The Phenix developers are pleased to announce that version 1.21.1 of Phenix is
now available (build 1.21.1-5286). Binary installers for Linux, Mac OSX, and
Windows (under Windows Subsystem for Linux), and the source installer, are
available at the download site:
For anyone who is confused:
Unfortunately, the link given here (https://phenix-online.org/download/) says
that the latest release is 1.19.2-4158! That’s very odd because the same URL
without the trailing slash (https://phenix-online.org/download) gets to a
different page with the right
The Phenix developers are pleased to announce that version 1.21 of Phenix is
now available (build 1.21-5207). Binary installers for Linux, Mac OSX, and
Windows (under Windows Subsystem for Linux), and the source installer, are
available at the download site:
Dear Colleagues,
The Phenix developers will be holding a day-long satellite workshop on July
29th, prior to the ACA meeting in Portland, Oregon. This Phenix user
workshop will focus on using predicted models for crystallography and
cryo-EM.
The format of the workshop will be demos of the use
The Phenix developers are pleased to announce that version 1.20 of Phenix is
now available (build 1.20-4459). Binary installers for Linux, Mac OSX, and
Windows platforms, and the source installer, are available at the download site:
http://phenix-online.org/download/
Highlights for the
Robbie joosten says it is fixed - a bug seen by pdb- redo from an old
version of Phoenix. Message him for more detail... cheers Eleanor
On Fri, 31 Dec 2021 at 22:27, Pavel Afonine wrote:
> Hi All,
> who produced this file? If phenix.refine added water with chain S given
> that protein chains
Hi All,
who produced this file? If phenix.refine added water with chain S given
that protein chains named S were already in that model, then it is a bug
that I need to fix.
Cheers,
Pavel
On Thu, Dec 30, 2021 at 11:05 AM Eleanor Dodson <
176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote:
> I
Thanks Robbie - so we dont need to bother much about it...
E
On Fri, 31 Dec 2021 at 15:21, Jon Cooper <
488a26d62010-dmarc-requ...@jiscmail.ac.uk> wrote:
> I was going to suggest returning to this topic in 3 months time. It has
> that sort of quality ;-?
>
>
> Sent from ProtonMail mobile
>
>
I was going to suggest returning to this topic in 3 months time. It has that
sort of quality ;-?
Sent from ProtonMail mobile
Original Message
On 31 Dec 2021, 15:17, Robbie Joosten wrote:
> Hi Eleanor,
>
> This seems to be a caused by a bug in an older version of Phenix. We
Hi Eleanor,This seems to be a caused by a bug in an older version of Phenix. We used to see quite a few examples of this on the PDB-REDO server, but not recently. Renumbering is the only solution I'm afraid.Cheers,RobbieOn 30 Dec 2021 20:05, Eleanor Dodson
I am not sure whether I have this straight but someone has sent a pdb file
from phenix refinement with these atoms in the pdb file..
ATOM 5580 N GLY S 18 36.182 44.368 56.021 1.00 79.25
N
ATOM 5581 CA GLY S 18 37.168 44.349 57.091 1.00 74.78
C
ATOM 5582 C
*Subject:* [External] Re: [ccp4bb] phenix refinement for bent DNA
Hi Dhiraj,
I have structure with bent DNA. I am trying to refine the
structure using phenix. do I need to turn off the DNA secondary
structure restraints during refinement?
Application of secondary structure
On 30/03/2021 02:52, Srivastava, Dhiraj wrote:
I am sorry about phenix related question. But since the question was
refinement related I thought it will be ok to ask on ccp4bb.
For the record, it's not wrong, it just that questions about Phenix are more likely to get accurate and
timely
Cc: CCP4BB@jiscmail.ac.uk
Subject: [External] Re: [ccp4bb] phenix refinement for bent DNA
Hi Dhiraj,
I have structure with bent DNA. I am trying to refine the structure using
phenix. do I need to turn off the DNA secondary structure restraints during
refinement?
Application of secondary
Hi Dhiraj,
I have structure with bent DNA. I am trying to refine the structure
> using phenix. do I need to turn off the DNA secondary structure restraints
> during refinement?
>
Application of secondary structure restraints depends on the quality of the
experimental data. The most basic
Hi Dhiraj,
I have structure with bent DNA. I am trying to refine the structure
> using phenix. do I need to turn off the DNA secondary structure restraints
> during refinement?
>
probably not, unless you have reasons to do so otherwise.
