Dear Shawn,
cpptraj from amber has a large number of parameters it can calculate,
with some specific routines to nucleic acids.
My hello to Rutgers, too!
Jorge
On 12/26/24 20:46, Shawn R wrote:
Dear Colleagues,
I am trying to characterize nucleic acid duplexes with paramet
Dear all,
I have learned that a common Ag/AgCl electrode should not be used with
solutions containing Tris (what buffer else?), proteins, some other, due
to the contact of silver to these components - precipitation, I believe.
I have learned a Ross type electrode can overcome this problem (du
ted,
another way to do build-by-rotamer is with these awk programs that I
wrote long before coot was a thing. I still find them useful for
certain tasks. I have created a git repo for them here:
https://github.com/jmholton/build_pdb
HTH,
-James Holton
MAD Scientist
On 2/6/2024 8:24 AM, J
Dear all,
As I cannot find by myself, maybe someone can indicate here.
I would like a program, command line - not gui, that I would simply
indicate residues and the desired rotamer, and so it will change the
coordinate file to complete/change side chains accordingly, say, somehow
lik
far as we can tell [3]
Cheers
Clemens
[1] https://www.globalphasing.com/autoproc/
[2] a paper describing this in detail is under review atm
[3] like most software developers we tend to get feedback if
something doesn't work ;-)
On Tue, Oct 31, 2023 at 10:48:54AM -0400, Jorge I
Hi,
Well, it seems there are already many good indications to study and to
work on.
Thanks, Oliver, Kay, Harry and Graeme!
Now, brain and hands on!
Jorge
Forwarded Message
...
Dear all,
I have found many fundamental studies on image processing and
refine
Dear all,
I have found many fundamental studies on image processing and
refinement indexes concerning the decision on cutting resolution for a
dataset, always meant to get better models, the final objective. Paired
refinement has been a procedure mostly indicated.
I have been searching studi
On Wed, 20 Jul 2022 11:10:04 -0300, Jorge Iulek mailto:jiu...@gmail.com>> wrote:
>Dear all,
>
>
> We had some data collections at a Synchrotron. Crystals are a
>kind of brush like (lattice strains, to use a term by Dr. Bergfors,
>though we e
inning" (in contrast to merohedral twinning,
which involves two twin domains); maybe this helps to find
additional pointers.
best wishes,
Kay
On Wed, 20 Jul 2022 11:10:04 -0300, Jorge Iulek mailto:jiu...@gmail.com>> wrote:
>Dear all,
>
>
>
Dear Dom.
Yes, Zanuda must also give more insights, well pointed (it goes
straight to my question "Should I look at anything else to establish
twin P1 is the best way to refine this structure?"). By the way, though
we have not gone through P1 in/extensively for while, a brief overview
ha
Thank you, Edward, for sharing this. I will read through the (extensive)
details of the work.
J.
On 7/22/22 10:25 PM, Edward A. Berry wrote:
As for your second question, whether refining in a lower symmetry
affects the R-factors,
On 7/20/22 10:10 AM, Jorge Iulek wrote:
Related, and a
Thanks Kay and Ralf for your input.
I will check out the reference pointed and search for more.
Best wishes,
Jorge
Forwarded Message
Subject:symmetry possibilities
Date: Wed, 20 Jul 2022 11:10:04 -0300
From: Jorge Iulek
To: CCP4BB@JISCMAIL.AC.UK
Dear
Dear all,
We had some data collections at a Synchrotron. Crystals are a kind
of brush like (lattice strains, to use a term by Dr. Bergfors, though we
employed good effort for purification), but we took advantage of the
Synchrotron microfocus.
Some of the datasets (images) clearly s
Dear all,
We had some data collections at a Synchrotron. Crystals are a kind
of brush like (lattice strains, to use a term by Dr. Bergfors, though we
employed good effort for purification), but we took advantage of the
Synchrotron microfocus.
Some of the datasets (images) clearly sh
Dear all,
Just going to test some polycarbonate coverslips, I wonder what
alternatives might there be for sealing wells (using traditional 24 well
plates) besides vacuum grease. One idea was to move forward "lower
plastic disposal" and recover them (slips) after an "easy" cleaning. I
cou
As a matter of fact, no, it is not. But it must be available soon!
Yours,
Jorge
On 08/30/2018 01:13 PM, Pius Padayatti wrote:
this sounds like an ABC transporter structure
just a guess
On Tue, Aug 28, 2018 at 6:03 AM, Jorge Iulek <mailto:jiu...@gmail.com>> wrote:
e indicated.
