Replicate is a good option with its own problems as it can be seen as
referring to exact copy which multiple measurements clearly aren't. It does
have an advantage of being the word used by non-crystallographers though.
As a lame attempt at joke, use of terms redundancy and multiplicity to
describ
Pozharski (
epozhars...@som.umaryland.edu). References will be requested as needed.
Edwin Pozharski, PhD
Assistant Professor
Department of Biochemistry and Molecular Biology
Center for Biomolecular Therapeutics
University of Maryland School of Medicine
Institute for Bioscience and Biotechnology
On Mon, 2010-11-29 at 14:30 +, Jyotica Batra wrote:
> is there
a way I can switch to phenix.refine by retaining the same
>
R-frees, I have from refmac
If you actually mean the test set,
then you don't need to do anything
other than use the same
mtz-file. Keep in mind though that in phenix b
nt as they will skew the
statistics and possibly the B-factor
>>> restraint model.
>>
>> Zero occupancy may be a bad idea for yet another
reason - the atoms will
>> displace bulk solvent and produce
what is essentially a hole in the
>> structure. It may be
justified
arameters?
> Thanks for
any suggestions
>
> Regards,
> Yuan SHANG
>
--
Edwin Pozharski, PhD
University of
Maryland, Baltimore
uld not be using Luzatti plots to estimate error.
(Actually, I'm not sure what "Luzatti SigmaA Rfree" means in the first
place).
You should instead use the ESU values from either Maximum Likelihood
or from the Cruickshank DPI empirical indices. These are given
in the PDB file outp
copies to do the refinement, forseeing that there
will be a huge Rfree drop from 42% because I account for the extra
density using the 4th copy. BUT TO MY SURPRISE, THE RFREE INCREASE TO
65%.
Can you teach me what is going wrong? Thank you
Yanming
--
Edwin Pozharski, PhD, Assistant Professor
S, Building 101, Room F363
> P.O. BOX 12233 111 T.W. Alexander Drive
> RTP, NC 27709 RTP, NC 27709
> Tel (o): 919-316-4634
> E-mail: [EMAIL PROTECTED]
>
--
Edwin Pozharski, PhD, Assistant Professor
University of Maryland, Baltimore
--
we use ??
Example : shifting from Refmac to CNS. There appears to be an increase
in rmsd of bonds even without refining the structure in CNS. Is the
estimation methods are different or am i doing something wrong !!
Thanks for your valuable inputs.
regards
john
--
Edwin Pozharski, PhD
ter. Best - MM
Mischa Machius, PhD
Associate Professor
UT Southwestern Medical Center at Dallas
5323 Harry Hines Blvd.; ND10.214A
Dallas, TX 75390-8816; U.S.A.
Tel: +1 214 645 6381
Fax: +1 214 645 6353
--
Edwin Pozharski,
/ or
(averaged over all the reflection in a given resolution shell)?
--
Edwin Pozharski, PhD, Assistant Professor
University of Maryland, Baltimore
--
When the Way is forgotten duty and justice appear;
Then knowledge and wisdom are born along with hypo
hat's
not such a problem.
--Christopher Putnam, Ph.D.
Assistant Investigator
Ludwig Institute For Cancer Research
Mischa Machius, PhD
Associate Professor
UT Southwestern Medical Center at Dallas
5323 Harry Hines Blvd.; ND10.214A
Dallas, TX 75390-8816
he drawbacks of using Rmerge as a measure of the quality of a
data set is that it can be
intentionally and unintentionally manipulated. "
Cheers,
Ed.
--
Edwin Pozharski, PhD, Assistant Professor
University of Maryland, Baltimore
--
When the Way i
know which column to look at, but you
will satisfy the other half.
Bernie
On Fri, January 18, 2008 1:39 pm, Edwin Pozharski wrote:
There are two opposing views on this.
First: Rmerge doesn't matter. Don't even look into that column in
scalepack output, you will be upset over nothing.
program which to use
for Rfree set, but needs to be set, since it is not default.
again, not exactly sure what the problem is, but i hope some of this
helps. feel free to email with further questions if needed. best of
luck!
cheers,
nick
--
Edwin Pozharski, PhD, A
hD
Manager, Structural Biology Resource Center
Rockefeller University
1230 York Avenue
New York, NY 10065-6399
phone: 212- 327-7429
fax: 212-327-7389
--
Edwin Pozharski, PhD, Assistant Professor
University of Maryland, Baltimore
--
When the Way is forgotte
x27;s a question I already asked in the appropriate forum.
