamination" from e
Well - try the coordinate utility recommended by Martyn Winn to convert
cif to pdb
coord_format xyzin ./1ivo.cif xyzout 1ivo.pdb
Hi,
I would like to get some feedback on the type of media that people are
using for insect cell culturing.
We have happily made a transition last year from using Invitrogen's
SFM medium and cellfectin to Insect-Xpress (Lonza) and
polyethyleneimine for transfection. We are moving several pro
Hello everybody,
I have a 16 mer peptide which is predicted to be positively charged alpha
helix and has 50% of its sequence hydrophobic.
Could any one recommend the best way to dissolve it, and then it can be used
for crystallization trials.
thanks
--
rashmi
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