:* [ccp4bb] Phaser and Molrep gave different solutions
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
Hi,
It's not a bad idea to read the Phaser manual for molecular replacement;
see http://www.phaser.cimr.cam.ac.uk/index.php/Molecular_Replacement
Soon after the start, in a table on the right hand side, there is: TFZ
score 5, have I solved it ? No.
Hence with a TFZ score of 3.8 you do not
Have you tried using the DNA as your search model? - I have had success this
way round - certainly more phasing power than your protein model, I guess.
Also, refine with your DNA in place, and your phases/ map should improve -
hopefully allowing you to place your protein molecules with ease.
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On
Behalf Of Hubing Lou
Sent: Thursday, July 21, 2011 6:46 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Phaser and Molrep gave different solutions
Dear all,
I am stuck
] *On Behalf Of
*Hubing
Lou
*Sent:* Thursday, July 21, 2011 6:46 AM
*To:* CCP4BB@JISCMAIL.AC.UK
*Subject:* [ccp4bb] Phaser and Molrep gave different solutions
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
Hi,
Although it's pretty much true that if TFZ8, the solution is correct, there
are hard cases where a correct solution has a significantly lower TFZ score.
Also, we've been finding that TFZ scores are generally lower for monoclinic
space groups like P21, at least in the search for the first
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:
Does anyone know where to look for an error when PHASER outputs this
message?
Eleanor
.
*
*** Phaser Module: AUTOMATED MOLECULAR REPLACEMENT
2.1.4 ***
Hi Eleanor,
A bit more context about what Phaser was doing at the time might help... As a
first guess, it looks like there was an odd character in a text file (PDB
file?). Do you have a PDB file with funny line terminators or something like
that?
Regards,
Randy
On 17 Jan 2011, at 11:50,
CCP4-o-philes,
Has anyone experienced issues with Phaser outputting P3 symmetry
MTZ and PDB files from H3 (R3) input files? I've worked on a
couple of structures in H3 in the last few months, and for some
reason Phaser is changing the symmetry of the
Hi all,
I am trying to use PHASER in space group P1. I has expected that PHASER would
have centered the first protein molecule or at least placed an atom at the
origin of the P1 unit cell. Is this how PHASER works or am I mistaken?
Thanks for your help.
Ray
ray-br...@att.net
Hi ccp4ers,
I am currently trying to process a crystallographic data set from a
20kDa dumbbell shaped protein which was collected on a Bruker Proteum
series detector. The crystal was badly twinned so the Bruker program
CELL_NOW was used to find twin domains within the data. While it
Two suggestions for the data processing:
1) The more recent versions of Pointless (since 1.4.3, and better since 1.4.9)
can read SAINT output and may do a better job than combat
2) You could scale the data in the Bruker programs and import merged data to
CCP4
Phil
On 15 Jun 2010, at 10:19,
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
Just to avoid any problem
pdbcur xyzin X.pdb xyzout X-nohyd.pdb
DELHYD
END
Eleanor
Francois Berenger wrote:
Markus Rudolph wrote:
Hello,
long ago I had a case when HG1 etc. were interpreted as mercury by
phaser.
Could that be relevant to your case?
I hope not.
However, as I have
The increase in RFZ is relatively small and not entirely unexpected.
While hydrogens only contribute one electron (as opposed to carbon (6),
nitrogen(7), oxygen(8) and sulfur (16)), there are many hydrogens (in
fact, almost as many as all the other atoms combined). For instance, in
lysozyme you
Dear all,
In the phaser .sol file what do the two LLG's correspond to on the
SOLU SET line eg
SOLU SET RFZ=20.7 TFZ=35.4 PAK=0 LLG=1699 LLG=2821
Do they show an initial and a refined LLG or do they correspond to the
rotation and translation function as in the Z scores?