Edwin Pozharski, PhD, Assistant Professor
University of Maryland, Baltimore
--
When the Way is forgotten duty and justice appear;
Then knowledge and wisdom are born along with hypocrisy.
When harmoni
It should be according to the manual
http://www.ccp4.ac.uk/html/refmac5/keywords/xray-principal.html#solv
If you using CCP4i, I believe this is done by unchecking the "Calculate the
contribution from the solvent region" box in Scaling section.
---
I don't know why the sacrifice didn't work. The
>
>
>
> Good luck!
>
> Herman
>
>
>
> *Von:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *Im Auftrag von
> *Edwin Pozharski
> *Gesendet:* Montag, 4. Februar 2019 22:35
> *An:* CCP4BB@JISCMAIL.AC.UK
> *Betreff:* [EXTERNAL] [ccp4bb] refmac same residue dif
Consider removing sulfate from the mother liquor after crystals are
formed. I recall having success replacing ammonium sulfate with sodium
malonate (it's a nice cryoprotectant as well). This is assuming that
ammonium sulfate is your major precipitant. If it's just an additive (say,
your conditio
But my 80 symbols... :)
On Wed, Feb 20, 2019 at 3:08 AM John Berrisford wrote:
> From July 1st 2019 onward, mmCIF format files will become mandatory for
> crystallographic depositions to the Protein Data Bank. PDB format files
> will no longer be accepted for deposition of structures solved by
Dear Daniel,
with all due respect, I do believe that you are making several mistakes in
your argument.
English is not my native tongue, but I suspect that there is a substantial
difference between "author" and "signatory". What people are asked to do
here is essentially to sign a petition, not t
>
>
> In the absence of such you can resort to carefully bending the loop or
> bending the pin (Jim Holton made a nifty device for bending the pin) while
> keeping the xtal bathed in the cold stream.
>
>
I would also mention these
https://hamptonresearch.com/product-Adjustable-Mounted-CryoLoop-38
I expect this not to exist, but is there a way to define a variable in a
cif-file (e.g. a global esd target for, say, angles)?
I am certainly capable of putting together a bash script to emulate this,
so please don't bother with suggesting a workaround unless you really enjoy
that kind of thing :)
Anyone knows what happened at SSRL? Remote access of all sorts appears
to be down (including ssh, nx, website, webice).
Filip,
if you have a way to measure the fraction bound (say you see two
conformers and your data is good enough to refine occupancies), and if
the binding constant for the two peptides in solution is measurable then
you can derive your "effective concentration". What would that really
tell y
If you need reducing agent, the best choice is probably TCEP. If you
are to choose between the BME and DTT, I'd recommend DTT, since BME
tends to modify cysteines (sometimes in active site which may be quite
annoying, although post-crystallization DTT soaks can remove some of
these). On the o
I think the bash-compatible startup script has disappeared from CNS
distribution at some point. The one that was distributed with cns 1.1
still works though, and I attach my copy of it.
On 07/12/2012 11:24 AM, Dirk Kostrewa wrote:
Dear Fulvio Saccoccia,
along the lines of Ian Tickle's reply:
7;ll
add hydrogens in a naming scheme consistent
> with CNS? (reduce
doesn't do this).
>
>
> Thanks!
>
> F
>
>
>
>
>
-
> Francis E. Reyes
PhD
> 215 UCB
> University of Colorado at Boulder
>
--
Edwin Pozharski, PhD
University of
Maryland, Baltimore
;>
people's views. Thanks very much.
>> Narayan
>
> After refinement, what is R-free in the last shell? If it is
significantly
> better
> than random, say around .4 or
less, that could be taken as evidence that
> there
> is
data in the last shell.
> Also check the e
http://www.ysbl.york.ac.uk/ccp4bb/2001/msg00383.html
>
Rsym...what's that?
>
> JPK
>
> On Wed,
Jul 18, 2012 at 9:12 AM, Edwin Pozharski
>
wrote:
>
>> As has been
shown recently (and discussed on this board), Rsym is not
>>
the
>> best me
p; Molecular Biology
> Johns Hopkins
Malaria Research Institute
> 615 North Wolfe Street, W8708
> Baltimore, MD 21205
> Office: +1-410-614-4742
>
Lab: +1-410-614-4894
> Fax: +1-410-955-2926
>
http://lupo.jhsph.edu
>
>
>
>
>
--
Edwin Pozharski, PhD
University of
Maryland, Baltimore
One of many possible ways is to use rms_cur command in pymol.