P.S.: There is a Phenix mailing list for Phenix
Hi
I have structure with bent DNA. I am trying to refine the structure using
phenix. do I need to turn off the DNA secondary structure restraints during
refinement?
Thank you
Dhiraj
To unsubscribe from the CCP4BB
The Phenix developers are pleased to announce that version 1.19.1 of Phenix is
now available (build 1.19.1-4122). This fixes bugs in the 1.19 release. If you
have previously downloaded 1.19 we recommend upgrading to 1.19.1. Binary
installers for Linux, Mac OSX, and Windows platforms, and the
The Phenix developers are pleased to announce that version 1.19 of Phenix is
now available (build 1.18.2-3874). Binary installers for Linux, Mac OSX, and
Windows platforms, and the source installer, are available at the download site:
http://phenix-online.org/download/
Please note that
Thanks for the advice Pavel!
I don't want to celebrate prematurely, but I just re-ran the same
refinement in both the stable and in nightly 4070, and it _seems_ to be
corrected in the nightly. Will let you know if it pops up again.
- Igor Petrik, PhD
On Thu, Dec 3, 2020 at 9:16 AM Pavel
Thanks Nigel,
I will put together the input and output file from my latest refinement and
send them to you and Pavel later today.
- Igor Petrik, PhD
On Wed, Dec 2, 2020 at 9:46 PM Folmer Fredslund wrote:
> Dear Igor
>
> There's a phenix bulletin board for question like this, which is where
Hi Folmer,
I would choose to not do the real space refinement in phenix.refine during
> the last rounds of refinement of a model, when sidechain positions are
> essentially correct.
>
by design it is supposed to place and fit side chains as good as possible,
satisfying both map fit and geometry
Dear Igor
There's a phenix bulletin board for question like this, which is where you
should post the question. ( I crosspost here)
I would choose to not do the real space refinement in phenix.refine during
the last rounds of refinement of a model, when sidechain positions are
essentially
Igor
There is a Phenix BB for your Phenix related questions. You can subscribe
here.
http://www.phenix-online.org/mailman/listinfo/phenixbb
In the meantime, please send the Phenix version and OS to myself and Pavel
privately and I'm sure we can help. We may also need the inputs (privately,
of
I am refining a 1.71A X-ray structure with phenix refine. I have everything
modelled in - ~150 residues in the ASU and a heme - and my R-work/R-free is
0.17/0.22. But when I went to deposit it, PDB pointed out that two of my
sidechains have distorted geometries. One is a His, and looking at it in
Dear Colleagues,
The Phenix developers will be holding an online *Phenix User Workshop on
the 17th and 18th of November at 8am-12pm PDT.* These times will work best
for researchers in North and South America, Europe and Africa. We plan to
hold a future workshop at a time better suited to
Dear Clemens,
If the working model and reference model are exactly identical, you may try
to use the same file in both the working and reference model to see if it
works. I don't see anything strange in the pdb lines you attached. I'm
happy to have a closer look if you are willing to share
Dear All,
I am not getting any reference model matches in Phenix:
Reference Model Matching Summary:
reference file: reference.pdb
Model: Reference:
Total # of matched residue pairs: 0
Total # of reference model restraints:
The Phenix developers are pleased to announce that version 1.18 of Phenix is
now available (build 1.18.2-3874). Binary installers for Linux, Mac OSX, and
Windows platforms, and the source installer, are available at the download site:
http://phenix-online.org/download/
Please note that
Dear Colleagues,
please make a note of upcoming Phenix workshop focusing on crystallography
and Cryo-EM tools for structure solution, August 2nd 2020 in San Diego,
California. This is a day-long satellite workshop prior to ACA meeting. For
schedule and registration see ACA 2020 web site:
Postdoctoral Researcher
Lawrence Berkeley Laboratory
Job ID: 89267
Division: Molecular Biophysics & Integrated Bioimaging (Computational
Crystallography Initiative)
Date Opened: 12/23/2019
Summary: Berkeley Lab’s Molecular Biophysics and Integrated Bioimaging
Division has an opening for a
Postdoctoral Researcher
Lawrence Berkeley Laboratory
Job ID: 89267
Division: Molecular Biophysics & Integrated Bioimaging (Computational
Crystallography Initiative)
Date Opened: 12/23/2019
Summary: Berkeley Lab’s Molecular Biophysics and Integrated Bioimaging
Division has an opening for a
The Phenix developers are pleased to announce that version 1.17 of Phenix is
now available (build 1.17.1-3660). Binary installers for Linux, Mac OSX, and
Windows platforms, and the source installer, are available at the download site:
http://phenix-online.org/download/
Please note that
Hi Structural biologists, particularly students and postdocs!
