San Diego Supercomputer Center
Postdoctoral Fellow
Summary: We are looking for two highly motivated post-docs as part of our new
project “Compressive Structural Bioinformatics” funded by the US National
Institutes of Health (NIH) Big Data to Knowledge (BD2K) initiative.
The Challenge: To enable
Computational and Data Science Research Specialist
The Structural Bioinformatics Group at the San Diego
Supercomputer Center (SDSC) is seeking an exceptional scientific
software developer to work on our new project “Compressive Structural
Bioinformatics” funded by the US National Institutes of Hea
Hi Chen,
I followed instructions on this page and it seems to be working:
http://www.geo.mtu.edu/geoschem/docs/putty_install.html
One thing I think is worth mentioning is that in Putty-connection-SSH-X11, I
put localhost:0.0 instead of 10.0, as for putty itself, it is requesting from
Xming for
Hi,
I have successfully forwarded OpenGL applications like PyMOL
using VirtualGL http://www.virtualgl.org/.
Takanori Nakane
On 2015年07月02日 14:09, Dale Tronrud wrote:
Then I would worry that your local X11 server doesn't support glut.
3d graphics is an additional layer to the protocol and
Then I would worry that your local X11 server doesn't support glut.
3d graphics is an additional layer to the protocol and not every
server supports it, since the performance over the network is quite
poor in the best of circumstances.
Dale Tronrud
On 7/1/2015 4:05 PM, Chen Zhao wrote:
> Than
The RCSB PDB is seeking exceptional Developers, and we know we're not alone in
our search. So why choose to work with us? Our team values open discussion and
contribution. Starting from your first day, you will shape software and
services used by thousands of people around the world. Our organiz
Hi Eric,
Since you are asking your question on the CCP4 bulletin board, I will give a
CCP4 answer. Take your model refined to 2.7A and through it into PDB_REDO with
the full 2.3A dataset. It will automatically do paired refinement and pick a
resolution cut-off in REFMAC. No mucking about with a
Hello All,
Sorry for giving incomplete information. The protein is 75KDa membrane
protein and it exists as tetramer in ASU. Structure is solved by MR.
Overall completeness of data is 98% wiith multiplicity of 4.8. Density
looks great after refinement having ANISOU record in PDB.
Any suggestions an
Hi,
In order to do a paired refinement you need 2 sets of Rwork/Rfree at each
resolution. The first is just the normal figures from refinement, the second
is from the structure refined at higher resolution but with the R/Rfree
calculated at the lower resolution. You can calculate this using s
4 Angstrom resolution is pretty low and there has to be other info
associated with that to get more help from here.
How big is your protein? How are you solving the phases? How complete is
your data at that resolution? What kind of multiplicity are you getting? I
think you have other issues that ar
Dear CCP4 users,
I am refining a structure at 4A resolution. Crystal diffracted
anisotropically and after refinement in both PHENIX and REFMAC, electron
density in one of the domain of protein is represented by discontinuity and
poor maps. Therefore i did the aniosotropy correction using anisotropy
Hi all,
I have a dataset processed in XDS to 2.3 A (based on CC1/2). I'm trying to do
"paired refinement" to determine the optimal resolution cutoff. Here is what I
get at different resolutions set in Phenix:
Final Rfree/Rwork:
2.7—> 0.2498/0.2027
2.6—> 0.2519/0.2009
2.5—> 0.2567/0.2025
2.4 —>
Thank you Dale, but when I added " localhost:10.0" to X display location,
the problem still exist, just without the phrase "localhost:10.0" in the
warning. My X11 forwarding is enabled all the time and all other GUIs work
just fine.