But fundamentally such number is meaningless, since root mean square
deviation is only useful when the average shift between the two
structures is (close to) zero.
On 07/23/2012 11:06 AM, Theresa Hsu wrote:
Dear all
I have two p
Scott,
you are asking for opinions when you should be asking for hard data.
CNS, refmac and phenix all can regularize a structural model. If your
primary consideration is speed, you should simply try all three and
compare cpu time.
Cheers,
Ed.
On 07/23/2012 12:50 PM, Scott Foy wrote:
He
;
>
> cns_solve: command not found
>
> I
don't know how to trouble shoot.
> Any help is appreciated.
>
> Thanks
> Yogi
>
--
Edwin Pozharski, PhD
University of Maryland, Baltimore
e/CNS/cns_solve_1.3
>>
>>
>> yogesha@yogesha-laptop:~/work$
cns_solve
>>
>>
>> cns_solve: command not
found
>>
>> I
> don't know how to trouble
shoot.
>> Any help is appreciated.
>>
>>
Thanks
>> Yogi
>>
>
>
>
--
> Edwin Pozharski, PhD
> University of Maryland,
Baltimore
--
Edwin Pozharski, PhD
University
of Maryland, Baltimore
problems. Try using the same unit
cell/orientation on all datasets, it's easy to do if you abandon gui and
feed input file directly to denzo.
--
Edwin Pozharski,
PhD
University of Maryland, Baltimore
On 08/02/2012 04:37 AM, Careina Edgooms wrote:
Dear ccp4
I ask a very fundamental question because I have not had formal
training in this and I would like to understand.
How can I obtain the multiplicity (z) from the space group? So for
example if the space group is P222 how do I know that th
Note that gel filtration columns need to be calibrated separately for
different buffer. S100 is a preparative column not quite intended for
molecular weight determination, but if that is what you are doing, it's
important to do your own calibration.
On 08/07/2012 03:20 AM, MT wrote:
Have a l
On 08/08/2012 09:00 AM, Jose Duarte wrote:
To my knowledge PISA by itself is not able to do interface prediction
To my understanding PISA is not *intended* to do interface prediction
On 08/09/2012 03:55 AM, rashmi panigrahi wrote:
Does any one have the experience of doing ITC or Biacore(SPR) at 10 or
15 degrees?
You can do ITC at any temperature your instrument allows, certainly no
problems at 4oC. To share a trick, at least on a MIcrocal instrument
cooling down is very
Michelle,
On 09/04/2012 06:14 PM, Michelle Deaton wrote:
Is there a straightforward way to obtain this value from my data?
From what I understand, most of my options involve going back and
obtaining unmerged intensities. I am hoping there may be a way for me
to avoid having to backtrack that
Mary,
consider re-posting with log-files attached
Cheers,
Ed.
On 09/05/2012 08:44 AM, Mary Ortmayer wrote:
Hi,
My scala and scaleit programmes are failing with "bad input labels" for both my
data and the ccp4 tutorial data. I would be grateful for any help.
Thanks,
Mary
On 09/06/2012 07:48 PM, Qing Luan wrote:
I built a molecular replacement model
What is the model based on (i.e. how much sequence identity you have)?
Did you try something other than CNS (specifically for twinning detection)?
Did you check the patterson map and/or self-rotation for off-origin pe
And also - I presume p6 does not work?
On 09/06/2012 07:48 PM, Qing Luan wrote:
which I can scale in P3, P31, P32, P321, P3121 and P3221 with similar
statistics:
Matt,
On 09/07/2012 09:56 AM, Matthew Franklin wrote:
I'm also a bit dubious about the 4.3 A limit; your useful data may be
ending around 4.6 instead, despite the high I/sigma numbers.
Why? I would rather suggest Qing extends resolution to where
I/sigma~1. Other than Rmerge, I don't see wh
All you need is scipy library to get those pesky statistic functions :)
On 09/12/2012 11:11 AM, Pete Meyer wrote:
Python's relatively easy to learn, and more flexible than octave/R;
but it doesn't have the built-in statistic functions that octave and R
do.
