Dear list,
Is there a way that for a binding site (defined as the protein surface
atoms N Angstroms around a ligand molecule) we can assign a (preferably
normalized) hydrophobicity score to the binding site?
- I would prefer something that I can run offline rather than
a webserver (but a we
;Nil illegitimo carborundum"/- /Didactylos
--
Best regards,
Francois Berenger.
https://www.linkedin.com/in/fberenger
Be careful that running data intensive jobs over NFS
is super slow (at least an order of magnitude compared
to writing things on a local disk).
Not only the computation is slow, but you may be slowing down
all other users of the cluster too...
F.
On 07/30/2013 11:28 PM, Adam Ralph wrote:
Dear S
You need to source the CCP4 config file.
At my site:
# for Bash
source /usr/local/src/ccp4/ccp4-6.3.0/setup-scripts/ccp4.setup-sh
I guess that would be the first command in the script
you send to your cluster via qsub.
Regards,
F.
On 07/02/2013 11:55 PM, AFL wrote:
Dear Group Members,
I'm
I think pdbset from CCP4 can renumber a PDB and hence get rid of the
uggly insertion codes.
On 06/26/2013 03:33 PM, herman.schreu...@sanofi.com wrote:
Dear Rain,
Insertion codes are still a sore point for many CCP4 programs and one of
the reasons I prefer Buster over Refmac. Refmac5 does not re
On 06/25/2013 12:36 AM, Tim Gruene wrote:
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Hello Kay,
the rotation can be achieved with 'set xtics rotate by 30'
I did not know about xticlabels, suggested by Abhinav - very useful!
My preferred gnuplot reference:
http://security.riit.tsinghua.ed
On 06/07/2013 06:10 AM, Ho Leung Ng wrote:
Hello,
Are there any issues with crystallography related software on
Windows 8, especially with PyMol or Coot?
The operating system you are mentioning is unobservable, non causal
and has a response time far greater than one second.
To me, as an
On 06/06/2013 08:47 AM, Bosch, Juergen wrote:
Hi Yuri,
http://fpocket.sourceforge.net
http://sts-fw.bioengr.uic.edu/castp/calculation.php
I think GHECOM also compute this.
GHECOM uses morpho maths operators in 3D. Quite beautiful.
http://strcomp.protein.osaka-u.ac.jp/ghecom/
Just to name 2
On 05/29/2013 04:30 PM, Gang Dong wrote:
Try FTsite: http://ftsite.bu.edu/.
I have seen people using metapocket:
http://projects.biotec.tu-dresden.de/metapocket/
Gang
On Wed, May 29, 2013 09:17, Karsten Niefind wrote:
Dear colleagues,
please allow me to ask crystallography experts for adv
On 05/13/2013 06:34 PM, Evgeny Osipov wrote:
Hello everybody,
I am trying to evaluate solvatation energy of my protein and.
Unfortunately the protein highly glycosilated and it seems that PISA
does not take into account hydrogen bonds between mannose from one
molecule and symmetry related molecul
Hello,
Is there a way to tell the new phaser to not
use more than N threads when running?
I have a problem with it overloading some cluster
nodes.
Thanks a lot,
F.
You can try to run your program under strace in order to
get more info about what went wrong.
Look at the end of the trace to have an idea.
strace
On 03/08/2013 02:47 AM, Roger Rowlett wrote:
OK, here is a strange one: I have 4 client machines (3 absolutely
identical hardware) all running ccp4
Hi,
The command:
$ aptitude install fort77
would install an f77 command on Ubuntu/Debian Linux.
In fact that's a wrapper for f2c, but maybe it behaves like
a real f77 compiler, I would give it a try personnally.
On 03/06/2013 06:48 PM, vellieux wrote:
Hello,
For those who still know the Fortra
It is easy to use and even nice looking.
Regards,
F.
On 02/13/2013 04:51 AM, Emmanuel Levy wrote:
Hello,
I have been looking for a tool to measure the "Protein accessible
surface area", which could be defined exactly as the solvent ASA
except with a probe of larger radius.
