Dear Yusuf --
On 8 Aug 2008, at 06:01, Yusuf Akhter wrote:
My data is 95.4% of completeness at Signal/noise
=-3.
I noticed that in the header of out-put PDB file from Refmac shows
100%
completeness.
Could you precise where do you see 100% completeness in the PDB
header (overall reflect
The PISA tool at the EBI can calculate surface area contact, interacting
residues and salt bridges/hydrogen bonds between proteins and lots of
other things. And it's easy to use.
http://www.ebi.ac.uk/msd-srv/prot_int/pistart.html
Alan
Skrzypczak-Jankun, Ewa wrote:
What is the best and user
Wikipedia claims Hasselbach is a misspelling:
http://en.wikipedia.org/wiki/Henderson-Hasselbalch_equation
Since Wikipedia has now replaced the social consensus as the final
arbiter of truth ...
On Aug 7, 2008, at 3:22 PM, Juergen Bosch wrote:
Just on a side note, can someone clarify why Ha
Just on a side note, can someone clarify why Hasselbach is not
Hasselbalch or vice versa ? Or is that the same guy just somewhere
sometime misspelled and for ever in the records ?
See here:
http://www.britannica.com/EBchecked/topic/261188/Henderson-Hasselbach-equation
Jürgen
On 7 Aug 2008,
Good points!
Not only citrate is inappropriate for buffers in the pH 6.5-7.5 range,
but also (as pointed out by your colleagues at UCSC, but probabbly elsewhere,
polyprotic acids are hard to handle, as their pKa change in a significant
fashion depending on their concentration.
In this case, the H
Sorry, that equation should read:
Buried_Surface_Area = ASA_unbound1 + ASA_unbound2 - ASA_bound
ASA = Accessible Surface Area
The way I wrote it before would give you a negative value.
Regards,
Steve Darnell
--
Steven Darnell
Department of Biochemistry
University of Wisconsin-Madison
Madison,
Ewa,
What is the best and user-friendly program to calculate a surface of
the interface between two proteins?
If you want a list of interface residues...
The Protein-Protein Interface Database
(http://ppidb.cs.iastate.edu/ppidb/InterfaceResidues) is easy to use,
but it is only for structu
Crystallizer Position Available--
The Almo laboratory of the Albert Einstein College of Medicine is seeking
a skilled crystallization technician to support high throughput protein
crystal structure determination for the New York Structural Genomics
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Thank you very much to Artem, Lijun, Dale and Paul for giving me great
suggestions regarding my earlier query on D to L amino acid residues.
Now one more problem is in same 3 A structure refinement. For those who not
remembered my case. I have processed a diffraction data-set at 3 A using XDS. I
a
What is the best and user-friendly program to calculate a surface of the
interface between two proteins? Or two domains?
Is there any common criteria how to define boundary for that interface
(other than van der Waals distance)?
Thanks in advance for good tips - Ewa
There are 3 pKa's for citric acid:
3.15, 4.77, and 5.19
so it is going to be a lousy buffer at pH 6.7 to 7.25. Also, you need
to know what concentration your buffer is, and whether that
concentration is with respect to the citrate ion or what. It won't be
tribasic with respect to ammoniu
Dear All
Sorry for non crystallographic query.
Can any body mail me how to prepare Ammonium citrate
tribasic (citric acid triammonium salt) buffer pH 6.7
to 7.25 and also what is the pKa value.
Thanking you in advance
Rajakumara
E. Rajakumara
Postdoctoral Fellow
Strcutural Biology Program
phenix.reflection_file_converter did the job (thanks Peter). I tried CAD,
but don't think it can output a column type if that type is not included in
the input (at least not as an option in the GUI)
Cheers
David
CAD (in ccp4) should be right program. You input an mtz file and write-out
> any c
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University of Limerick, Ireland
Applications are invited for the above Scholarship positions (two positions are
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National Institutes of Healt
Hi Yanming:
Using zsh shell, this is very easy.
I have the following pre-defined in ~/.zshrc
autoload -U zmv
alias mmv='noglob zmv -W'
so all I have to do is type
mmv foo_10[0-9][0-9].img foo_1[0-9][0-9].img
mmv foo_11[0-9][0-9].img foo_2[0-9][0-9].img
mmv foo_12[0-9][0-9].img foo_3[0-9][0-9]
Hi all,
I have an MTZ file with I, SIGI in which Friedel pairs are on separate
lines, i.e.
LIST OF REFLECTIONS
===
-6 -6 -624173.00898.47
6 6 623523.00872.92
-7 -5 -560313.00 1232.77
7 5 558022.00 1288.21
All I want to do i
Is your "problem" Mosflm related ?
Then you could have used the command
Template XXX_.img
Jürgen
On 7 Aug 2008, at 01:40, yanming Zhang wrote:
All UNIX gurus,
I need to change 300 image file names sequentially, such as:
XXX_10001.img to XXX_101.img
XXX_10002.img to XXX_102.img
...
try the unix tool mmv.
jan
On Aug 7, 2008, at 1:40 AM, yanming Zhang wrote:
All UNIX gurus,
I need to change 300 image file names sequentially, such as:
XXX_10001.img to XXX_101.img
XXX_10002.img to XXX_102.img
Obviously, using UNIX 'mv' to work on 300 files is stupid. Anyone
My original posting on this question generated quite a few replies,
for which many thanks.
I found the most useful pointer to the required algorithm was the link
to Mark Gerstein's site given by Ian,
and I have now programmed this in a C++ class using Clipper routines,
which I can make avai
Dear Xie,
In order to run DISTANG for the command line you must type something
like this
distang xyzin your_PDB.file
If you just type `distang` the message below will appear.
Adam
On Wed, 6 Aug 2008, Xie Jiabao wrote:
> Hello,
>
>
> I am trying to run the CCP4 program DISTANG from the c
Hi there, this should work:
!/bin/tcsh
#renames 080123_131f07.osc to 0801123_131f07_.osc
#run by typing ./rename.com
for fil in `ls 080123_131f07[0-9][0-9][0-9][0-9]*`
do
echo $fil
new=`echo $fil | sed -e 's/080123_131f07/080123_131f07_/g'`
mv $fil $new
done
Cheers
Ole
___
Hi Yanming
You don't even need a shell script, there's a Unix command to do
precisely this: 'rename'.
Sadly usage does vary between distributions, e.g. Debian & RedHat based
distributions differ, so type 'man rename' and follow the instructions!
HTH!
-- Ian
> -Original Message-
> From
In /sh/bash/ksh/zsh something like
for f in XXX_10[0-9][0-9][0-9].img
do
mv -vi $f XXX_${f#XXX_10}
done
Cheers
Clemens
PS: no guarantee ...
On Thu, Aug 07, 2008 at 01:40:44AM -0700, yanming Zhang wrote:
> All UNIX gurus,
>
> I need to change 300 image file names sequentially, such
All UNIX gurus,
I need to change 300 image file names sequentially, such as:
XXX_10001.img to XXX_101.img
XXX_10002.img to XXX_102.img
Obviously, using UNIX 'mv' to work on 300 files is stupid. Anyone can give me a
very simple UNIX shell file to finish the job quickly? Thank y
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