If I remember for coefficients with FOM and a precise PHI calculated, A =
FOM*cos(phi) B = FOM*sin(phi) C=D=0
If you have a probability curve for PHI. 0 to 360 such as you get from
experimental phasing, A B C D mirror this bimodal curve better ..
On Fri, 9 Feb 2024 at 09:58, Nitin Kulhar <
Dear sir
Thank you for clearing that. I checked back to see that HLC/D are
invariably 0 for all reflections, with the non-zero HLA/B supposedly having
been originated from the probability distribution of phases *calculated* by
phaser. Hopefully, I have not misunderstood it.
Thanks and regards
Hi,
Hendrickson-Lattman coefficients are just a way of storing phase probability
information, and they can come from different sources including atomic models.
Phaser puts in HL coefficients because they could be handy under some
circumstances for combining the phase information from
Dear all
Is anomalous diffraction necessary for determining experimental phases and
the Hendrickson-Lattman coefficients (HLA, HLB, HLC, and HLD)?
MR solution from Phaser 2.8.3 (interfaced in ccp4 8.0.000 suite) seems to
be generating HLA/B/C/D coefficients from an x-ray diffraction dataset.
On 31/03/2021 04:37, rohit kumar wrote:
I tried to remove H atoms in pdbcur in ccp4 but still there are lots of HD and HH atoms present in the pdb.
Could anyone please suggest how to fix this problem.
PDBCUR would want to use the element column in order to identify that the atom
is a Hydrogen
Thanks to Damian for the clear explanation!
Just a bit more background. Airlie put this feature in because, with small
fragments such as helices (which our collaborator Isabel Usón uses in
ARCIMBOLDO), the initial translation function scores are often higher for
trials where symmetry-related
Hi Silvia,
Looking at the end of the log file, it looks like you have a very clear
solution and are ready to go!
This message means that a better solution from the Fast Translation Function
was excluded because it failed the packing test (too many clashes with
neighboring molecules).
Hi,
The old approach of counting the number of clashes was changed to the
percentage of trace atoms (typically CA atoms) involved in clashes largely
because, as people like Eleanor pointed out to us, the number of clashes grows
with the size of the problem and solutions can be rejected when
Dear CCP4bb members,
I found in the newer CCP4 Phaser MR version (I use CCP4 7.0.0 in Win7),
there is no "allow maximal clash..." option anymore. There are only two
options "pairwise percent packing" and "accept all solutions". I used to
increase the number in the "allow maximal clash" (let's
Hi,
The syntax of the PACK command has changed, but the commands generated by the
GUI have also changed in synch, so this problem shouldn't normally arise.
Our best guess is that the user is attempting to rerun an old job, and ccp4i is
getting confused when trying to interpret the saved old
That is a very high nTCS vector (78% of the origin. Are you sure your unit
cell isny doubled
ie cell is not 94.2073 148.003 72.9967 90 97.6686 90
But
47.136 148 7390 98 90
What does pointless suggest for theSG
Eleanor
On 26 November 2016 at 18:56, KAUSHIK H.S. <
Dear Dr. Read,
For the first time, Phaser gave the following warning.XXXWarning:
Input/Default tNCS NMOL (2) does not match suggested NMOL (4): Please check
cell content analysis and tNCS to confirm NMOL
Warning: tNCS is present but correction factors NOT applied
XXX
Hence, I set NMOL=4
Hi,
That message should mean that you didn't ask for a number of molecules
divisible by the order of the tNCS. With that vector you need to search for an
even number of copies.
Let me know if that doesn't explain what you're saying.
Best wishes,
Randy Read
Randy J. Read
> On 25 Nov
Hello,
I have a crystal in C2 spacegroup (94.2073 148.003 72.9967 90 97.6686 90) and
Xtriage predicts 923 residues in ASU. My protein could be anywhere between 95
to 110 residues long (assuming the terminals could be cleaved). Using a
homolog, Phaser gives me a solution with LLG=1072 and
Hi everyone,
I think I have finally got a solution in Phaser (screen shot attached) as
the TFZ is 10.
However the solution PDB has 30 molecules in it as the search model was an
NMR solution.
As I have 0.944 Angs resolution data pretty complete, I thought of building
the initial model in ArpWarp.
