The original poster just told me that the map file is 2.6 GB. Please don't
encourage him to attach it to a ccp4bb email!
-James Holton
MAD Scientist
On Tue, Jul 13, 2010 at 2:58 PM, wrote:
> Actually, zero spacegroup should be tolerated by the CCP4 library now.
>
> We were recently alerted to
Actually, zero spacegroup should be tolerated by the CCP4 library now.
We were recently alerted to another problem, caused by non-zero origin in the
EM map header. But I think this is different to the problem of the original
poster.
It's probably fair to say we haven't tested enough against rea
On Tue, Jul 13, 2010 at 09:39:12PM +, KUMARASWAMI MUTHIAH wrote:
> http://bit.ly/98W5FY
Spam, spam, spam, spam, spam. But he got 1088 of us so far.
http://bit.ly/98W5FY+
Bah.
-b
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Dear All,
I took over this project last September. Since the information in the
lab are not well managed, it's kind of starting over (WRONG plasmids
sequences; even WRONG oligo length/sequence in the complex which has been
successfully crystallized. Those crystals only gave low resolution da
Hi Ariel,
here is how the R-factor is defined and computed in phenix.refine and
related tools (such as phenix.model_vs_data):
http://cci.lbl.gov/~afonine/FandR/Fmodel_and_Rfactor.pdf
and here is the link to almost exactly the same questions asked a few
days ago on ccp4bb:
http://www.mail-
There may be several reasons:
It looks strange. Something seems to be wrong in protocols
1) Check free R flags. I have seen in few cases wrong free R.
Generally number of reflections for free should be less than for work
reflections
2) Check TLS refinement. You may need to restart TLS refinem
Hello,
we have found that there are some minor issues in MRC files using in Em
that can make them unpalatable to the CCP4 map library. You can easily
look at header fields in Python - here is a sample program to quickly
check some of the more common problems.
from struct import *
header=
It means that the CMBI's server migration is still ongoing. The problem should
be temporary.
Cheers,
Robbie
> Date: Tue, 13 Jul 2010 13:03:05 -0700
> From: xtald...@gmail.com
> Subject: Re: [ccp4bb] Judging a PDB
> To: CCP4BB@JISCMAIL.AC.UK
>
> On Jul 13, 2010, at 5:49 AM, Robbie Joosten wrote:
Hi Fred,
Also, at such a high resolution you might want to do individual atomic
anisotropic temperature factor refinement.
And unless it has changed recently, there is no such temperature factor
refinement in Phenix.
it's available in phenix.refine since 2005 or so. Please update your
vers
On Tuesday 13 July 2010 12:32:48 pm Ariel Talavera wrote:
> Hi CCP4ers,
>
> Is there any differences in the way of calculating the Rfactor between
> PHENIX.refine and other programs implemented in CCP4i, like Refmac5 or
> sfcheck, or the EDS server?
>
> I asking this because I have a structure so
Received from Peter Zwart:
> Message du 13/07/10 22:02
> De : "Peter Zwart"
> A : "Frederic VELLIEUX" , "Pavel Afonine"
> Copie à :
> Objet : Re: [ccp4bb] differences Rfactor calculations
>
> > Also, at such a high resolution you might want to do individual atomic
> > anisotropic temperature
On Jul 13, 2010, at 5:49 AM, Robbie Joosten wrote:
For a quick overal test you can look at the summaries of the
PDBREPORTs (http://swift.cmbi.ru.nl/gv/pdbreport/) of each PDb entry.
"The requested URL /pdbreport/cgi-bin/nonotes was not found on this
server."
Does that mean the structure pa
Hi,
There are differences in the algorithm used by Phenix and (for example) Refmac
for the solvent treatment. These can
account for a 3 to 4 percent difference in Rfactor. I do not understand why
there is such a large discrepancy in
your case, unless you have for example a solvent model in Phe
Hi CCP4ers,
Is there any differences in the way of calculating the Rfactor between
PHENIX.refine and other programs implemented in CCP4i, like Refmac5 or
sfcheck, or the EDS server?
I asking this because I have a structure solved at 1.4 Å resolution.
Phenix,refine was used for its refinement and
Does anyone know if the ZM-M215W and ZM-M240W Zalman monitors work in 3D
with Coot and Pymol (would use them on Mac OS10.6)? If so, does the
increased resolution improve things compared to the ZM-M220W?
Thanks,
Daniel
Hello James,
You can try the map2map from the SITUS package (
http://situs.biomachina.org/fguide.html) or em2em (
http://www.imagescience.de/em2em/)
Cheers
Filip Van Petegem
On Tue, Jul 13, 2010 at 5:32 AM, James Whittle
wrote:
> Hi all-
>
> I'm trying to convert a cryoEM map from FREALIGN f
It is possible that the map is just too big. You might run into
"problems" with file I/O in general if it is bigger than 2 GB. If you
have a 64-bit machine with CCP4 completely re-compiled in 64-bit mode,
then it "should" be able to read the large files (but I have not had
much luck with this
An opening is available in the laboratory of Dr. Stephen Fesik
(http://www.vicc.org/dd/display.php?id=4451) for a postdoc in the field of
protein x-ray crystallography. Responsibilities will include protein
expression/purification and all aspects of x-ray crystallography, including
preparatio
Dear Pranjal,
Some measure of a structure's "quality" compared to another is the number of
rotamer outliers, bad bond angles, ramachandran outliers and interpenetrating
atoms or "clashes" in a given structure. I would suggest using the Molprobity
website
http://molprobity.biochem.duke.edu/
r
I am sorry, I have a very basic quarry regarding the PDB structures. How one
can judge the quality of a deposited PDB data set? Suppose,for e.g., two
PDB's have same R-values and have determined at same resolutions with same
completeness.
You may want to work your way through this tutorial:
Hi James,
I had similar problems with MRC maps. As a solution, a colleague of
mine, working with EM, read the MRC map into SPIDER and saved it as a
CCP4 map. That worked for me. Unfortunately, my colleague is absent for
some time, and I'm still not familiar with EM software. But maybe, you
f
Dear Pranjal,
For a quick overal test you can look at the summaries of the PDBREPORTs
(http://swift.cmbi.ru.nl/gv/pdbreport/) of each PDb entry. The full WHAT_CHECK
reports on the same site will give you many details. If you want to look at
specific parts of a structure you should look at the
Hi all-
I'm trying to convert a cryoEM map from FREALIGN for use with various CCP4
programs, or with MAPMAN. Even though the MRC format is derived from the
CCP4 map file format, every program I've tried fails to open it, (except for
Chimera which displays the map but cannot save it to another form
Dear Sir,
I am sorry, I have a very basic quarry regarding the PDB structures. How one
can judge the quality of a deposited PDB data set? Suppose,for e.g., two
PDB's have same R-values and have determined at same resolutions with same
completeness.
Thanking you,
Pranjal
A crude purification prior loading the metal-chelating column (like ion
exchange chromatography) can help and speed up the binding to the column
(remark not specific to Fos-cholin). Fos-choline is, contrary to
popular belief, a quite harsh detergent and this may affect the
purification yield a
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