Most tools that calculate ASA however do not work with a probe radius
of a
Hello,
Would it be possible to have pdbset take care of only the ATOM
lines in a given PDB?
I managed to make it do what I want but in case there are
ANISOU lines, I want to ignore them.
Currently, I'm using grep before pdbset, but I would prefer
to avoid it as I am doing some computational expe
Especially the renumber command that changes
residue insertion codes into an increment of
the impacted residue numbers.
Regards,
F.
For those interested, I think I'll go for Chimera and its support for
.bild files.
And that will be the end of this not so much xtal-related topic. ;)
Sorry for the noise.
Regards,
F.
On 10/29/2012 09:47 AM, Francois Berenger wrote:
On 10/27/2012 05:32 AM, Pete Meyer wrote:
Just o
protein representation, etc.
So, if I go for some pymol-supported format,
I will do all my visual inspection in pymol.
Pete
Francois Berenger wrote:
Hello,
For some new project, I'd like to be able to generate things
and store them in PDB format.
For example, a triangle, a line segment, a squa
On 10/26/2012 12:29 PM, Francois Berenger wrote:
On 10/26/2012 12:16 PM, James Stroud wrote:
This sounds like something that a PDB file is not intended to do. I
think everyone has universally agreed to the PDB specification at the
RCSB, which makes no provisions for arbitrary objects, as cool
ispaces or even the pymol wiki, pointing
to your implementation that you keep on github.
James
On Oct 25, 2012, at 7:25 PM, Francois Berenger wrote:
Hello,
For some new project, I'd like to be able to generate things
and store them in PDB format.
For example, a triangle, a line segme
set up a home page using wikispaces or even the pymol wiki, pointing
to your implementation that you keep on github.
I do have a github page, and do open source what's worth it. ;)
Thanks,
F.
James
On Oct 25, 2012, at 7:25 PM, Francois Berenger wrote:
Hello,
For some new project, I
Hello,
For some new project, I'd like to be able to generate things
and store them in PDB format.
For example, a triangle, a line segment, a square,
a cube, a sphere, an arrow, etc.
Being able to change the color and "line width" would be nice.
Is there some official recommended way of doing th
On 10/07/2012 12:02 AM, Boaz Shaanan wrote:
Hi
If you want to calculate the electrostatic properties of your protein/mutants
you can use Delphi or APBS. Calculation of the dielectric constants is most
challenging. I think that these two programs use some approximations to
estimate the variati
On 10/04/2012 04:09 PM, sreetama das wrote:
Dear all,
Is there any CCP4 module/ other software/ web server
which can determine which particular residues form the surface of a
pocket/ binding-site in a protein?
Do you mean "residues not far from any ligand atom"?
And you know wher
On 10/03/2012 12:09 AM, Christopher Browning wrote:
Dear All,
I was wondering if anybody knows how one can have two transparent
surfaces overlapping but then being able to see how the 2 intersect
using PYMOL. At the moment, if I have two transparent surfaces
overlapping I don't see how they over
On 09/01/2012 07:48 PM, Rex Palmer wrote:
Dear CCP4BB
Does anyone know how to convert a .pdf file into a meaningful Word file.
Maybe through Google doc you can do something for free (if you are OK
with Google looking into your PDF file).
On Linux, there are the pdftohtml and pdftotext commands
Hello,
Quite interesting article:
http://bioinformatics.oxfordjournals.org/content/28/15/1972.abstract
Regards,
F.
On 07/11/2012 11:36 AM, dengzq1987 wrote:
> Hi all,
> recently，I want to use
> DelPhi to calculate the Electrostatic potentials of DNA.but in the
> manual,i can not find the method to create the inputfile fort.11
> 、fort.12 and fort.13.Does anyone have experience on this? Please suggest
Why no
More seriously, there is the babel command from Open Babel
in case the second format you show has a known name.
On 05/08/2012 04:46 PM, Francois Berenger wrote:
Hello,
The tool is called awk.
There is also another tool called Perl, but I won't recommend it.