Just throw your phaser-placed model into Buccaneer
JPK
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of xaravich
ivan
Sent: Monday, June 29, 2015 3:10 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Phaser solution and solvent content for arp warp
Hi everyone,
I think I
I think I would be tempted to chainsaw one of the ensemble chains of
2IT8 (they look very similar except for side-chain disposition) and use
1 or 2 of these as search models in a Phaser run. If this works, you
should see good Z-values and the final result inspected in Coot should
show good
From: CCP4 bulletin board
[CCP4BB@JISCMAIL.AC.UK] on behalf of Randy Read [rj...@cam.ac.uk]
Sent: 22 April 2015 09:04 To: CCP4BB@JISCMAIL.AC.UK Subject: Re:
[ccp4bb] Phaser going into infinite loop in Ample
Hi Dale,
It must actually be AMPLE deciding
Hi Dale,
It must actually be AMPLE deciding how many copies to search for. Phaser will
give you some information about how consistent the specified composition is
with the Matthews volume, but it just searches for the number of copies that
it's instructed to look for. We haven't put the
Dear Dale,
Isabel Uson's ARCIMBOLDO-LITE works well for coiled coils and has the
same resolution
requirements (2.1A or better) as AMPLE because both use SHELXE to expand
the solution.
It also employs PHASER to place a small fragment but it is often
sufficient to let it search for
just two or
Dear Dale,
as George points out, you may be interested in trying ARCIMBOLDO, as it has
been successfully applied to coiled coil proteins recently, as in the case
of
Franke et al (2014) Open Biology, 4. p. 130172 or Sammito et al (2013)
Nature Methods 10: 1099-1101 . Different models can be
@JISCMAIL.AC.UK] on behalf of Randy Read
[rj...@cam.ac.uk]
Sent: 22 April 2015 09:04
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Phaser going into infinite loop in Ample
Hi Dale,
It must actually be AMPLE deciding how many copies to search for. Phaser will
give you some information about how consistent
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
We are having a problem with AMPLE and hope someone can help.
The protein is about 70 amino acids long and we suspect it forms a
coiled-coil. Our previous attempts at molecular replacement have
failed so we hoped that AMPLE, with its ability
Hi all,
Actually, what I think has happened here is that Phaser has limited the
resolution to what it estimated was needed to get a clear enough solution, and
then the final refinement was carried out with all the data. The
signal-to-noise is lower with limited data, but it’s a price that
The Z-values may be marginal, but of course you should inspect the
solution in Coot to see if the electron density makes sense, and the
packing of the protein molecules in the unit cell (look at symmetry
mates) is sensible. If this passes the sniff test, then you should clean
up your model
Hi Jeorge -
Something seems to have changed for the worse in this MR run. In your
earlier posting, where you failed to find a solution in P222, your log
file had solutions with RFZ=23.4, generally a clear indication of a
correct rotation function solution. (You didn't include this log file
Thank you so much to all for your kind concern.
Jeorge
On Mon, Jan 26, 2015 at 5:55 PM, Kay Diederichs
kay.diederi...@uni-konstanz.de wrote:
Dear Jeorge,
you'll find some information about this in
http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Space_group_determination
. A
Dear Jeorge,
you'll find some information about this in
http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Space_group_determination
. A practical and easy way is described in
http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Pointless
HTH,
Kay
On Mon, 26 Jan 2015 11:24:27
Dear Jeorge,
XDS make no claim to determine the SPACE GROUP but rather the LAUE
GROUP, as only the latter is taken into account during data integration.
This is definitely so during the indexing step (IDXREF.LP), but even in
CORRECT, when systematic absences are sometimes indicated, XDS does not
Dear Jeorge,
I can’t see anything in that output saying whether the systematic absences that
would allow you to detect screw axes were covered in your data collection.
In any case, it’s not necessary to reintegrate. All that happens when going
from P222 to any one of the other 7 possible
Dear all,
i am solving a structure of 2.5 A resolution by PHASER but every time i got
this following warning.
$TEXT:Warning: $$ Baubles Markup $$
-
Large non-origin Patterson peak indicates that translational
Dear Rohit,
Are you sure about your space group? I think you should look at this first
Hope it helps.
Etienne
Etienne Rebuffet, PhD
Tel: +334 86 97 73 34
Laboratory of 'integrative Structural Chemical Biology (iSCB)'
Cancer Research Center of Marseille (CRCM)
CNRS UMR 7258; INSERM U 1068;
Hi Jurgen,
You could send me a logfile off-list, and maybe I would spot something in there.