Ethan,
I think majority of your complaints about python result from its very
purpose - to be readable/portable for the sake of facilitating rapid
implementation. There are many other languages that provide tools to
accomplish what Jacob wants to do (well, I would stay away from P''),
but pyt
You can do unrestrained refinement in refmac, at your resolution it may
be OK. If you want to keep protein restrained, you can either use
harmonic restraints or come up with a special cif-file for your ligand
with large esd targets. There is no direct way to tell refmac to
exclude specific r
On 09/14/2012 12:30 AM, Eric Bennett wrote:
Actually it's a bit of a hindrance. In Perl I can call the int function on
anything and get a sensible answer. In python if you call int on a string that
contains a floating point number the default behavior is that it will crash:
The sensible ans
This may be tricky if binding is too weak, but could you use some
ultrafiltration with, say, 5kDa filters? The idea is that peptide will
not go through if it is associated with protein. Another option is size
exclusion, although that is not always straightforward as weakly bound
ligands may c
If you are looking for reflection files, the tricky part is that in CNS
format they did not include the unit cell parameters. Just to locate
them, it may be helpful to know that they contain a header that looks
like this
NREFlection= 49238
ANOMalous=FALSe { equiv. to HERMitian=TRUE}
DECLa
On 09/24/2012 07:09 AM, Harm Otten wrote:
Why is it so hard to break the symmetry for two (seemingly) different monomers?
Because it's present in your data?
In P1, do you still have the electron density that suggests the
"overlap" (it's not entirely clear to me what you mean by that - a
figu
Tim,
On 09/25/2012 09:51 AM, Tim Gruene wrote:
I would assume that someone who publishes crystallisation conditions has
given up solving the structure or some other reason to encourage others
to pick up the project
there could be several situations when this is not so. Sometimes a
crystalliz
ince 6.3.0, but I do not see any mention of freerflag in updates
summary.
I can supply the input mtz file that produces the
error if needed.
Thanks,
Ed.
--
Edwin Pozharski, PhD
University of Maryland, Baltimore
I guess for such vehicle to be "extremely contagious" (or contagious at all
for that matter) it should be capable of rapidly multiplying inside the
host, so that it outruns immune system mediated destruction for at least
some time in order to be present in high enough concentration to
effectively s
There are tools such as hbplus
https://www.ebi.ac.uk/thornton-srv/software/HBPLUS/
that will calculate predicted hydrogen bonds (including ligands, you just
need to define their chemistry) throughout a structure. These tools usually
go beyond simple distance considerations and analyze further geo
https://pymolwiki.org/index.php/Rms_cur
On Fri, Nov 12, 2021, 9:05 AM Kyle Gregory <
3632e92fcc15-dmarc-requ...@jiscmail.ac.uk> wrote:
> Dear CCP4 bulletin board,
>
> I was wondering if there are any tools to determine the RMSD of the entire
> molecule (two domains) when only aligning one dom
Any molecular dynamics simulation would have a temperature parameter.
GROMACS is free and easy to use. And do find a computational biology expert
to consult with if this is more than an excercise.
On Wed, Nov 10, 2021, 11:20 PM Dr Muhammad Saleem
wrote:
> Dear All,
>
> I was wondering if there i
One could use PISA to get a rough distribution of oligomerization states of
proteins in the PDB and compare bacterial vs mammalian... there always will
be a question though of whether any bias is inherent in proteins or driven
by crystallizability itself.
Personally, I always though that bacterial
CCP4 package manager doesn't work for me when I try a fresh ccp4
installation. It goes through all the question dialogs, but then fails to
download the actual installation package, complaining of broken network
connection. Multiple tries don't help. Obviously, I can get around this
by downloadin
I know space is cheap these days, but is there a reason for Refmac to
generate all those extra columns in the output mtz file? Refmac (as well
as phenix.refine and buster-tnt) output mtz file is almost always used for
only one purpose - look at the map in coot. You only need 4 columns for
that, n
will get
corrected by Garib, Gerard and Pavel).
Cheers,
Ed.
Edwin Pozharski, PhD, Assistant Professor
University of Maryland, Baltimore
--
When the Way is forgotten duty and justice appear;
Then knowledge and wisdom are born along with hypocrisy.
By default, iMosflm excludes corners from processing. Is there a simple
way to make it the default to go all the way to the corner instead of
detector edge? I could of course set the max resolution for processing to
some outrageous value that is guaranteed to be outside of the image, but
perhaps
The most pertinent question is, of course, what is the average frequency of
the disordered chain controversy flareup. Once we figure that out, some
profound mysteries of the Universe will reveal themselves. I am betting
it's a simple combination of the solar cycle, inflation adjusted price of a
b
I don't know the explicit answer to your question, but you can always copy
active site residues into a separate model and use different representation
for that.
On Tue, Aug 27, 2024 at 8:52 AM Firdous Tarique
wrote:
> Hello everyone.
>
> Is there any way to show stick representation of the selec
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