A Phenix crystallography/cryo-EM workshop will be held after the last day
of Understanding Biology through Structure 2020 (https://cvent.me/4kq9P,
the meeting is March 16-19, 2020 in Santa Fe,NM; the workshop is March 20
and the
Hi Jonathan,
send me files off list and I will have a look. From your description it
isn't clear to me what the problem is. You need to add H or D or H and D
only once (and phenix.ready_set is the right tool to do it!), then just do
refinement and all should work. Coot indeed may not play well
Dear Jonathan,
since structure for neutron data are usually pre-refined and you are
only interested in the small print, you can also use SHELXL for
refinement (https://doi.org/10.1107/S1600576713027659). That gives you
full control over what you want to achieve.
With PDB2INS
On 20/06/2019 17:44, Jonathan Cooper wrote:
I am trying to refine a neutron structure for someone and I have come across a couple of things which I need
help with.
I am struggling to get the occupancy refinement of the hydrogens/deuteriums on the N-terminal nitrogens to
behave right. Some of
I am trying to refine a neutron structure for someone and I have come across a
couple of things which I need help with.
I am struggling to get the occupancy refinement of the hydrogens/deuteriums on
the N-terminal nitrogens to behave right. Some of them get deleted by readyset
but the trick
The Phenix developers are pleased to announce that version 1.15 of Phenix is
now available (build 1.15.2-3472). Binary installers for Linux, Mac OSX, and
Windows platforms, and the source installer, are available at the download site:
http://phenix-online.org/download/
Highlights for
The Phenix developers are pleased to announce that version 1.14 of Phenix is
now available (build 1.14-3260). Binary installers for Linux, Mac OSX, and
Windows platforms, and the source installer, are available at the download site:
http://phenix-online.org/download/
Highlights for
r/ ,
http://lcrbw.pharmacie.univ-paris5.fr/spip.php?article18
De : Nigel Moriarty <nwmoria...@lbl.gov>
À : CCP4BB@JISCMAIL.AC.UK
Envoyé le : Vendredi 2 mars 2018 8h25
Objet : Re: [ccp4bb] phenix refinement about cis-proline
Shijun
You can ask all the questions you like about Phenix on P
Shijun
You can ask all the questions you like about Phenix on PhenixBB. However,
to answer your question, you can set all peptides to trans using
apply_all_trans=True
or more specific control using
apply_cis_trans_specification {
cis_trans_mod = cis *trans
residue_selection = None
Dear all
I am refining a structure which has cis-Pro and trans-Pro, the tans-Pro is
gone when I set the "threshold degrees for cis-peptide " from default 45 to 65,
but still has cis-Pro. While no significant change when I set it to 15. My
question is how to set in phenix refinement to clear
The Phenix developers are pleased to announce that version 1.13 of Phenix is
now available (build 1.13-2998). Binary installers for Linux, Mac OSX, and
Windows platforms are available at the download site:
http://phenix-online.org/download/
Highlights for this version:
-
The Phenix developers are pleased to announce that version 1.12 of Phenix is
now available (build 1.12-2829). Binary installers for Linux, Mac OSX, and
Windows platforms are available at the download site:
http://phenix-online.org/download/
Highlights for this version:
New tools for
Hi all,
The Phenix website is still currently down due to scheduled electrical work
in the building. Power has not been restored to the building and there is
no firm estimate on when power will be available.
--
Billy K. Poon
Research Scientist, Molecular Biophysics and Integrated Bioimaging
Is the phenix website down? Anyone know when it will be back up?
Sosa
Sent: Tuesday, November 22, 2016 7:51 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Phenix on Windows
I am trying to install Phenix on a Windows (windows 7) machine using the
windows installers (64 or 32) but when clicking on the downloaded installer
.exe file, it not only fails to install
I am trying to install Phenix on a Windows (windows 7) machine using the
windows installers (64 or 32) but when clicking on the downloaded installer
.exe file, it not only fails to install, but the file itself gets deleted (??).
Does anybody who has installed Phenix on Windows have any tips to
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Hi Paul,
thank you for the answer. I was curious, especially since there was a recent
paper on anomalous phasing with neutron scattering (doi:10.1038/srep31487),
and wondered if this was related. I also appreciate seeing development in
neutron
Hi Tim,
you are correct as it is scattering by the nucleus. Support for ions means
that users can use an “ion name”, e.g. Ca+2 for an atom and the appropriate
scattering factors will be used. The neutron scattering table previously didn’t
include the ionic names.