Regards,
F.
On 05/08/2012 04:
Hello,
The tool is called awk.
There is also another tool called Perl, but I won't recommend it.
Regards,
F.
On 05/08/2012 04:02 PM, K Singh wrote:
Dear All
I was looking for a script or an informatics tool enabling me to
change the sequence from FASTA format to something like following:
FAS
Hi,
There is the exact same problem when releasing a software,
possibly open source, before the corresponding article is accepted.
And I don't know a correct solution to this problem.
Regards,
F.
On 04/19/2012 05:34 PM, Yu Wai Chen wrote:
Dear Marc,
As a reviewer I find it difficult to “vis
On 03/27/2012 12:20 PM, Ethan Merritt wrote:
On Monday, 26 March 2012, Francois Berenger wrote:
Dear list,
If I take all the fasta files for proteins in the PDB,
are the sequences complete?
I mean, do they have holes sometimes (missing amino acids)?
In theory the SEQRES records describe the
Dear list,
If I take all the fasta files for proteins in the PDB,
are the sequences complete?
I mean, do they have holes sometimes (missing amino acids)?
Sorry for the maybe stupid question but I know that sometimes
the PDB files have missing residues, I am hoping that
it is not the case with t
I wonder if it's not in the output of pisa from ccp4mg.
On 03/05/2012 12:30 AM, Bart Hazes wrote:
Hi Fred,
The SSBOND server has indeed been moved as we have relocated to a new
building. SSBOND is still available at the new server address:
http://hazeslab.med.ualberta.ca/forms/ssbond.html
This
On 02/08/2012 12:47 PM, Mike Lawrence wrote:
Hi Francois
Here's a one-liner. The major concept behind the Sc coefficient is that it measures the
extent to which, "on average", the normal vectors between closest-neighbour
opposing points within the molecular interface are antiparallel.
Sc=1 im
Hello,
After following the discussion on
"[ccp4bb] shape complementarity between protein and DNA surface",
is there someone here able to explain simply what the SC software
of CCP4 is calculating?
I mean, is there some intuitive/easy to understand explanation of what
SC is calculating?
I know
On 02/04/2012 08:11 PM, Vellieux Frederic wrote:
I believe Procheck generates drawings such as those. It generates
PostScript files, and if you need to have (eg) jpg files, a PostScript
interpreter, screen capture and there you are (Gimp to select only the
areas you're interested in)
The conver
On 01/27/2012 04:00 PM, Shiva Bhowmik wrote:
Dear All,
I was wondering if there is any IOS5 based app to display protein
models, which are not in public database, on Iphone.
Better than this: Jolecule from Dr. Bosco Ho.
"Jolecule works in HTML5 browsers such as Chrome and Safari, mostly in
F
On 12/22/2011 06:56 AM, David Schuller wrote:
Fedora releases are supported for about a year from initial release.
Red Hat Enterprise, Centos and Scientific Linux are all supported for
about 5 years.
Ubuntu has long term support distributions as well:
"Starting with Ubuntu 12.04 LTS [...] ver
On 12/08/2011 05:11 PM, Petr Leiman wrote:
Dear Bostjan,
There is Chimera for almost anything you can think of.
Not coot, you are sure?
Because (i) Chimera is not part of CCP4 and (ii) usually
coot does everything on this mailing list. :)
> Search for "Structure-Based Sequence Alignment" on
On 11/09/2011 07:21 PM, Pascal wrote:
Le Tue, 8 Nov 2011 16:25:22 -0800,
Nat Echols a écrit :
On Tue, Nov 8, 2011 at 4:22 PM, Francois Berenger
wrote:
In the past I have been quite badly surprised by
the no-acceleration I gained when using OpenMP
with some of my programs... :(
You need big
Hello,
How faster is the OpenMP version of Phaser
versus number of cores used?
In the past I have been quite badly surprised by
the no-acceleration I gained when using OpenMP
with some of my programs... :(
Regards,
F.