We’ve put some effort into putting more intelligence into the Phaser search, so
that it adapts to the initial perceived difficulty of the problem in setting
the initial parameters, and then adapts to
Hi again,
I should have mentioned that, if you have a good enough model, it’s often
possible to solve the structure in P1. The molecular replacement solution will
settle on one of the twin domains (or you may end up with more than one
solution, related by the twin law(s)). Then the symmetry
Dear Jurgen,
Thanks for your interest in DIALS - we are working hard at the moment on
testing the software and finding bugs (and fixing them!) and I would say
right now it's not quite ready for the general user, but we do plan to make
an alpha release of the software before the end of the year.
Thanks Randy,
so from your reply it seems that cutoff is differently treated. And if I
interpret your email correctly it is better to provide Phaser with a truncated
versus a full data set. I tried both cases, but I had assumed that if you
restrict the resolution within Phaser it would be the
Dear BB, or in particular Phaser developers :-)
This must be part of British humor right (or was that the Canadian influence
Randy) ?
eLLG indicates that placement of ensemble ensemble_1 will be straightforward
The data are sufficient to exceed the eLLG target
The search space is finite 143
Just to add to what Herman said:
The statistics are good for placing the domain represented by ensemble 1
(TFZ=14.3) and the first copy of the domain represented by ensemble 2
(TFZ=11.9), but not for the two possible solutions for placing the second copy
of ensemble 2 (TFZs of 4.5 and 4.7).
Or perhaps there is only 1 copy and more solvent than you expect? This is not
that uncommon.
On 20 Sep 2014 12:09, Randy Read rj...@cam.ac.uk wrote:
Just to add to what Herman said:
The statistics are good for placing the domain represented by ensemble 1
(TFZ=14.3) and the first copy of
Dear CCP4 members,
Recently I have collected native data at 3.3 A resolution. The structure of the
protein should have two domains. The structure of c terminal domain from
homologous (30 seq similarity) is known. I took n terminal domain from another
homologous protein. I ran the phaser using
Salvatierra maps.fa...@gmail.com
Date: 2014-06-03 9:49 GMT+02:00
Subject: Re: [ccp4bb] phaser issue MR
To: Airlie McCoy ajm...@cam.ac.uk
Dear Airlie,
don't worry, actually it was you who gave me the clue when you told me what
the error was standing for. I will try to be a clear as possible:
1
to misunderstandings at the
end.
Best wishes,
Have a nice day.
Almudena
-- Forwarded message --
From: Almudena Ponce Salvatierra maps.fa...@gmail.com
Date: 2014-06-03 9:49 GMT+02:00
Subject: Re: [ccp4bb] phaser issue MR
To: Airlie McCoy ajm...@cam.ac.uk
Dear Airlie
Dear all,
I am using Phaser for Molecular replacement. After Phaser places part of
the structure, I would like to run it again, giving this time as search
ensembles new pieces of structure. I thought what I had to do was simply to
put in know solution the .sol file coming out from the previous
Hello Everyone,
I'm trying to using Phaser to perform molecular replacement, however each time
I run my input script Phaser ends with a segmentation fault. Here is the error
phaser0.inp: line 29: 1414 Segmentation fault (core dumped) phaser
EOF
My input script can be found here:
Looks like you need to search for more molecules.
Best,
Herman
Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Amanda
Blythe
Gesendet: Montag, 16. Dezember 2013 11:46
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [ccp4bb] Phaser output problem
I am trying to solve a structure
like you need to search for more molecules.
Best,
Herman
*Von:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *Im Auftrag von
*Amanda Blythe
*Gesendet:* Montag, 16. Dezember 2013 11:46
*An:* CCP4BB@JISCMAIL.AC.UK
*Betreff:* [ccp4bb] Phaser output problem
I am trying to solve
Just to follow up on this:
The enormous increase between the TFZ= and TFZ== numbers is surprising, so I
focused on that in my original answer to Fred's question. However, if anyone
wants to know the difference between these, it's documented on this web page:
Hiyya all,
I have a question about the latest Phaser output, concerning TFZ = and
TFZ == .
I do not know how to interpret outputs of the type
TFZ = 5.2 TFZ == 54.1;
TFZ = 5.8 TFZ == 63.0;
TFZ = 6.4 TFZ == 19.7 (these are real TFZ figures coming from Phaser log
files).
