I've been able to build and run hbplus / ligplot and thought that others
may be interested in the experience. Ligplot is not part of the ccp4
suite, but it is very widely used among structural biologists. Therefore
this may be of interest to some of you.
1- Compilation is performed with the follow
Dear Colleagues,
We would like to remind everyone that the deadline for
registration for the Structural Biology Symposium is fast approaching.
Also, if you haven’t already done so, I encourage you to submit a
poster abstract now, as space is limited.
We
Has anybody heard about what happened in the end with the Ajees et al
debacle which raised so much dander?
Jacob Keller
***
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
Dallos Laboratory
F. Searle 1-240
2240 Campus Drive
Dear All
I'm trying to locate heavy atoms. SO I started with
Revise from CCP4. But it fails with error message
#CCP4I TERMINATION STATUS 0 " REVISE: Duplicate
column labels in output file"
#CCP4I TERMINATION TIME 15 Apr 2008 14:50:34
#CCP4I MESSAGE Task failed
Any help pls
Thanks
Sajid
yang li wrote:
Hi All,
We have several substrate-soaked data with resoltuion from
3.1~3.6A, after refinement
with the native structure, the rfree are in the range of 0.29~0.34. We
found in the expected
active site there do have extra densities, but not very clear. In some
chains the densi
Off the top of my head:
Phoenix Robot: ~2min (incl. reformatting)
Hydra2plusOne: ~5min (incl. reformatting and washing of needles)
Mosquito: ~2min (no reformatting, needles are disposable)
Cartesian: ~20min (incl. washing)
At 11:10 PM 4/14/2008, JOE CRYSTAL wrote:
Hi,
Does anyone have inform
Hi,
Apologies for the off topic question. I am curious if the CNS/Explore
language is a derivative of Lisp. In that case, how does it invoke
C/Fortran routines? There seems to be something called "Lush" which
does it inline and supports GPL/maths libraries..
Cheers, Partha
Hi,
I cannot tell you how to make density better. However, you can verify if
the substrate is in by anomalous signal if you can replace an atom in
you substrate, or add one to it with the absorption edge in
synchrotron-tunable energy range.
In any case, you should keep in mind that depending on you
Hi All,
We have several substrate-soaked data with resoltuion from
3.1~3.6A, after refinement
with the native structure, the rfree are in the range of 0.29~0.34. We found
in the expected
active site there do have extra densities, but not very clear. In some
chains the densities
are big while in
Hi all,
Does someone have a table, or a web link to a table of dielectric constants for
solubilized states of all PEGs (and related compounds) commonly used in
macromolecular crystallography? Non-Merck Index suggestions please.
A related question: can anyone recommend any freely available arti
There is a binary to slot over the existing installation, details here
http://www.ccp4.ac.uk/problems/mac_4_2.php#48
Charles
On 15 Apr 2008, at 10:49, Eva Kirchner wrote:
Dear ccp4bb readers,
when I'm trying to run Procheck in CCP4i or with "procheck xxx.pdb
'resolution' ", it starts, but
Dear Eva,
I reported the same problem a few days ago and Charles Ballard of ccp4
kindly sent me a new "proclean" file which solved the problem.
I will send you the file in a separate message, I assume it will soon
also appear on the ccp4 problems page for everyone to download, or be
part of
We also have this machine (Cartesian Honeybee X8 ) and can verify that
dispensing 3 drops per condition increases the overall build time about
30 seconds.
We have also recently acquired a Cartesian Honeybee 963 which will do
the whole experiment setup, including dispensing precipitant into the
Being one of those succesgul users I can say that this is great news!
Thanks Santosh,
Inge
-Original Message-
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of
Santosh Panjikar
Sent: dinsdag 15 april 2008 9:45
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Auto-Rickshaw:
We use Cartesian Honeybee X8 machines (8 tips). They take about 10 minutes to
set a 96-drop plate including the washes of the tips. 3 or 4 drops per
condition wouldnt take much longer. Optimisation and additive/detergent screens
take a little less time.
The plates are pipetted under a close-f
Dear Eva,
I reported the same problem a few days ago and Charles Ballard of ccp4
kindly sent me a new "proclean" file which solved the problem.
I will send you the file in a separate message, I assume it will soon
also appear on the ccp4 problems page for everyone to download, or be
part of
I had the same problem. I had to build it from source to get it to
run. I changed the g77 compiler to fortran in the Makefile:
chernev 18% diff Makefile*
6c6
< F77 = gfortran # Your FORTRAN compiler
---
> F77 = g77 # Your FORTRAN compiler
I can't remember if this was required or not. My
Ph.D. Student Position in Structural Biology in Bochum, Germany
We are looking for a highly motivated Ph.D. student interested in
biochemical and structural studies
on intracellular signaling systems with relevance to aging &
diseases. Our laboratory (for more info:
http://www.ruhr-uni-bochum.d
Dear ccp4bb readers,
when I'm trying to run Procheck in CCP4i or with "procheck xxx.pdb
'resolution' ", it starts, but remains "running" forever. In the log file,
it says that it started (or tried to start) the "Clean-up program CLEAN"
(interface) or "Running clean-up on file: xxx.pdb" (without in
Dear Colleagues,
Have you ever heard of Auto-Rickshaw?
Auto-Rickshaw is the EMBL Hamburg automated structure determination
platform, which is now available as a web service. Try it out and solve your
structure in minutes.
The EMBL-Hamburg beamline user have been successfully using this system fo
Thanks Leo for your introduction.
However, the link is broken.
Please look at the following page.
http://pfweis.kek.jp/protein/Robot/PXS/index-e.html
Best regards,
Yusuke
---
Yusuke Yamada, Ph.D.
Photon Factory
High Energy Accelerator Research Organi
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