On 11/09/2011 02:59 AM, Dr G. Bunkoczi wrote:
Hi Ed,
in the CCP4 distribut
On 10/14/2011 06:31 PM, Ian Tickle wrote:
Hello all, some Fortran developer out there must know the answer to
this one. I'm getting a "forrtl: severe (41): insufficient virtual
memory" error when allocating dynamic memory from a F95 program
compiled with Intel Fortran v11.1.059. The program was
Hello,
The more I read this mailing list, the more I feel
the crystallographer is a very special human being:
- he lives in the Fourier space
- when he goes to the Cartesian space, he restricts
himself to a small box that is replicated to the infinity
using symmetry operators and origin shif
On 10/05/2011 07:25 AM, Jun Liao wrote:
Dear All,
These days, I want to calculate the surface curvature for my proteins in
a quantitative way and show the results in a graphics software such as
Pymol. Does someone have a good idea of which program will do a nice job?
If you are a C++ expert an
On 09/29/2011 09:46 AM, William G. Scott wrote:
On Sep 28, 2011, at 5:26 PM, Jacqueline Vitali wrote:
Dear colleagues,
I need some advice for a new computer.
(1) I have the option of an HP Z210 8 GB with a low end Quadro Nvidia 400 512
MB.
--How does Coot run with this card?
OK
--I am
On 09/27/2011 09:55 AM, David Veesler wrote:
Hi François,
Chainsaw should do the job for you if you input a clustal alignment.
Cheers
David
Thanks! I'm happy I asked. I'll give a try at chainsaw.
Hope to not cut one of my fingers during the process...
Le 26 sept. 2011 à 17:44
Hello,
I have one bound complexe (a ligand + a protein in holo conformation).
I also have the apo structure for a very similar protein.
Is there a tool to create a new PDB, whose coordinates are
taken from the holo structure but residue names and numbers
are taken from the alo structure (by look
On 08/18/2011 09:34 PM, Andreas Förster wrote:
Since we're on the subject... I've been tempted on and off to encrypt my
hard drive, but after getting burned once a hundred years ago when
encrypted data turned into garbled bytes all of a sudden I've been
hesitant. I've gone so far as to install Tr
On 08/18/2011 04:13 AM, Jrh wrote:
Dear Colleagues,
My institution is introducing concerted measures for improved security via
encryption of files. A laudable plan in case of loss or theft of a computer
with official files eg exams or student records type of information stored on
it.
Files, f
Hello,
Recently I was advised PULCHRA on phenixbb for such task
(http://www.pirx.com/pulchra/index.shtml).
I wonder if there is another tool in the CCP4 treasure chest
for the same kind of task (preferably open source).
Regards,
F.
On 07/29/2011 06:30 PM, Robbie Joosten wrote:
Jung-Hoon,
This is a so-called WaReZ request, which could get you banned a lot of webfora.
Of course, we are all guilty of it at some occasions. The best way to get an
article is to ask the authors, they are allowed give away free copies
(dependin
On 07/21/2011 01:45 PM, Hubing Lou wrote:
Dear all,
I am stuck in a molecular replacement case and looking for advices.
I have been working on a protein-DNA complex structure.
Data was processed by HKL2000 to 2.6Ang and some of the data statistics
are shown below:
Space group: P21,
Unit Cell: 5
Hi Obayed,
If I understood your question well,
you are looking for something called "secondary structure prediction".
I googled these keywords and found this server:
http://bioinf.cs.ucl.ac.uk/psipred/
You may find other interesting servers on the web and
some literature comparing them.
I thin
On 06/17/2011 05:25 PM, Armando Albert wrote:
Does anyone has got some information about how to get a mac version (intel), of
the old unix program naccess?. It was meant to calculate the solvent
accessibility per residue from a pdb file.
Armando
Maybe this server can do the job:
http://cgal.
On 06/13/2011 04:55 PM, DUFF, Anthony wrote:
It may require some tricks, such as the creation of walls of CA atoms,
but Kleywegt's FLOOD will give an answer in terms of number of water
molecules.