I used to analyse
Hi Fred,
Send me the logfiles (off-line), because this shouldn't be happening and I'd
like to have a look. That said, we've been seeing some similar problems in
certain circumstances, i.e. B-factor refinement refines to significant negative
B-factor values, and data at high resolution have
Hi,
I need (reluctantly!) to install CCP4 on 20 fairly ancient Windows XP machines
for a course. I have installed CCP4 on a central server with network-mounted
drive and applied all the updates. CCP4 is then runnable on the individual
computers. However when I run a Phaser job the output in
Dear All,
Installed the CCP4 6.4.0 version recently on CentoS 5. When I try to run
phaser I get the following error. Apparently I can reproduce the error
for different reflection file. This happens after getting the rotation,
translation and packing function. Any suggestions to this problem
Dear Petr,
Presumably you're just talking about Phaser for molecular replacement, because
Phaser still produces HL coefficients for SAD phasing.
There were two major reasons we made this change. First, the presence of HL
coefficients can fool some programs into thinking that you have
Dear Randy,
Thank you for your quick response. Obviously, you have given this a lot
of thought.
I would like to have the HL coefficients in the phaser output file for
downstream compatibility with density modification programs such as
resolve.
Thank you,
Petr
On 07/03/2013 10:46 AM, Randy
I have just found out that phaser v. 2.5.2 in ccp4 6.3.0-021 does not
output columns with HL coefficients. I cannot find a combination of
buttons in CCP4i GUI to enable this extremely useful feature. This is
the first time I tried phaser in the latest CCP4 release and I am
shocked this problem
On the whole it is good practice to refine the 7 molecules you have - correct
sequence etc etc, all with NCS restraints a 3A, then if you like use one of
your improved molecules as the search model. But don't you have some NC
symmetry such as dimers or tetramers - if so take one of the complete
if you are sure about it's position, why not put the 8th molecule by hand?
why believe what a program does more than you can see by eye?
(this is nothing against Phaser, it is a great program)
Mark J van Raaij
Laboratorio M-4
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia -
Hi all,
we have been running into a space group issue when we start phaser (2.5.1)
through ccp4i since the installation of ccp4-6.3.0:
We typically scale data in the point group and then let Phaser go through
various space groups. Even though the corresponding line appears in the input
file
Hi,
As of last week, this is a known bug (defined as one where I got around to
adding it to the list on our Phaser Wiki). It has been fixed in the latest
nightly builds of Phenix, and a new executable will be released through CCP4 in
a few weeks, coordinated with the next stable release of
The ensemble should be a set of coordinates
Eleanor
On 15 Aug 2012, at 04:42, 李华 wrote:
Dear ccp4er,
I try to use Phaser MR to solve a structure. A mtz file from oasis was
used as a ensemble. All of the parameters containing protein MW, nucleic acid
MW, extent of X, Y, Z and center of
No, it's possible also to specify a model in the form of the molecular
transform in an MTZ file, derived either from coordinates or a density map.
I see that I failed to Reply all in my earlier reply to this email, which was
the following:
=
Does the MTZ file from oasis contain electron
, but not OASIS -
PHASER. Or do you have some special idea？
Zhang, Tao
发件人: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] 代表 李华
发送时间: 2012年8月15日 11:42
收件人: CCP4BB@JISCMAIL.AC.UK
主题: [ccp4bb] phaser with MR--search ensemble
Dear ccp4er,
I try to use Phaser MR to solve
Dear ccp4er,
I try to use Phaser MR to solve a structure. A mtz file from oasis was
used as a ensemble. All of the parameters containing protein MW, nucleic acid
MW, extent of X, Y, Z and center of X, Y, Z and RMS error were assigned.
However, when I ran phaser mr, the program complain
(MRC,RAL,RCAH)
Cc: ccp4bb
Subject: Re: [ccp4bb] Phaser Fatal runtime error.
We have an in-house Agilent (Oxford) system and routinely use data with CCP4.
You will need to run sortmtz, scala (w/constant scale), and truncate to prep
the data properly. This can be done via batch file or GUI.You may
Data from Crysalis in mtz format are not merged I think - you have to go
through the scale and merge step in Scala first ...
Jan Dohnalek
On Tue, Jun 26, 2012 at 11:21 PM, Steiner, Roberto
roberto.stei...@kcl.ac.uk wrote:
Don't know where the exact problem is. However, it is definitely
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Jan
Dohnalek
Sent: 27 June 2012 07:30
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Phaser Fatal runtime error.
Data from Crysalis in mtz format are not merged I think - you have to go
through the scale and merge step in Scala
I suspect you didn't request the FreeR assignment on the TRUNCATE interface?
This calls amongst other programs, CAD and CAD makes sure that the reflection
list is unique and that it is in a standard asymmetric unit. Most people do it
by default so don't hit these problems...