Cheers,
Paul
>
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Dear Paul,
I am surprised by the mentioning of support for ions in the neutron scattering
tables.
Would you have a reference? I always though neutron scattering was independent
of the electronic state of an atom.
Best,
Tim
On Wednesday, November
The Phenix developers are pleased to announce that version 1.11.1 of Phenix is
now available (build 1.11.1-2575). Binary installers for Linux, Mac OSX, and
Windows platforms are available at the download site:
http://phenix-online.org/download/
Highlights for this version:
New tools
Dear Weifei,
You'd better ask this question on phenixbb as here is ccp4bb.
But the environment variable file (.bashrc or .bash_profileis) in your home
folder(specific user) or in /etc/profile (all user). Source Phenix in this
file. Next time you run the terminal, the file will be
Dear all,
Sorry to disturb you.
I have install Phenix to my computer Centos 7.0.
When I want to use it I need to
cd /usr/local/phenix-1.9-1692/
and
. /usr/local/phenix-1.9-1692/phenix_env.sh
then type phenix in the command line every time.
I wish to use phenix in every terminate window and
...@outlook.com
Envoyé : vendredi 26 juin 2015 15:05
À : CCP4BB@JISCMAIL.AC.UK
Objet : [ccp4bb] phenix installtion problem
Dear all,
Sorry to disturb you.
I have install Phenix to my computer Centos 7.0.
When I want to use it I need to
cd /usr/local/phenix-1.9-1692/
and
. /usr/local/phenix-1.9-1692
. By careful only to translate, not to rotate.
Best,
Herman
-Ursprüngliche Nachricht-
Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von
Tim Gruene
Gesendet: Mittwoch, 15. April 2015 09:58
An: CCP4BB@JISCMAIL.AC.UK
Betreff: Re: [ccp4bb] Phenix: heavy atoms
the best,
Tom T
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Natalia O
[natalie.c...@gmail.com]
Sent: Tuesday, April 14, 2015 9:24 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Phenix: heavy atoms
Dear All,
I am new to the crystallography and I am
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Dear Natalia,
you can use Coot to generate the symmetry related molecules and see if
the substructure matches your model.
If your space group is polar, as in e.g. P2(1) or P2(1)2(1)2(1), your
coordinates may float freely along the polar axis and
board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag
von Tim Gruene
Gesendet: Mittwoch, 15. April 2015 09:58
An: CCP4BB@JISCMAIL.AC.UK
Betreff: Re: [ccp4bb] Phenix: heavy atoms
Dear Natalia,
you can use Coot to generate the symmetry related molecules and see
if the substructure matches your model
option. By careful only to translate, not to rotate.
Best,
Herman
-Ursprüngliche Nachricht-
Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Tim
Gruene
Gesendet: Mittwoch, 15. April 2015 09:58
An: CCP4BB@JISCMAIL.AC.UK
Betreff: Re: [ccp4bb] Phenix: heavy atoms
Dear All,
I am new to the crystallography and I am seeking for an advice considering
data processing. I have a dataset with 2.8 A resolution. I used hybrid
substructure search program in phenix, I got the heavy atom sites
(selenium), and then I submitted the site to the autosol. With autosol
Lawrence Berkeley Laboratory
Career-track Research Scientist
Job ID: 80447
Division: Physical Biosciences
Date Opened: 1/14/2015
https://lbl.taleo.net/careersection/2/jobdetail.ftl?lang=enjob=80447
Summary: A research scientist position is available to work on developing new
methods for
Change ad to and in selection.
Sent from Jack's iPad
On Nov 26, 2014, at 7:16 AM, Almudena Ponce Salvatierra
maps.fa...@gmail.com wrote:
Dear all,
I am refining my structure with Phenix refine and I get the following error
message just before starting:
no atom selected, name CA ad
FYI, there is a phenix BB for phenix questions.
Sent from Jack's iPad
On Nov 26, 2014, at 7:16 AM, Almudena Ponce Salvatierra
maps.fa...@gmail.com wrote:
Dear all,
I am refining my structure with Phenix refine and I get the following error
message just before starting:
no atom
Hi Almudena,
I am refining my structure with Phenix refine and I get the following error
message just before starting:
no atom selected, name CA ad chain A and resname CA and resseq 1.
this is due to atom selection syntax error that you provided:
after CA must be and not ad .