Some more tools are referenced here:
http://hollow.sourceforge.net/
However, I did not tried them.
This tool looks cool also (especially to all the maximum likelihood fans
of this list I guess):
http://www.theseus3d.org/
---
Theseus is a program that simultaneously superimposes multiple
macromolecular structures. Instead of using the conventional
least-squares criteria, Theseus finds the opt
Sorry,
I forgot to mention about what is the .obj file I need.
It is a pure ASCII geometric description of a polyhedra.
Cf. http://en.wikipedia.org/wiki/Wavefront_.obj_file
It looks rather easy to parse compared to some VRML file, for example.
Thanks,
F.
Francois Berenger wrote:
Hello
Hello,
What are the good software to do this?
I already know of Pymol and Jmol.
Both can export the result to a .obj file, which is interesting for
later processing.
However, Pymol's algorithm is not exactly what Connolly described,
cf.
http://www.mail-archive.com/pymol-users@lists.sourceforg
Hello,
Does someone know some good articles on this particular topic?
I'd like to implement the thing myself, however if there is
a good software doing the job (with readable source code),
I might use and cite it.
Best regards,
Francois.
Hello,
For me the citation format is also a major problem.
When the title of the paper is not shown, it really hinders the work
of trying to find which references are worthwhile reading.
I think it may even have a negative impact on the number of citations
a paper get.
I don't know if it has be
James Stroud wrote:
On Nov 16, 2010, at 10:57 PM, Ethan Merritt wrote:
Bleah. Virtually none of those are human-readable, no matter what the
wikipedia page may choose to put as a heading title.
What kind of data are you dealing with? PDF would indeed be an odd
format for
diffraction images,
--- Begin Message ---
Kay Diederichs wrote:
""
Datum:
Sun, 14 Nov 2010 21:37:10 +
Dear all,
Thanks for your suggestions. From what I learned new GPUs from NVIDIA are using
the Optimus technology which does not support Linux, meaning that only the
dedicated graphics on the system will be
Hi,
This is the first time I read about "shape complementarity statistics".
According to:
"A structural basis for the activity of retro-Diels–Alder catalytic
antibodies: Evidence for a catalytic aromatic residue"
As seen here:
http://www.pnas.org/content/99/15/9674.full
---
[...] compute the
Edward A. Berry wrote:
I'm helping set up crystallography programs on a ubuntu system, and we're
stuck because one program (scalepack) needs the library libg2c.so.0 .
Maybe compat-libf2c
I understand this is absent from modern distributions because gcc
discontinued
support for g77 and f2c in
Laboratory: Zhang Initiative Research Unit,
Advanced Science Institute, RIKEN, Japan.
(Unit Leader: Dr. Kam Zhang)
Job title and Job description: Postdoctoral Researchers
Job description:
We are seeking a highly motivated and experienced computational
structural biologist to join the Zhang Ini
Reply to myself:
The author changed his program so that only the
2 first columns are needed now, and they are obvious enough.
Regards,
F.
Francois Berenger wrote:
Hello,
First, sorry for this not directly CCP4-related question.
I have some software here that requires a seq.data file as one
Hello,
First, sorry for this not directly CCP4-related question.
I have some software here that requires a seq.data file as one
of its inputs: any idea on how to create such a file from a FASTA file?
Here is how the expected file looks like for protein 101M (it is named
seq.dat):
---
1
Hi,
What is the motto/slogan of coot?
I read so often about it on ccp4bb.
If there is not one yet, I propose:
"coot, the crystallographer's swiss knife"
:'D
Regards,
F.
Tim Gruene wrote:
Hello Florian,
you can read the .hat-file into coot and save it from there, changing the
suggested file-e
Hello,
I know at least the following papers on this topic:
---
"High resolution protein structure prediction and the crystallographic
phase problem"
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2504711/
"Prospects for de novo phasing with de novo protein models"
http://www.ncbi.nlm.nih.gov/pmc/
Hello,
Is there some C or C++ code out there doing what you described in 1).