I checked the
I think the second LLG value is after refinement. But sometimes I see that
the second LLG goes negative and I wonder what it means. For example:
RFZ=3.1 TFZ=17.2 PAK=0 LLG=238 LLG=-603
-Konstantin
On Wed, 30 Sep 2009, Simon Kolstoe wrote:
Dear all,
In the phaser .sol file what do the two
In a Phaser automated molecular replacement job, it does almost
everything at a working resolution and then a final refinement at a
final resolution. By default, the working resolution is 2.5A and the
final resolution is the full resolution of the data set. So the
second-last LLG is the
Hi
This is probably an obvious one but I'm having trouble getting Phaser to
run. It simply says the status is starting and will not give me more
information in the log file. I suspect the problem has to do with the F
and Sigma F values but I am not sure what to assign them as?
Any help would
Hi,
is the problem related to one of the problems listed below?
(taken from the CCP4i troubleshooting page
http://www.ccp4.ac.uk/ccp4i/trouble_shooting.html ):
If I recall correctly, once I saw similar behaviour when my
$CCP4I_TCLTK/tclsh was pointing to an incorrect directory.
I hope that
Hi, Sylvia:
Did you also install Phenix in your machine? Phenix contains another
version of phaser and will alias phaser to the phaser in Phenix. Try
to type which phaser. If your command is not aliased to the phaser in
your ccp4 version. Just use runview com file in the ccp4 and type in
the
On Mon, Aug 24, 2009 at 12:30 PM, Joseph Ho
j...@medusa.bioc.aecom.yu.eduwrote:
Did you also install Phenix in your machine? Phenix contains another
version of phaser and will alias phaser to the phaser in Phenix.
No, it will be called phenix.phaser. The Phenix environment scripts
Dear CCP4BBer,
I'm using Phaser 2.1.4 to solve a structure containing both protein and DNA.
The packing function works find with the protein, but does not recognize the
trace of the DNA. Does anyone know precisely what should be the pdb format ?
Here is the format that I'am using :
ATOM 1 P
Hi,
Thanks a lot for the replies. It seems that Randy¹s solution works fine.
Marie-Ln
Le 6/08/09 13:54, « Randy Read » rj...@cam.ac.uk a écrit :
Hi,
That's actually the last question answered on our FAQ page!
http://www-structmed.cimr.cam.ac.uk/phaser/faq.html
Basically, you'll want
Original message:
Dear all,
When running phaser with ccp4i the program exits with a message
saying that the program had a fatal runtime error and that it could
not open the mtz file. All other programs I use with ccp4i manage to
run without problems.
Solution:
For some reason there was an old
Hello Aaron,
this usually means that you have a second version of phaser installed,
e.g. from the phenix package. To find out, go to a terminal from which you
would start ccp4i and type 'which phaser'. My guess is that the answer to
that command does not show phaser in the ccp4-directory.
On Thu, May 21, 2009 at 11:04 PM, Tim Gruene t...@shelx.uni-ac.gwdg.dewrote:
this usually means that you have a second version of phaser installed, e.g.
from the phenix package. To find out, go to a terminal from which you would
start ccp4i and type 'which phaser'. My guess is that the answer
Dear all,
When running phaser with ccp4i the program exits with a message
saying that the program had a fatal runtime error and that it could
not open the mtz file. All other programs I use with ccp4i manage to
run without problems.
Any ideas?
Thank's for any input.
Aaron
Hello all,
I have a structure that has been solved by MR and now have experimental SAD
phases that I hope will improve the map.
I used Phaser for this from within the CCP4i suite but I would like to take
the solution and work with it further in CNS.
Is there a way to generate a .hkl file from
The CCP4 mtz2various will do this. A sample script
and instructions for using the CCP4i GUI can be found at
http://capsicum.colgate.edu/chwiki/tiki-index.php?page=Phase+Solution#File_preparation.
The example cited is for preparing a file for EPMR, which is a simple
hklF listing.
Cheers,
--
Dear Kelly-Anne
2009/3/27 Kelly-Anne Twist wils...@rockefeller.edu:
Hello all,
I have a structure that has been solved by MR and now have experimental SAD
phases that I hope will improve the map.