I suggest you just
Just to be clear, Phaser does not require the reflections to be in a
standard asymmetric unit, only that they are unique (as the error message
thrown says).
Airlie
On Jun 27 2012, Eleanor Dodson wrote:
I suspect you didn't request the FreeR assignment on the TRUNCATE
interface? This calls
We have an in-house Agilent (Oxford) system and routinely use data with
CCP4. You will need to run sortmtz, scala (w/constant scale), and truncate
to prep the data properly. This can be done via batch file or GUI.You may
also have to reset/reassign the space group for some space groups due to an
Dear CCP4bb
I have collected a data-set using the supernova x-ray generator from Agilent
and taken the mtz file generated by the data processing software in crysalis
pro forward for structure solution. The data collection was straight forward
and the software seemingly processed the data
Don't know where the exact problem is. However, it is definitely possible to
use a Crysalis-Scala-Truncate-Phaser pipeline without runtime errors. I have
done a few times.
I am sure you will be able to get help from Agilent people. If not, feel free
to get back to me.
Best
Roberto
On 26 Jun
The new CCP4I interface for PHASER removed the menu item where you could
change the number of clashes. It's not set as a default to 5% of the
number of C-alpha atoms. Where is the default file?
I found the phaser_MR.def file in share/ccp4i/tasks, and changed the
parameter value, but it still used
If you install the .tcl update from the CCP4 site, you will find the clash
menu setting under advanced options, IIRC.
Roger Rowlett
On Jun 20, 2012 6:08 PM, Santarsiero, Bernard D. b...@uic.edu wrote:
The new CCP4I interface for PHASER removed the menu item where you could
change the number of
, 2012 8:20 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] phaser: high z score but no sol
Hi all,
I am trying to solve one structure by molecular replacement with
phaser in CCP4. This a complex of a multi-domain domains with small
ligand. I
Subject: [ccp4bb] phaser: high z score but no sol
Hi all,
I am trying to solve one structure by molecular replacement with phaser in
CCP4. This a complex of a multi-domain domains with small ligand. I have
structues of this protein in apo state and with other similar ligand. The
space group
P21.. You sure about this space group? (very high confidences for space group
and laue group in pointless?)
F
On Apr 19, 2012, at 12:20 AM, LISA wrote:
Hi all,
I am trying to solve one structure by molecular replacement with phaser in
CCP4. This a complex of a multi-domain domains
Hi all,
I am trying to solve one structure by molecular replacement with phaser in
CCP4. This a complex of a multi-domain domains with small ligand. I have
structues of this protein in apo state and with other similar ligand. The
space group of this crystal is P21. This crystal should have 4
Hi,
If you have the correct solution, clashes may be due to loops. It may be
an idea to clip these off for the molecular replacement calculations
(loops might be shorter in the structure-to-be-solved than in the search
model, they may have different conformations in the
Hi,
My first guess would be that this crystal possesses translational NCS, and that
you're using the old (distributed with current old CCP4) version of Phaser
that can't handle tNCS. You can tell if this is the case by looking at whether
there's a large off-origin peak in the native Patterson
As Randy pointed out, you should check Patterson map for off-origin
peaks. There is also a small chance that you actually have P2 -
systematic absences may result from tNCS nearly colinear with
crystallographic axis.
On Thu, 2012-04-19 at 14:20 +0800, LISA wrote:
Hi all,
I am trying to solve
This was resolved offline. It turns out that there's an obscure bug in Phaser
triggered if you search for the same model twice as an alternative for itself
(e.g. SEARCH ENSEMBLE ensemble1 OR ENSEMBLE ensemble1 NUM 1). When the input
was fixed (SEARCH ENSEMBLE ensemble1 NUM 1), Phaser didn't
Hi CCP4 community.
While running the Phaser in the CCP4 GUI, It was terminated and giving the
error message.
#CCP4I TERMINATION STATUS 0 child killed: segmentation violation
#CCP4I VERSION CCP4Interface 2.0.6
CCP4 Version ccp4-6.1.13
Thanks in advance.