If not, is there a very detailed explanation of this procedure
somewhere, detailed enough in order to implement it (just getting
the best fit vector and its "length", no other parameters)?
Thanks a lot,
Francois.
To
By the way,
I used this one recently:
http://zhang.bioinformatics.ku.edu/TM-score/
It computes a lot of scores: TM-score, MaxSub-score, GDT-TS-score and
GDT-HA-score.
All of this with a single Fortran file (so nothing more needed except
a Fortran compiler), I was impressed.
Regards,
F.
Pavel A
at some moment.
And, I also agree that things made only "in the computer" have
to be checked using some experimental data in order to be relied on.
Francois.
Fred.
Francois Berenger wrote:
Hello,
I am not a crystallographer, so I will ask
a maybe stupid question.
When you say &qu
Hello,
I am not a crystallographer, so I will ask
a maybe stupid question.
When you say "After molecular replacement you should check the result
with the model building program of your choice and correct as many
errors as possible before running a refinement program."
Can this step be automated
Hello,
I used this script once just to have a look
at some NMA-moved structures:
---
#!/bin/bash
if [ "$#" -ne "1" ] ; then
#0 1
echo "usage: phaser_nma.sh INPUT.PDB"
exit 1
fi
name=`echo $1 | sed "s/\.pdb$//g"`
phaser << EOF
TITLE moved by some low frequen
Hello,
This is not what you asked for, but I think
it is good to know: Intel compilers don't seem
to like non-Intel CPUs:
http://www.agner.org/optimize/blog/read.php?i=49
Regards,
F.
Terry Lang wrote:
Hey Everyone,
I am considering switching from gcc to the Intel compiler in the
hopes
Hello,
Just for your information, there is a mailing list for CNS:
http://groups.yahoo.com/group/cnsbb/
And there is some activity on it.
Regards,
F.
AMIT wrote:
Just type in CNS refine.inp in the atom select option:
{===>} atom_select=(not((chainid A and resid 10:15 ) or (chainid B and
resi
Hello,
Is there a tool to apply both the scale and overall B-factor
correction found by the wilson plot to a given MTZ file?
After applying these corrections, is there another way
than redoing wilson to check that the output MTZ is
on absolute scale?
Thanks a lot,
Francois.
?
Thanks,
Francois.
Francois Berenger wrote:
Hello,
While doing a rotation search with Patterson maps,
what is the standard way to find the minimum* and maximum**
radius to be used while correlating maps?
* to avoid the origin peak
** to avoid inter molecular-vectors
Is there a CCP4 tool to give me
Hello,
While doing a rotation search with Patterson maps,
what is the standard way to find the minimum* and maximum**
radius to be used while correlating maps?
* to avoid the origin peak
** to avoid inter molecular-vectors
Is there a CCP4 tool to give me this if I provide it with
a model?
If
Hello,
Is there a ccp4 tool to find automatically the smallest virtual
orthogonal "box" that contain a given PDB ?
Even if your favorite tool is not part of ccp4, I would be happy
to know about it. ;)
Thanks,
Francois.
Hello,
I was recently advised to have a look at James Holton's videos
to have an idea of the effects of various parameters.
http://ucxray.berkeley.edu/~jamesh/movies/
There is a video "The importance of Phase":
http://ucxray.berkeley.edu/~jamesh/movies/dephase.mpeg
This is not an explanation,
are multiple copies in the ASU.
So, we should scale both data sets to absolute scale.
This is illustrated in the tutorials here:
http://www.ccp4.ac.uk/dist/examples/tutorial/html/heavy-tutorial-mad.html#step_4a
Best wishes,
Graeme
On 12 March 2010 08:17, Francois Berenger wrote:
Hello,
Is
Hello,
Is there a magic tool doing the job of scaling 2 MTZ to the same scale?
For the moment I know with ccp4:
rwcontents then wilson then mtzutils
with phenix:
lsq_scale (in fact I am lying, I was forced to run ccp4's cad before)
Is there a simpler way with ccp4?