I knew
Thank you all very much for your replies.
However I am sorry this ad was a typing mistake of mine while
transcribing the message.
I have signed up for the phenixbb mailing list.
And I will look up at the restraints that may still be there for this atom
that I removed.
Thanks again,
best
Your .eff file must be explicitly referencing the Ca that you removed. Since it
doesn't
exist, phenix stops. Search your .eff file for the string
name CA and chain A and resname CA and resseq 1
(maybe a geometry.edit) and remove the reference.
I think the CCP4 bylines specifically encourage
Dear All
I am planning to purify monoclonal antibody. In this concern
I found Pseudospecific ligands such as histidine, tryptophan,phenylalanine
etc. can be used to purify a wide range of bio-molecules and especially
immunoglobulin. I wish to know the structural mode of binding of
The Phenix developers are pleased to announce that version 1.9 of Phenix is now
available. Binary installers for Linux, Mac OSX, and Windows platforms are
available at the download site:
http://phenix-online.org/download/
Highlights from this version:
Significant changes to the
Dear all,
Hello! I am now running into a simple technical problem but I just cannot
figure it out. I am trying to create a composite omit map by phenix, but
when I typed in the command phenix.composite_omit_map XXX.eff based on the
instructions on
Hi Chen,
I will answer you on the phenix mailing list!
All the best,
Tom T
On Apr 21, 2014, at 10:53 AM, Chen Zhao wrote:
Dear all,
Hello! I am now running into a simple technical problem but I just cannot
figure it out. I am trying to create a composite omit map by phenix, but when I
typed
Dear all,
I'm refining a structure with three modified amino, ccp4 code: CY3, DTR,
and MPT respectively. However I don't know how to give phenix.refine the
adequate libraries as to obtain the correct geometry for three amino acids.
I tried to add the cif libraries downloaded from ccp4 to the
The Phenix developers are pleased to announce that version 1.8.4 of Phenix is
now available. Binary installers for Linux, Mac OSX, and Windows platforms are
available at the download site:
http://phenix-online.org/download/
Highlights from this version:
Automated MR/ligand
Dear all,
I'm aware this may not be the right BB for this question but I've searched for
some time and am all out of ideas, if you could help it would be much
appreciated.
I've stupidly lost a .phenix folder and hence can't import the associated data
into the phenix GUI, is there another way
The Phenix developers are pleased to announce that version 1.8.2 of Phenix is
now available. Binary installers for Linux, Mac OSX, and Windows platforms are
available at the download site:
http://phenix-online.org/download/
Highlights from this version:
Ensemble refinement, updated
The Phenix developers are pleased to announce that version 1.8.1 of Phenix is
now available. Binary installers for Linux, Mac OSX, and Windows platforms are
available at the download site:
http://phenix-online.org/download/
Some of the new features in this version are:
Graphical
The Phenix developers are pleased to announce that version 1.8 of Phenix is now
available. Binary installers for Linux, Mac OSX, and Windows platforms are
available at the download site:
http://phenix-online.org/download/
Some of the new features in this version are:
Graphical
Dear all,
Sorry for the non-CCP4 question.
My crystal is a complex of two proteins. I use Se-Met SAD method to
solve the structure, and only one of the proteins is Se-Met protein.
When I use phenix.autobuild to auto-build the model, how do I input the
sequences? in a file or two files?
Hi Qixu Cai,
first off -- as a reminder, there is Phenix mailing list to post
Phenix-related questions:
http://www.phenix-online.org/
Your first question: yes, give it one sequence file containing all.
Your second question: see here
http://phenix-online.org/documentation/autobuild_gui.htm
Pavel
Matthew Vetting
Enzyme Function Initiative
Structural Biology
Albert Einstein College of Medicine
- Reply message -
From: Pavel Afonine pafon...@gmail.com
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] PHENIX: sequence files input problem
Date: Wed, Jun 13, 2012 4:51 pm
Hi Qixu Cai,
first
Hello Fellow PHENIX users (and others!)
I had been using PHENIX to generate iterative build composite OMIT maps. I was
able to perform these runs with automated settings for two of my data. With the
third one (1.2 A structure) I get an error. I am pasting a part of the message
below:
On 13 December 2011 17:59, James Holton jmhol...@lbl.gov wrote:
A small but potentially important correction:
FC_ALL PHIC_ALL from REFMAC are indeed the calculated structure factor of
the coordinates+bulk_solvent, but AFTER multiplying by the likelihood
coefficient D (as in 2*m*Fo-D*Fc ).