Yours,
Jorge
On Tue, Aug 28, 2018 at 6:03 AM, Jorge Iulek <mailto:jiu...@gmail.com>> wrote:
Dear all,
I am working currently on a structure that, nicely, presents
two different orientations between its domains when one compares
monomers of the te
Dear all,
I am working currently on a structure that, nicely, presents two
different orientations between its domains when one compares monomers of
the tetramer in the asymmetric unit.
I notice, in this nature gift, that a helix, probably central (in
its role) for the relation (orie
nar
with the
six-membered ring. As always, check you CIF!
Dale Tronrud
On 5/17/2017 12:46 PM, Jorge Iulek wrote:
Dear all,
I came across some difficulty to refine a NAD molecule in
Dear all,
I came across some difficulty to refine a NAD molecule in a
structure, specially its amide of the nicotinamide moiety.
A (very) brief search in deposited structures seems to point
that not so ever the C2N-C3N-C7N-N7N dihedral is
d not investigate. My hypothesis why this occurs agrees with yours. Nothing should prevent you to make use of this effect!
best,
Kay
On Mon, 20 Feb 2017 08:24:58 -0300, Jorge Iulek wrote:
Dear all,
I have been noticing, with many datasets, processed the
tes, but then less shells are the consequence. The best compromise will probably sit in a shallow optimum, so it does not matter too much if you deviate from it.
best,
Kay
On Mon, 20 Feb 2017 08:19:09 -0300, Jorge Iulek wrote:
Dear all,
Is
Dear all,
I have been noticing, with many datasets, processed the duet
xds/scale, that when one integrates to a resolution limit which
is (a little) higher than the one used for scaling/merging, the
statistics (and here I mean R-symm, R-meas,
Dear all,
Is there any study to recommend the (minimum) number of
reflections for adequate statistics in each shell during image
processing? I mean, for indexes like R_meas or R_symm or CC1/2,
it might be important to know the number of total
om source, so for now use the workaround
above.
Marcin
On Sun, May 17, 2015 at 11:10:41AM -0300, Jorge Iulek wrote:
Thanks Carlos Contreras-Martel and Lu Zuokun for pointing me to check
graphic driver problems (or update them from the vendor, by the way,
controller model Intel HD 4000). Takin
question, though maybe it escapes the discussion
list scope, that I must search further: how (and where) different are
the resources used by the virtual machine compared to the host machine,
such that this graphical behavior is different.
Yours,
Jorge
On 05/16/2015 08:39 PM, Jorge Iulek wrote
Dear all,
My machine has openSuSE 12.3, a lenovo ideadpad with 8 cores (4 are
virutal) and 8 GB memory.
For a number of coot versions in it (including the newest one),
coot answers slowly to rotating, but specially the space bar translate
is even more slow (from residue x to x+1 etc.)
tallographica F, co-editor
e-mail: mbfro...@post.tau.ac.il
Tel: ++972-3640-8723
Fax: ++972-3640-9407
Cellular: 0547 459 608
On Jun 27, 2012, at 21:00 , JORGE IULEK wrote:
I thank for the references and the comprehensive discussion from Dr.
Holton. Also, for the reference indicated by Dr. B
TH,
-James Holton
MAD Scientist
On Tue, Jun 26, 2012 at 2:34 PM, Edward A.
Berry
wrote:
Maybe figure 4 in
Viatcheslav Berejnov et al. Vitrification of aqueous solutions
J. Appl. Cryst. (2006). 39, 244–251 ?
JORGE IULEK wrote:
Hi, all,
I thought I could easily find a reference to comment u
Hi, all,
I thought I could easily find a reference to comment upon the relative
intensity of rings in an image due to diffraction by polycrystal ice, but
no luck googling for that. A reference that would contain a picture (with
visual relative intensities) would be even better. Of course absol
Concerning what Pierre asked, one point to remember at structure
refinement is to test and probably use TLS tensors. I had one case with
serious anisotropy in the data due a libration axis parallel to a
crystallographic axis. TLS lowered dramatically the R's and maps were neatly
better.
ee to be
too close to R ?
here they appear to be too different !
in other words: if Rfree is not 'really free due to twin law' i would
expect R/Rfree to be too close, not too far !
A.
On Oct 23, 2007, at 13:58, Jorge Iulek wrote:
John,
One other point to be added, althou
John,
One other point to be added, although that might not justify all your
observations, is to be sure that the R-free set was chosen respecting the
twin law. Both phenix and CNS (not automatically) can do this. Of course, as
pointed before, when you change your R-free set, you should "ann
Dear all,
Please, maybe you could give some suggestions to the problem below.
1) Images show smeared spots, but xds did a good job integrating them. The
cell is 229, 229, 72, trigonal, and we see alternating strong and weak rows
of spots in the images (spots near each other, but rows more sepa
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