As I am not a crystallograph
Alejandro Buschiazzo wrote:
Dear all,
I know this can be done with any statistics program, or even by
handbut, just for practical reasons and having to deal with a bunch
of pdb's, is there any (CCP4...or eventually other) program containing
an embedded feature to calculate the best straig
On 2/27/2010 10:10 PM, David Roberts wrote:
I have a quick question about linux for all. Is there anybody running a windows pc with
linux on a bootable cd or bootable drive/flash drive/??? that works for crystallography
apps? I have a colleague who does molecular dynamics calculations and he
James Stroud wrote:
This seems to be a temporary condition.
The page is back up now.
Alternatively, if you put the address in Google
(http://www.doe-mbi.ucla.edu/~sawaya/anisoscale/), then
you click on the "Cached" link of the first result, then
you will access the page as Google remembers it.
Ethan Merritt wrote:
On Thursday 04 February 2010 05:14:24 hari jayaram wrote:
> [...]
The program run with command: /mega/ccp4-6.1.3/ccp4-6.1.3/bin/sortmtz
HKLOUT "/mega/hj-8-2-1/hjbr5-1/hjbr5-1_sorted_mosflm.mtz"
has failed with error message
ERROR: ld.so: object '/usr/NX/lib/libesddsp.so.0'
sensible,
but I think in this particular the fault doesn't lie with reforigin.
Cheers
-- Ian
-Original Message-
From: owner-ccp...@jiscmail.ac.uk [mailto:owner-ccp...@jiscmail.ac.uk]
On
Behalf Of Francois Berenger
Sent: 27 January 2010 06:50
To: CCP4BB@JISCMAIL.AC.UK
Subject: refor
Hello,
I am playing with ccp4's reforigin to verify some MR solutions.
If I translate a copy of the pdb.org's PDB 2FKA (from spacegroup F432)
by +/-0.5 fractional in any unit cell direction, then reforigin will
find back this translation and consider it as valid for this spacegroup.
But for
e
certainly different.
-James Holton
MAD Scientist
Francois Berenger wrote:
Hello,
1) In the case I know the true structure (I am verifying I use Phaser
correctly), is there a program to do so?
Some other questions, if I am to write this program by myself:
2) is there a list somewhere of the t
Francois Berenger wrote:
Hello,
1) In the case I know the true structure (I am verifying I use Phaser
correctly), is there a program to do so?
Some other questions, if I am to write this program by myself:
2) is there a list somewhere of the translation ambiguities for
each spacegroup
Hello,
1) In the case I know the true structure (I am verifying I use Phaser
correctly), is there a program to do so?
Some other questions, if I am to write this program by myself:
2) is there a list somewhere of the translation ambiguities for
each spacegroup?
For example, in P1 it wo
Hello,
By the way, does anyone got this LCD in Japan?
My team is interested to know the model's exact
reference as well as from where you ordered it.
Thanks a lot,
Francois.
see if I can make Phaser
output atom numbers from what was read from the PDB.
Regards,
F.
Regards,
Markus
On Tue, 12 Jan 2010, Francois Berenger wrote:
Hello,
I have 4 molecules.
If I use Phaser's AUTO_MR with all default parameters on them,
I get the following scores:
no_
Hello,
I have 4 molecules.
If I use Phaser's AUTO_MR with all default parameters on them,
I get the following scores:
no_modif remove_H
molecule RFZ TFZ RFZ TFZ
16.9 9.6 7.0 9.4
25.2 5.9 5.4 6.2
34.2 4.5 4.7 5.2
44.9 6.8 5.2 6.7
Hence, here are my e
enables progress bar
[-w | --workers n] number of local worker threads
must have n >= 0
n == 0 can be useful to only run
the server
---
I hope it can be useful to other people.
Rega
Sorry, I forgot to mention my previous message concerns using Phaser.
Francois Berenger wrote:
Hello,
Is there any way to search in AutoMR mode but have the
translation only being brute forced?
Regards,
F.
Hello,
Is there any way to search in AutoMR mode but have the
translation only being brute forced?
Regards,
F.
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