PHIC wont do any harm - you may need it for various reasons - I use it
mostly as input for a DANO map to check out possible metal sites..
The reason for not using a refmac output mtz as input for the next run is
1) the refmac output Fobs has been scaled by the anisotropic scale so
all
On Tue, 2011-12-13 at 02:31 +, Yuri Pompeu wrote:
Hi Ed,
I just had a chance of looking at your comment more closely.
You are right it only uses PHIC if in refmacs set up you choose to refine
with prior phase information -AFAIU.
So what exactly is the info contained in the output
A small but potentially important correction:
FC_ALL PHIC_ALL from REFMAC are indeed the calculated structure factor
of the coordinates+bulk_solvent, but AFTER multiplying by the likelihood
coefficient D (as in 2*m*Fo-D*Fc ). So, if you subtract ( FC_ALL
PHIC_ALL ) from ( FC PHIC ) you will
This is very uncommon...
Can you look at the final plot of R and Rfree against resolution.
Sometimes there is an awful hiccup somewhere -
ice rings?
high resolution data somewhat fictional -
low resolution data saturated and also somewhat fictional ..
I also check the completeness which is uin
The Phenix developers are pleased to announce that version 1.7.3 of Phenix is
now available. Binary installers for Linux, and Mac OSX platforms are available
at the download site:
http://phenix-online.org/download/
Some of the new features in this version are:
Graphical interface:
Hi Ed,
I just had a chance of looking at your comment more closely.
You are right it only uses PHIC if in refmacs set up you choose to refine with
prior phase information -AFAIU.
So what exactly is the info contained in the output refmacX.mtz besides map
coefficients for COOT? If it is not just
-BEGIN PGP SIGNED MESSAGE-
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Dear Yuri et al.,
I like the fact that one must not use the output mtz-file from refmac as
input to the next round of refinement. It encourages to think about why
this is and then makes you realise what your data really are: the result
of data
On Sun, 2011-12-11 at 05:28 +, Yuri Pompeu wrote:
In refmac however the newly generated refmacX.mtz file contains phase
info as PHIC calculated from your model. Using this for subsequent
rounds of refinement results in terrific looking maps as they are now
biased (even more so) by the
Precisely, one should not use it! I have seen people do it either
because they dont fully understand what is going on or are not at all
familiar with the documentation.
In phenix the output .mtz contains Fo plus x% Rfree flag=1, so one may
try and do this for refmac because of one of the two
PHENIX has an otpion under the reflection editor program that will create R
flags that are compatible with ccp4 programs.
Another point worth mentioning is in phenix.refine it is appropriate to use the
data.mtz files generated each round of refinement, as these are the raw data
plus the Rfree
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Dear Petr,
there may be a couple of reasons, e.g.
- - your data are not really 1.1A, but you simply integrated a lot of noise
- - you entered some odd command or another option which allows refmac5
such a deviation
- - your model is incomplete
- -
Hi Everybody,
First off, thanks for the replies. They definitely fixed my problem. It
was indeed as Garib Murshudov said. The flags got swapped, and therefore
the percentage of Rfree reflections were 95%.
So, if Rfree is created from CCP4.use Rfree flags with a value of 0
and a value of 1 if
Hi Christopher,
just a remark: for phenix.refine it does not matter where the flags come
from and what is the test/work value since it automatically scores the
values in the flags array and guesses the right one. Still one can imagine
corner case, so it's good to be careful -:)
Pavel
On Fri,
On Fri, 2011-12-09 at 05:45 -0800, Pavel Afonine wrote:
just a remark: for phenix.refine it does not matter where the flags
come from and what is the test/work value since it automatically
scores the values in the flags array and guesses the right one. Still
one can imagine corner case, so
Hi Ed,
changes like this generate more confusion then good, I guess. Current
phenix.refine behavior does not create any problem for phenix.refine users,
so I don't feel a strong reason for changing anything. It's not just a
flipping the flag value somewhere, but it's updating the documentation,
Dear All,
Question: Has anybody ever refined the same structure using PHENIX and
then tried REFMAC to see what happens?
I did and I stumbled on something funny. I'm refining a structure at
1.1A resolution which was solved with Iodine phasing using PHENIX
AutoSolve. Got a great map and the
Christopher,
if you send me the input PDB and data files (off-list, of course) I will
have a close look and then explain what exactly happens and why. I also
promise to post the summary on this mailing list (without revealing the
identity of your structure, of course).
If you send me the command
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