Seconday structure assignement by Pymol is poor and unreliable to say
the least. This behavior is very common. Best is to assign secondary
structure using other software and then tell Pymol explicitely from
where to where the starnds and helices run
Remy Loris
Vriej universiteit Brussel
On
You should type Dss into pymol and this will assign more appropriate secondary
structure
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of meisam
nosrati
Sent: Tuesday, 24 July 2012 9:47 a.m.
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Problem with making PDB from Coot
4Mb attachments, posted to a mailing list NOT COOL.
On 24/07/2012 14:40, Niks wrote:
Dear All,
I am trying to crystallize a recombinant dehydrogenase protein. Got
five hits in PEG ION Screen from Hamptons (20% PEG 3350 with 0.2M
Sodium Acetate, 0.2M Potassium acetate, 0.2M ammonium
Hi Bernhard -
Having the spots in regular lines indicates that this is a single
crystal diffraction pattern (to a first approximation). I have seen ice
rings which contain a few strong spots, probably from microcrystals of
ice, but I haven't yet seen ice diffraction that shows a lattice of
Dear all,
I am looking into a 2D-bar code scanner to read Hampton pins barcodes.
Something we can plug directly to any computer running Windows, Mac or Linux,
via a supplied USB cable, and feed the barcodes into Excel.
Does anybody know a cheaper alternative to the FOCUS MS-1690-38?
Grazie,
CCP4ers,
a log file from Refmac_5.7.0027 presents me with this line:
fromLog
Problem with the ADP of the atom N A 3 ADP is non-positive
-1.7740907E+35
/fromLog
I did not explicitely refine ADPs or TLS.
Should I modify my model when I encounter such a message? If yes, does the
Dear Zhijie:
I saw this for under $300 at Amazon's Showroom and wondered the same thing. I
can verify that the LG TV will work with coot, etc., as long as you turn OFF
all stereographic processing and allow the software to do the work. There is
an extremely detailed review of this at
The diffraction you see is probably not the best diffraction you could
obtain from these crystals. I have found long thin needles are
very susceptible to manipulation.
I would highly recommend seeding (I like the Hampton Seed Bead personally,
Dear Nishant,
To me, the diffraction looks like powder diffraction from a salt. In
your case, I would look at the protein buffer to see if there are
components present (phosphate, detergent etc.) which might be prone to
form crystals on their own and see if you can find a minimal buffer
where
On Tuesday, 24 July 2012, wtempel wrote:
CCP4ers,
a log file from Refmac_5.7.0027 presents me with this line:
fromLog
Problem with the ADP of the atom N A 3 ADP is non-positive
-1.7740907E+35
/fromLog
I did not explicitely refine ADPs or TLS.
Should I modify my model
Hmmm..I just fail to see 'lines' in that diffraction map. I see spots along
something that could be segments of diffraction rings, i.e. a number of
these crystals in some clustered random orientations, similar to ice as you
mention. I also wonder how there could be true diffraction 'lines': If it
Dear Colleagues,
Does anyone have access to this article? It is not in my library and they
cannot find it via interlibrary loan. I know the limitations and that it
is best not to ask papers via the newsgroup but I have even tried to ask
the author for a reprint and my email was returned to me.
There are atom records for C, O and CA (B-factors 42, 43, 40A**2,
respectively), but not for N, as density tapers off going to the amino
terminus (well, without the amino in this case). Residue 3 is the
lowest-numbered residue in its chain. B-factors of N, CA of residue 4 are
38, 33A**2,
1- if i have anomalous peak of unknown heavy atom, How can i identify this
heavy atom in general. (different methods)
2- in my case, i see anomalous peak in heavy atom binding site (without any
soaking). preliminary i did mass spec. i got Zn++ and Cu, How can i know which
one give the
On Tue, Jul 24, 2012 at 10:14 AM, Haytham Wahba haytham_wa...@yahoo.com wrote:
1- if i have anomalous peak of unknown heavy atom, How can i identify this
heavy atom in general. (different methods)
2- in my case, i see anomalous peak in heavy atom binding site (without any
soaking).
On Tuesday, July 24, 2012 10:22:18 am Nat Echols wrote:
On Tue, Jul 24, 2012 at 10:14 AM, Haytham Wahba haytham_wa...@yahoo.com
wrote:
1- if i have anomalous peak of unknown heavy atom, How can i identify this
heavy atom in general. (different methods)
2- in my case, i see anomalous
On Tue, Jul 24, 2012 at 10:33 AM, Ethan Merritt
merr...@u.washington.edu wrote:
As to the home source - no.
Neither Cu nor Zn has appreciable anomalous signal when excited with a
Cu K-alpha home source.
http://www.bmsc.washington.edu/scatter
An element's emission edge (Cu K-alpha in this
Hello
Actually, if the home source uses a copper tube, neither copper nor zinc have
much of an anomalous signal at that wavelength (the energy is below the
absorption edge for both).
The best way is to check the location of the absorption edge at the
synchrotron. Cu+ and Cu++ can be
Perhaps also exafs should be mentioned--I believe the various ion species,
redox states, and even binding geometry can be determined.
JPK
On Tue, Jul 24, 2012 at 12:37 PM, Roberts, Sue A - (suer)
s...@email.arizona.edu wrote:
Hello
Actually, if the home source uses a copper tube, neither
Sent using BlackBerry® from Orange
-Original Message-
From: Jacob Keller j-kell...@fsm.northwestern.edu
Sender: CCP4 bulletin board CCP4BB@JISCMAIL.AC.UK
Date: Tue, 24 Jul 2012 12:55:31
To: CCP4BB@JISCMAIL.AC.UK
Reply-To: Jacob Keller j-kell...@fsm.northwestern.edu
Subject: Re: [ccp4bb]
I think it's done on a crystal itself, but others who know better than I
can comment.
JPK
On Tue, Jul 24, 2012 at 1:02 PM, Theresa Hsu theresah...@live.com wrote:
Does EXAFS requires same amount of samples as ICP-MS/ICP-AES?
Theresa
On Tue, 24 Jul 2012 12:55:31 -0500, Jacob Keller
Dear Haytham,
may I address your points (although some nice hints have already come
from previous replies)
1- if i have anomalous peak of unknown heavy atom, How can i identify
this heavy atom in general. (different methods)
To see anomalous peak I guess you have done the experiment at a
Dear Haytham,
It should be relatively simple (and quick) to determine the metal in your
sample employing either crystallized sample or solution using X-ray
fluorescence (http://en.wikipedia.org/wiki/X-ray_fluorescence) at any beamline
with a silicon drift detector
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