Hi Peng,
first off, there is Phenix mailing list for Phenix-related questions.
phenix.real_space_refine is Phenix program, not CCP4 so any issues related
to it are best addressed at appropriate mailing list (Phenix mailing list,
that is).
To answer your you question: please send me all inputs (1.
Dear all,
I met a problem when I tried to refine a EM structure using a reference model
in Phenix.
I used the command
phenix.real_space_refine 1.pdb 2.mrc reference.eff resolution=3.2
, but it did not work.
My reference.eff is following:
refinement {
reference_model {
enabled
Dear All
Morda at ccp4online has been updated to include 480 new entries.
The update is also available for existing local Morda installations and can be
installed from command line: change to installation directory (by default
MoRDa_DB) and type ./update_morda.
Both update and installation in
Dear Friends:
Happy New Year to all. May the many blessings of the Holiday Pig fall upon
you.
Sorry (not really) for the OT posting!
Artem
www.harkerbio.com
(brimming with the Holiday Pig spirit)
We are hiring for two *Research Scientist - Structural Biology *positions.
Desired qualifications
Dear All,
A postdoc position is available in a newly formed Structural Biology Section,
part of the US Military HIV Research Program, WRAIR in Silver Spring, Maryland,
USA.
The position involves the application of structural biology to understanding
viral glycoproteins and the immune response f
Dear all,
I am looking for a postbac for a membrane protein structure-function
project in my lab at the NIH. The NIH Postbac IRTA program provides
recent college graduates who are planning to apply to graduate or
professional (medical/dental/pharmacy) school an opportunity to spend
one or two year
It seems that I uploaded the wrong 64bit Linux version of shelxe on Dec,
3rd. I have now replaced it with the correct version 2016-3.
The versions on shelx.uni-goettingen.de for other operating systems
should already be correct. Apologies, George
On 01/03/2017 03:28 PM, Tim Gruene wrote:
Dear
I am very thankful to all.
>
Dear All
Yes, we are bundling the next update. We were missing the 64-bit linux build
until the 1st, but now putting it together.
Best regards
Charles
On 3 Jan 2017, at 13:26, Filip Leonarski wrote:
> Dear All,
>
> SHELXE provided with current version of CCP4 stopped working on Jan 1st
I guess that if one adds an EDO or GOL to a water position, and does not delete
the water, Coots wonderful real space refinement might place some atoms right
on top of each other. My advice would be to first delete the water, before
adding something else to the blob.
Best,
Herman
-Ursprüng
Your PDB file contains atoms that are less than 0.001 A apart. This doesn't
look like a good model. Please consider fixing it first.
Pavel
P.S.: There is Phenix mailing list for Phenix related questions.
On Tue, Jan 3, 2017 at 6:10 AM, Vikram Dalal
wrote:
> Hi all,
>
>
> I have added the water
On 03/01/2017 14:10, Vikram Dalal wrote:
Hi all,
I have added the water, EDO and GOL in coot in a protein structure. I got this
error message
(Fig 1) after running the phenix refinement.
Hello Vikram,
A flicker of confusion crosses my brow as I contemplate the on-going thought process tha
Dear Filip,
in case you don't want to wait, the new version of shelxe is already available
at the old shelx download site, http://shelx.uni-ac.gwdg.de/SHELX.
As you point this out I noticed that the shelx license file that comes with
CCP4 still lists the old shelx site, rather its new one,
htt
Dear All,
SHELXE provided with current version of CCP4 stopped working on Jan
1st. One can fix it by downloading new beta-version from SHELX webpage. Is
it possible to include new SHELXE version in the next CCP4 update?
Thank you,
Filip Leonarski
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