Dear Art,
I am the sysadmin, which is bad news since I am much better as a
crystallographer... and I was working on a different issue on the same
machine the past week.
Our institut has a good firewall so I believe we'll be fine, the
installation of Arp/warp was smooth after the modification of g
Hi Carlos,
We had the same problem trying to install ARP/wARP on our Debian 10
machines. TL;DR: you (or your sysadmin, since this requires root access)
have to enable vsyscall as follows:
echo 'GRUB_CMDLINE_LINUX_DEFAULT="vsyscall=emulate"' >> /etc/default/grub
update-grub
reboot
An explainer (m
Dear CCP4BB,
I am unable to install ARP/WARP on a server with Debian 10, it says:
Segmentation fault
*** ERROR ***
This machine cannot run ARP/wARP executables that
are statically linked to glibc.
*** INSTALLATION OF ARP/wARP 8.0 FAILED ***
Modified version exit status 1
-- after some diggi
Hi,
I've installed the entire CCP4 7.1 package (ShelX and arpWarp); however, I
can't find the arp/Warp binaries/scripts (e.g. auto_em.sh). Are these not
included with the CCP4 package? If not, why not? Thanks.
Best wishes,
Reza
Reza Khayat, PhD
Assistant Professor
City College of New York
D
Hi,
auto_tracing.sh “ARP/wARP 8.0 patch 1”, after a few cycles, prints
awk: Command not found., and exits a little later with:
Data line -- RESOLUTION 20 2.2
Data line -- REMOVE ATOMS 8 CUTSIGMA 1.0 FORCE NEGATIVE MERGE 0.7
Data line -- FIND ATOMS CHAIN Z CUTSIGMA 3.2 RESN DUM
T
Dear CCP4 Users
We would like to announce the joint release of ARP/wARP version 8.0
and CCP4-7.0.065.
ARP/wARP 8.0 provides a considerably improved performance for X-ray
crystallographic applications and it is now also capable of interpreting
cryo-EM maps at a resolution range 2.0-3.5 Å.
Install
Dear Colleagues,
We are happy to announce a redesigned and extended webservice for remote
ARP/wARP execution. In addition to the crystallographic protein chain
tracing, many other functionalities of ARP/wARP are now also available
online. These include:
- classic protein model building start
Dear colleagues,
If you are using ARP/wARP or Auto-Rickshaw remote services, we would like to
inform you that, as a preparation for the next ARP/wARP version, a few days ago
we moved the services to a new, faster and more powerful machine. Almost
everything is settled by now, but there are stil
Dear Monica,
On Jun 16, 2014, at 10:39 AM, Monica Mittal wrote:
> Dear all
> I am getting this error while running arp/warp to build DNA/RNA:
> PHIB is not assigned to an mtz label
> Input was merged data (.mtz)
> However no such problem while using arp/warp classic as i chose for automated
> mo
Dear all
I am getting this error while running arp/warp to build DNA/RNA:
PHIB is not assigned to an mtz label
Input was merged data (.mtz)
However no such problem while using arp/warp classic as i chose for
automated model building from existing model and not experimental phases.
Kindly help how
Dear colleagues,
ARP/wARP 7.4 Patch 2 is available for download on our FTP server, as well.
If you were installing ARP/wARP as a joint bundle with CCP4-6.4.0, you can
update ARP/wARP via automatic CCP4 update or download the patches from
http://www.ccp4.ac.uk/updates/
If you were installing A
representatives.
**
-Original Message-
From: Antony Oliver [mailto:antony.oli...@sussex.ac.uk]
Sent: Thursday, April 19, 2012 11:57 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Arp/WARP for multi-chain complex
Thanks Victor - for giving a rational and detailed
Thanks Victor - for giving a rational and detailed explanation. I obviously got
carried away with the number of alanines to intersperse!
With regards,
Tony.
On 19 Apr 2012, at 16:52, "Victor Lamzin" wrote:
> Dear Tony, Tongqing, Tim,
>
> Adding some alanine spacer is good for a simple rea
Dear Tony, Tongqing, Tim,
Adding some alanine spacer is good for a simple reason - during
sequence docking ARP/wARP checks the distance between the ends of the
fragments.
Imagine you have two chains, 10 residues each. If you concatenate them
together, terminal residues belonging to differ
Dear Tongqing,
On Apr 19, 2012, at 5:26 AM, Zhou, Tongqing (NIH/VRC) [E] wrote:
> I am trying to use Arp/wArp to build an antibody-antigen complex with 1.65 A
> data, there are three chains (heavy, light chains of antibody and the
> antigen) in the complex, my question is how to put the sequenc
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Hash: SHA1
Dear Tony, dear Tongqing,
the way I understand the working mechanism of arp/warp works I do not
see the point introducing the polyALA spacer into the sequence. Just
concatenate all sequences into one file as though it was one molecule.