I used Phaser for this from within the CCP4i suite but I would like to take
the solution and
Hi,
I've just run some tests with Phaser-2.1.4 (the version distributed
with CCP4 6.1 and with Phenix-1.3-final), and I get a .rlist file when
running the brute rotation function. Could you send me the logfile
from your job (probably better to do this off-line) so I can see
whether it's
Hi,
I've just double-checked this on my installation (6.0.99e still, but
shouldn't make a difference), and this command works.
I think that you've ended up with an older version of Phaser coming first
in your path. The syntax of the PACK command has changed (to allow it to
behave in a way
Hello,
I am running phaser from the ccp4 6.0.99 suite on an OSX 10.5.4 Leopard ,
Mac Pro machine .
I get the rather ominous error given below .
We have gotten similar malloc errors with large datasets before on this
machine. In those cases the same jobs ran fine on regular linux.
Thought I would
Hello Phil and thanks for your email..I was running a VMware fusion Ubuntu
session which was grabbing onto a large chunk of memory ( entirely my
fault). I didnt realize that virtualized sessions can divert memory away
from even the OS and make it essentially unavailable.
I am waiting for my
To the CCP4 community,
I have been trying to run PHASER to phase a nucleic acid structure by MR
using a partial template model. The problem is that symmetry-related molecules
generated from the output .pdb file coordinates spatially overlap with
extensive clashes. I understand from the
This turns out to be a failure in the (rarely exercised) code to read in
the substructure with a .ha file. We almost always use PDB files from Hyss
or SHELXD to enter the initial substructure, then Phaser .sol files if
there's a reason to carry on refinement.
The bug has now been fixed for
I am attempting to solve a 28kDa protein structure by sulfur anomalous
scattering in Phaser for EP (2.1.2). Phaser crashes immediately and I get the
following error in the log file. Thanks in advance for your input.
Sarah Wisecarver
EXIT STATUS: SUCCESS
Could you add information about
- operating system
- computer platform
- version of phaser
- how ccp4 was installed (binary or from source)?
Maybe you are trying to run a Mac binary on the wrong platform?
Tim
--
Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
Dear all,
I'm facing a particular MR problem:
I'm trying to solve the structure of a 20kDa protein (1 mol/AU) in a
cubic SG P432
(according to systematic absences and pointless)
Sequence homology is about 30%.
As I only get 'flat' scores with Phaser in P432, I lowered to SG P4
(with 6
I'm installing CCP4 and Phaser/CCTBX on a 64 bit machine (4 intel xeon cpus) running Ubuntu 8.04 with the 2.6.24-16-generic kernel (this linux was downloaded and installed just last week). I followed the instructions (untar ccp4*.tgz, untar phaser*.tgz, edit ccp4.setup, source ccp4.setup,
Message-
From: CCP4 bulletin board on behalf of Nathan I Nicely
Sent: Fri 5/16/2008 7:54 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Phaser compile errors
I'm installing CCP4 and Phaser/CCTBX on a 64 bit machine (4 intel xeon cpus)
running Ubuntu 8.04 with the 2.6.24-16-generic kernel
.
Ralf
- Original Message
From: Nathan I Nicely [EMAIL PROTECTED]
To: CCP4BB@JISCMAIL.AC.UK
Sent: Friday, May 16, 2008 5:54:28 AM
Subject: [ccp4bb] Phaser compile errors
I'm installing CCP4 and Phaser/CCTBX on a 64 bit machine (4 intel xeon cpus)
running Ubuntu 8.04 with the 2.6.24-16
To
Nathan I Nicely [EMAIL PROTECTED], CCP4BB@JISCMAIL.AC.UK
cc
Subject
RE: [ccp4bb] Phaser compile errors
It looks like you need to install python2.4 (and python2.4-dev if using
the package manager) and use that as the default during the build (remove
/usr/bin/python and symlink it to python2.4
Hi
I was running phaser on an 8 core Mac pro using the fink 10.5 (intel) ccp4
binaries provided by W.G Scott .