Sita Ram
Thanks for pointing out that link. The graph makes the point I was going to
mention, i.e. that you notice a big difference in using up to about 4
processors for typical jobs, but after that point the non-parallelisable parts
of the code start to dominate and there's less improvement. This is
Le Tue, 8 Nov 2011 16:25:22 -0800,
Nat Echols nathaniel.ech...@gmail.com a écrit :
On Tue, Nov 8, 2011 at 4:22 PM, Francois Berenger beren...@riken.jp
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
On 11/09/2011 07:21 PM, Pascal wrote:
Le Tue, 8 Nov 2011 16:25:22 -0800,
Nat Echolsnathaniel.ech...@gmail.com a écrit :
On Tue, Nov 8, 2011 at 4:22 PM, Francois Berengerberen...@riken.jp
wrote:
In the past I have been quite badly surprised by
the no-acceleration I gained when using OpenMP
--
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-3021 or -3068
Fax. +49-551-39-22582
---BeginMessage---
In my experience, writing efficient multithreaded code is much harder
than writing efficient
Could anyone point me towards instructions on how to get/build
parallelized phaser binary on linux? I searched around but so far found
nothing. The latest updated phaser binary doesn't seem to be
parallelized.
Apologies if this has been resolved before - just point at the relevant
thread,
Hi Ed,
in the CCP4 distribution, openmp is not enabled by default, and there
seems to be no easy way to enable it (i.e. by setting a flag at the
configure stage).
On the other hand, you can easily create a separate build for phaser
that is openmp enabled and use phaser from there. To do this,
On Tue, Nov 8, 2011 at 4:22 PM, Francois Berenger beren...@riken.jp wrote:
In the past I have been quite badly surprised by
the no-acceleration I gained when using OpenMP
with some of my programs... :(
Amdahl's law is cruel:
http://en.wikipedia.org/wiki/Amdahl's_law
This is the same reason
See page 3 of this
http://www-structmed.cimr.cam.ac.uk/phaser/ccp4-sw2011.pdf
On Wed, 2011-11-09 at 09:22 +0900, Francois Berenger wrote:
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
The new Phaser GUI does not seem to let me reset the number of clashes
for the packing search?
Is there something I have missed?
Eleanor
Hi Eleanor,
I think you should find it in the Additional Parameters section, second line,
labelled Packing criterion. The default (chosen largely because you had been
asking for something like this!) is to allow a number of clashes equal to 5% of
the number of residues.
Let me know if it
Subject: Phaser: ensemble not set
Hello:
I try to use Phaser under MR.
The program complain: ensemble not set.
The ensemble box keeps blank and does not allow to click.
I use: ccp4-6.2.0
Window Vista Business
Thanks for advice
ROS
Dear Randy and the Phaser team,
Phaser 2.3.0 brought us several enhancement, but similar to Alexander
Schiffer's experience, Phaser has failed several times now with a floating
point exception error at different stages of automated MR: it has stopped in
the beginning of RF and then in a new
Dear Petr,
Yes, please do send the log files, MTZ file and anything else needed to run the
job that shows the problem, so we can track it down. It's probably best to
send them off-line.
We couldn't reproduce Alexander's problem, but he tells me that it only occurs
when the script is started
Hi,
Could you send me some representative logfiles (probably off-list)? This might
give a hint. It must be something unusual, because we have a fairly wide range
of test cases and none of them have any problems.
Thanks and best wishes,
Randy Read
On 1 Sep 2011, at 14:58,
Hi Amir,
When this error was reported before, it turned out that the sequence file used
to define the composition had the one-letter code Z (presumably for Se-Met),
which Phaser-2.1.4 doesn't recognise. I'm not sure what the newer versions in
CCP4 and Phenix would do with this, but at the
Hi
Has anyone a solution to the following problem with Phaser (version 2.1.4)?
UNHANDLED ERROR: basic_string::_S_create
It seems to be data and model independent – there was an old thread from
earlier this year, but I cannot find a follow-up.
Thanks!
Amir
Dear all,
it would be really great if someone could point out to me how to enable the
openmp option for phaser during the compilation of the latest ccp4 release.
The system will be a SUSE 11.3 64bit using gcc.
Cheers,
Jochen
...@gmail.com
*To:* CCP4BB@JISCMAIL.AC.UK
*Sent:* Thu, July 21, 2011 6:39:49 AM
*Subject:* Re: [ccp4bb] Phaser and Molrep gave different solutions
I was worried as well with the low TFZ score. Usually successful cases with
score 8. I am still puzzled why Phaser and Molrep gave different
--
*From:* Hubing Lou louhub...@gmail.com
*To:* CCP4BB@JISCMAIL.AC.UK
*Sent:* Thu, July 21, 2011 6:39:49 AM
*Subject:* Re: [ccp4bb] Phaser and Molrep gave different solutions
I was worried as well with the low TFZ score. Usually successful cases
with
score 8. I am still puzzled why Phaser
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