Cheers,
Tim
O
In the absence of a likely, more sensible, answer - I think the trick is/was to
simply put everything in one pir file, but "link" each sequence with a run of
20 or so alanines i.e. sequence A followed by ... sequence B
sequence C.
There may well be a more el
Dear All,
I am trying to use Arp/wArp to build an antibody-antigen complex with 1.65 A
data, there are three chains (heavy, light chains of antibody and the antigen)
in the complex, my question is how to put the sequences in the *.pir file so
that it still identifies different chains. It looks
My two cents: I am installing arp/warp on my Mac since ages and it works ;-)
The only thing you need to make sure is that you grab ownership of the
/usr/local directory to you as a user, if you installed ccp4 from dmg. If you
do this by eg
sudo chown -R me.mygroup $CCP4
Then install.sh should
Hi,
I recently found the problem that after finishing the installation of
CCP4-6.2.0 on RHEL5, if the installation destination is not the default path
(/usr/local/), the ccp4.setup for csh wouldn't take the customized TCLTK
path correctly. No matter if I used sh or csh to install the CCP4 package.
Dear all,
I had no problem with Arp/wARP, but I didn't reinstall. Assume ccp4
sits in /installation/directory/ccp4 and arp in
/installation/directory/arp_warp_7.1. The new ccp4 doesn't recognize
the existing arp because the task interface is not installed. I run
./install.sh in /installati
Hello,
My reply is in the text below:
On Jul 28, 2011, at 6:00 AM, ccp4 wrote:
> A plea from West Australia too.
> I was sitting with someone yesterday who was trying to install it on a Mac
> , and finding it a nightmare.
We're working on improving this. I believe the main issue is that CCP4
Hello,
I'm one of the ARP/wARP developers. Sorry for the slow reply - this is down
to time differences. I'll install RHEL6 and try the ARP/wARP install and then
report back. This may take a day or so though.
My suspicion, based on previous bug reports, is that this problem is related to
the T
... strange, I have not seen any problems installing ARPwARP 7.1 on a new
CCP6-6.2.0 install on
- linux centos
- os-x snow leopard, here I initially ran into write permissions issues and
wound up changing the ownership of the /Applications/ccp4-6.2.0 directory
Cheers
Jan
On Jul 27, 2011, at 9:0
A plea from West Australia too.
I was sitting with someone yesterday who was trying to install it on a Mac
, and finding it a nightmare.
He finally got it set up as a local installation, whereupon it promtly
failed.
The message said See refmac-last.log but that told us nothing, and indeed
refmac
On Wednesday, 27 July 2011, you wrote:
> Hi Jonathan,
> seems to be a UW centered day today on the BB (Eric, Jan, you, me).
> Have the permissions changed ? I assume you are installing as root ?
> Wouldn't be surprised if Ethan replies soon :-)
Sure.
I hit the same problem trying to install Arp/w
Hi Jonathan,
seems to be a UW centered day today on the BB (Eric, Jan, you, me).
Have the permissions changed ? I assume you are installing as root ?
Wouldn't be surprised if Ethan replies soon :-)
Jürgen
..
Jürgen Bosch
Johns Hopkins Bloomberg School of Public Health
Departm
Hi all,
I have a RHEL 6 x86_64 machine I recently installed CCP4-6.2.0 onto; the
install went through fine, but when I went to install the ARP/wARP GUI (via
System Administration -> Install/uninstall task), I received the following
error in the shell window I started ccp4i from:
UnpackTaskArch
Hello Seema,
I believe this error occurs because ARP/wARP has not been setup within the
startup file for the shell that you are using. For instance, if you use bash
(the default under most Linux distributions) you need to add the following line
to the .bashrc file in your home directory:
sour
I've recently installed arp/warp(7.1) in ccp4 6.2 in linux i686,the problem is
whenever I'm trying to run arp/warp navigator or any other programs under
arp/warp it gives the error " cannot get environment variable for warpbin"
Please help.
Thanks in advance.
Seema Nath
On 9 Sep 2010, at 01:57, Leiman Petr wrote:
> Switch to the 64bit environment (source /sw64/bin/init.sh in a new terminal
> window). Install ARP/wARP while in this terminal (not sure if this is needed
> actually, probably not).
> Then copy all the files from these directories:
> /sw/share/xtal/ccp
Dear All,
My new Mac is affected by a bizarre software bug (or a feature), which has
been reported on this board earlier. In fact, it has been more than a year
since this problem was first reported, but it has not been resolved yet as
far as I can tell. Namely, it is not possible to add the ARP/wA
Dear Rafael,
We have seen this already twice, it is a bug, sorry. The fix is being
made and, when ready within a day or two, we will announce it.
With best regards,
Victor
Rafael Counago wrote:
Dear all,
I am getting an error message when I run arp/warp using CCP4i.