Although the many phaser jobs I have run in the last month have successfully
phased my data.
Today I saw a very strange error and phaser FAILED.
I did rerun phaser and have it work after
Hello Ethan Meritt,
Thanks for your reply,
I have only recently started using the 8 core Mac pro , and in the last
three days have faced many such issues with swapsize and running out of
memory (the machine has 4GB total).
Just Yesterday I had a problem on a different dataset with a cns simulated
Hi all,
in a rather weak molecular replacement the rotation solution that eventually
produces a decent translation search (Z9 with a couple of clashes) is way
down in the list of rotation function peaks. Sometimes this solution is
included in the translation function, in similar runs it is not.
On Sep 18 2007, Bryan W. Lepore wrote:
i wrote
(ensemble) / (sequence) to get a percent composition
i forgot to emphasize that i do not mean the Vm or the Z composition,
but the composition as one would enter e.g.
COMPosition ENSEmble mol1 FRACtional 0.22
or
COMPosition SCAttering
the phaser docs/tutorial indicate that phaser calculates what could be
called (ensemble) / (sequence) to get a percent composition, however i
cannot seem to find the direct result from this in any output (.sol, .sum,
.pdb, .log... other?)
any tips appreciated as to if this can be found /
i wrote
(ensemble) / (sequence) to get a percent composition
i forgot to emphasize that i do not mean the Vm or the Z composition,
but the composition as one would enter e.g.
COMPosition ENSEmble mol1 FRACtional 0.22
or
COMPosition SCAttering SCATTERING
-bryan
On Aug 31 2007, Bryan W. Lepore wrote:
if it doesn't now, will phaser be able to run a phased translation
function in the future?
-bryan
Yes, that's on our long to-do list!
Randy Read
if it doesn't now, will phaser be able to run a phased translation
function in the future?
-bryan
Hi all !!!
Is it possible to fix one domain and search for the second one in
phaser !!! What are the keywords to use.
I have a protein with two domains. It i give both the domains together or as
two ensembles it is not finding the solution. If i give only one domain it
is giving the
BSD
I donnot know what is wrong with the mtz file, it is simply
converted from a sca file
with scalepack2mtz, and now I am using molrep, it didnot give such
wrong information.
What is the problem? Thanks!
If you ran it through the GUI, did you click on the Run Truncate...
button to
You may have called the version of phaser installed in the phenix path. Type
wich phaser
in a terminal to check it.
Daniel
yang li a écrit :
Hi:
I am using CCP4 6.0.2, it has phaser contained in this package. When
I use it
to do mr, error occured:
Hi,
Anyone has used phser in ccp46.0.2 which is automatically installed with
ccp4? In previous ccp4 edition
I installed phaser seperately and it worked well, but now it seems has some
problems, it cannot read the
input mtz file, I tried several data, all gave the same error information
like
Hi,
You are almost certainly not using phaser that came with ccp4, but some
other version, e.g. phenix. From the window you start ccp4i from, type
'which phaser'. It should say '/your/path/to/ccp4-6.0.2/bin/phaser', but
it will say something different in your case (e.g.
Have you label your F and SIGF of mtz file?
On 3/26/07, yang li [EMAIL PROTECTED] wrote:
Hi:
I am using CCP4 6.0.2, it has phaser contained in this package. When I
use it
to do mr, error occured:
*
***
Quoting Andrew Wong [EMAIL PROTECTED]:
I was using Phaser for some MR with a data set in P1 (may not actually be
P1, but..), and in every run I always got a list of solutions that all
have TFZ=100.0, with a very small LLG (around 0 or even in the negative).
The RFZ is like 4 or less. The
On Mar 12 2007, Andy Purkiss wrote:
Quoting Andrew Wong [EMAIL PROTECTED]:
I was using Phaser for some MR with a data set in P1 (may not actually
be P1, but..), and in every run I always got a list of solutions that
all have TFZ=100.0, with a very small LLG (around 0 or even in the
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