And thank you for your clarification on the concept of server an
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Both the ssh client and server must be set up with "X11Forwarding
yes". The message sounds like your local computer is not set up to
accept X11 tunneling. (By the way, in the X11 world the remote system
is the "client" and your local system the "
Hi all,
Sorry to bother you, but I am trying to fix a long-standing problem that I
cannot run Coot and Pymol through Xming/PUTTY by SSH connection on a
windows client. The error messages are pretty similar for both:
Coot:
PuTTY X11 proxy: unable to connect to forwarded X server: Network error:
Con
A post-doctoral position is available for highly motivated candidates to
join a research group interested in investigating molecular mechanisms
underlying epigenetic regulation and DNA replication initiation. Projects
will involve structure determination of macromolecular complexes by X-ray
crystal
hi
You probably don't want to reprocess the data, but there is the "known cell"
option in iMosflm that would allow this at the indexing stage.
Harry
--
Dr Harry Powell, MRC Laboratory of Molecular Biology, Francis Crick Avenue,
Cambridge Biomedical Campus, Cambridge, CB2 0QH
Chairman of Interna
This is a cross-post from the cootbb last week, regarding the modelling of
multiple conformations in coot.
I know this has long been a tricky thing to do, and in the past I've always
managed to model multiple alternative conformers by hook or by crook, but
in some current structures I'm having a b
I think if you chose option "entering reflection transformation" from the
define transformation matrix button under reindexing details and then use:
h->k, k->l, l->h
i think you should be ok.
-Todd
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of
reindex k, l, h
you can use Pointless or Reindex
Phil
On 1 Jul 2015, at 16:04, D Bonsor wrote:
> Hi,
>
> I am trying to reindex a P212121 lattice to change the axis order from 32.62,
> 64.89, 103.16 to 64.89, 103.16, 32.62. Looking at the REINDEXING manual I
> can't find how to reindex the
Hi,
I am trying to reindex a P212121 lattice to change the axis order from 32.62,
64.89, 103.16 to 64.89, 103.16, 32.62. Looking at the REINDEXING manual I can't
find how to reindex the lattice. Does anyone know how I should do this and an
example of the execute script that I should use?
Than
Hi,
I am trying to reindex a P212121 lattice to change the axis order from 32.62,
64.89, 103.16 to 64.89, 103.16, 32.62. Looking at the REINDEXING manual I can't
find how to reindex the lattice. Does anyone know how I should do this and an
example of the execute script that I should use?
Thank
A valid concern particularly in this case, and related to a question
someone asked off-list. The model came from a collaborator when it was at
early stages of refinement (Rwork/Rfree 0.244/0.296). I followed up with
steps I knew would additionally confound cross-validation:
1. I assigned a new
I wasn't suggesting the space group was wrong - just a lower symmetry
equivalent of the true SG. e.g. all structures can be solved in P1 but
several of the molecules in the cell will be related by crystal symmetry
operators. The same is true for the associated P1 intensities. So IF you
had assigned
Dear Boaz,
One can equally well describe a R32 crystal with one molecule in the asymmetric
unit as P1 and 6 molecules in the asymmetric unit. In this case, the NCS in P1
is identical to the crystallographic symmetry in R32.
Best,
Herman
Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] I
Dear all,
A research technician position (Ref. MBP01379) is opening in my group to
support a biochemical and structural biology project on the
ubiquitin-proteasome system. Further details can be found at ;
http://www2.le.ac.uk/offices/jobs/opportunities/
Informal enquiries are welcome and shoul
Just wondering about Eleanor's interesting remark: would the Rf & Rw go as low as reported by Wolfram (0.22) in case of a wrong space group?
Boaz
Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben-Gurion Universit
Dear all,
We are advertising a research technician position in the Metabolic and Rare
Diseases group at SGC University of Oxford, which processes a variety of
human medically-relevant proteins in recombinant expression systems, and
purifies the proteins for structural and biophysical studies.
Cl
Dear Colleagues,
a reminder, the third CCP4 structure solution school at the Okinawa Institute
of Science and Technology (OIST), Okinawa. All details can be found at
http://www.ccp4.ac.uk/schools/OIST-2015 or contact ccp4_okin...@oist.jp
Title:
"CCP4 school: From data processing to structure
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