Try
sudo apt-get install ia32-libs lib32gfortran3
to install the required 32 bit libraries
On 26/12/2011, at 9:53 PM, 王瑞 wrote:
> Excuse me, could anyone can tell me how to install O on ubuntu11.10 ?Thanks a
> lot !
__
It seems some 32-bit libraries need to be installed to get recent versions
of O to run on 64 bit architecture. There is a 64-bit version undergoing testing
now, so you might want to just wait for it. or volunteer to be a tester.
Subscribe to o-info mailing list (at the below site) to keep up with
Did you try following these instructions:
http://xray.bmc.uu.se/alwyn/O_to_Go/O_to_Go_frameset.html
?
On Mon, 2011-12-26 at 18:53 +0800, 王瑞 wrote:
> Excuse me, could anyone can tell me how to install O on
> ubuntu11.10 ?Thanks a lot !
Excuse me, could anyone can tell me how to install O on ubuntu11.10 ?Thanks
a lot !
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Hi ,
I could not find error messages but only some warnings. Why do you think
anything goes wrong?
I recommend you repost your scientific question at the very end again
with a different thread as I guess that most readers will not have made
it th
I am sorry for a little off-topic! Could anyone tells me how to install
voidoo on 32-bits ubuntu11.10 ?
For its distribution kit on http://xray.bmc.uu.se/markh/usf/, I have
downloaded the distribution kit and Liniux_32_binaries executables, and
followed their tutorial, but something goes wrong:
if
This Ltest certainly doesnt look twinned.
But your R factors are indictive of "mostly correct but still problems".
Didnt someone suggest running Arp-Warp to rebuild the structure?
This might reinterpret any dodgy bits.
Eleanor
On 10/14/2011 02:52 AM, 王瑞 wrote:
> After L-test,the result are fol
After L-test,the result are follows:
TWINNING ANALYSIS:
First principles calculation of potential twinning operators using code by
Andrey Lebedev:
First principles calculation has found 0 potential twinning operators
No twinning detected
$TABLE: L test for twinning:
$GRAPHS: cumulative distribu
Dear Yuri,
Could you give out the details? Such as how you found the twins?
2-Could have twinning? I recently just got done working on a structure that
could be scaled in C 2 2 21 but turned out to really be an almost perfect P21
twin.
(of course in monoclinic there are certain conditions for tw
Similar to Tim's suggestion, but your low resolution limit may be too
low (check refmac's chart of R vs resolution to confirm this).
Pete
王瑞 wrote:
hello everyone:
Excuse me, could anyone give me some suggestions? Afetr several cycles of
refmac, it give me such a result:
Echoing whats been said:
1- Are you sure your crystal really is in C 2 2 21? If so How good is your data
(completeness, Rmerge, etc...)
2-Could have twinning? I recently just got done working on a structure that
could be scaled in C 2 2 21 but turned out to really be an almost perfect P21
twin.
On 10/13/2011 12:14 PM, 王瑞 wrote:
hello everyone:
Excuse me, could anyone give me some suggestions? Afetr several cycles
of refmac, it give me such a result:
InitialFinal
R factor0.2540 0.2531
R f
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Dear ,
- - how complete is your model compared to the sequence expected in the
crystal? If it is not very complete, yet, your R-values might diverge
- - Your RMS BondAngle is pretty high. Set the matrix weight manually to a
lower number (0.1 or less)
Possibility of twinning? A simple way to check this at this point is to turn
on the twin option in refmac and examine the log file. Twinning can cause
you to get stuck at high R values in unaccounted for.
Roger Rowlett
On Oct 13, 2011 7:14 AM, "王瑞" wrote:
> hello everyone:
>
> Excuse me, cou
hello everyone:
Excuse me, could anyone give me some suggestions? Afetr several cycles
of refmac, it give me such a result:
InitialFinal
R factor0.2540 0.2531
R free0.3499 0.3500
Rms BondLeng
Thank you for all your advice.They are all good suggestions!
2011/10/12 王瑞
> Dear Everybody,
>
> I am sorry for a little off-topic. Could anyone tell me how to
> determine a protein, peptide and ligand of a new pdb's b factor? I know
> there are rampage and sfcheck to validate in ccp4, but I
Hello,
2011/10/12 Xiaopeng Hu
> I made a simple script for this, perhaps you can edit it for your case.
> Just save it as baverage.sh, then run it as ./baverage.sh your.pdb.
>
Here is another option:
phenix.pdbtools model_statistics=true model.pdb
or
phenix.model_vs_data model.pdb data.hkl
w
Hi,
as Tim pointed out Rsym, I/sigma, Redundancy could not be obtained from a pdb,
but you find it in the ouptut of SCALA, XSCALE, or similar scaling programs. I
use Moleman2 from the Uppsala Software Factory to get the B values out of my
pdb. F.e. "Bf St Type" provide B-Factors for every compon
I made a simple script for this, perhaps you can edit it for your case.
Just save it as baverage.sh, then run it as ./baverage.sh your.pdb.
#!/bin/bash
echo "--"
grep '^ATOM' $1|cut -b61-66|cat |awk '{sum+=$1} END { print " Protein
Average B =",sum/NR;print
On 12/10/11 12:53, 王瑞 wrote:
> Dear Everybody,
>
> I am sorry for a little off-topic. Could anyone tell me how to
> determine a protein, peptide and ligand of a new pdb's b factor? I
> know there are rampage and sfcheck to validate in ccp4, but I only
> found a overall b factor in their result.
>
>
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Dear ,
A PDB file is a coordinate file. The quantities you mention, Rsym,
I/sigI, and Redundancy are quantities calculated from the measured data
and can therefore not be determined from a PDB file.
The PDB file also contains the B-factor, so in orde
Dear Everybody,
I am sorry for a little off-topic. Could anyone tell me how to determine
a protein, peptide and ligand of a new pdb's b factor? I know there are
rampage and sfcheck to validate in ccp4, but I only found a overall b factor
in their result. By the way, are there a software to det
Thank you for your replies.
With Regards,
Raju Gowriishankar
An excellent reference to start with..
Eleanor
James Stroud wrote:
Whether probing the bulletin boards for advice or probing nature for
her structural secrets, the first thing to do is to ask a good
question. The best advice I can give is to be specific with your
queries and do a little home
Hello Raju,
Welcome to crystallography! I don't have much information about predicting
structures, but have put together a list of resources about protein
crystallization:
http://tinyurl.com/ygmbpa3
Happy reading :)
Sean
Or, to avoid spending $63 and then finding out you want to do something
else, start here:
www.ruppweb.org/Xray/101index.html
Flip
James Stroud wrote:
Whether probing the bulletin boards for advice or probing nature for her
structural secrets, the first thing to do is to ask a good question. T
I have been there, and like most things that we want to learn the best way
is to practice them. suggest joining a lab that solves structures using
crystallography would be your best way to learn. there are introductory
textbooks that will also give you a feel for the subject (like
crystallography m
Whether probing the bulletin boards for advice or probing nature for
her structural secrets, the first thing to do is to ask a good
question. The best advice I can give is to be specific with your
queries and do a little homework before you venture formulate a
question.
A suggested starti
Hi Friends,
I am very new to the field of Crystallography.
I want to learn, how to crystallize the biological macromolecules and how to
predict the structures?.
So let me instruct the basic things to learn.
I am waiting for your reply.
Thanks in advance.
With regards,
Raju Gowriishankar
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