*/"QUITTING ... ARP/w
Dear Raphael and others who experienced this,
in some rare cases we have seen that the 'restraints' module of ARP/wARP
can have a malfunction. If this is the case for your data, then the best
you can do at the moment - while the fix is not there - is to deactivate
the use of this module in the
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The other possibility you might need to consider is wether or not you have java
running on your machine.
"restraints" is in java, and it seems that ARP/wARP stops just when starting
restraints.
As for the "error" message you're seeing, it is well
Dear Rafael, dear Li Chan,
is this the first time you run arp/warp on that particular computer? Maybe the
architecture of the binaries are not the correct ones.
You might search for the 'snow' binary (which leaves the empty log file) with
the command 'find ./ -name snow' issued from the arp/warp
Hi all,
I got the same errors as Rafael.
Please help.
Thanks
Peter
> Date: Tue, 16 Mar 2010 14:39:10 +1300
> From: rafael.coun...@otago.ac.nz
> Subject: [ccp4bb] arp/warp
> To: CCP4BB@JISCMAIL.AC.UK
>
> Dear all,
>
> I am getting an error message when I
Dear all,
I am getting an error message when I run arp/warp using CCP4i.
*/"QUITTING ... ARP/wARP module stopped with an error message:
RESTRAINTS
*** Look for error message in the file:
/home/rafael/MAD/CCP4/2_warpNtrace_build.last.log
[1] 11549/*
The only error message I can find on the ab
Hello,
we have been trying to run arp warp 7.1.0 from ccp4-6.1.2 starting from
experimental phases. As we hit the run or 'run& view comm script' button,
a window appears saying "Can't read 'wilsonb': no such variable"
followed by a polite apology and nothing else happens ever after.
What might
As Phil realized, the leading zeros in the refmac5 version number were
the culprit that broke the original installation script. His modified
version works beautifully.
Thanks.
Andreas
On 04/01/2010 11:27, Phil Evans wrote:
The attached slightly modified script fixes that problem
Phil
The attached slightly modified script fixes that problem
Phil
install_csh.sh.gz
Description: GNU Zip compressed data
On 4 Jan 2010, at 11:15, Andreas Förster wrote:
> Dear all,
>
> I downloaded ARP/wARP 7.1 from EMBL-Hamburg and executed ./install.sh. All
> tests pass up to and including re
Dear all,
I downloaded ARP/wARP 7.1 from EMBL-Hamburg and executed ./install.sh.
All tests pass up to and including refmac version check (see log below).
After that, a "Badly formed number" in an if test. What could be the
issue?
The system is Redhat EL 5.4, tcsh.
Thanks.
Andreas
ld-
Dear all,
First, I am happy that there is am easy solution.
Second, let me clarify that ARP/wARP CCP4i GUI uses standard CCP4i
library functions to read in files etc etc.
I am sorry to get technical, but what I do is simply:
CreateInputFileLine line \ [...lines deleted...]
-setfile
On Tue, Dec 01, 2009 at 04:57:38PM +, Eleanor Dodson wrote:
> One easy suggestion - try buccaneer and refinement!
> Eleanor
> The Arp/warp people will have to fix this..
It's also possible that this is due to a ctruncate problem: if the CAD
job adds the SHARP MTZ file (with C2) and a MTZ file
Hi all,
I ran into that several times in the monoclinic space groups. ARP/wARP does
not seem to like the C121 notation, yet likes the C2 notation. Same for P121
vs. P2. Re-assigning the SG eg. in CAD using the correct notation or the SG
number is an easy remedy.
Cheers
Jan
On Tue, Dec 1, 2009 at
Dear Jan,
that is an annoying thing with Arp/wARP - it sometimes does not
recognise some space groups, esp. the monoclinic ones with eg can be
called C2 or C121 etc.
Run the mtz file again through CAD, use SG 5 or C2. That should work.
and it does! Thanks a lot.
Let's hope these ann
One easy suggestion - try buccaneer and refinement!
Eleanor
The Arp/warp people will have to fix this..
Anita Lewit-Bentley wrote:
Dear all,
I have a nice MAD map produced by Sharp and would like to trace a chain
into it using Arp/wArp. When I input the mtz file via the CCP4i
interface, I
Dear all,
I have a nice MAD map produced by Sharp and would like to trace a
chain into it using Arp/wArp. When I input the mtz file via the CCP4i
interface, I get the following message:
"Cannot extract ARP/wARP asymmetric unit limits
The job will fail if run"
Well it DOES fail when run!
M
Hello Tassos,
'that command' (sorry about this expression, _I_ should have know how
silly a description that is) was the mtzdump.
Could you please clarify which is 'that commend'? Is that something like
warp_tracing.sh my_cp4i_par_file_from_above.par
That's what I was looking for. Issued at
Hi Tim,
First, we do not have access to Debian squeeze so I am afraid I cant
say much about it.
The gui asks about the Wilson plot, and, when run as 'run and view com
file' shows the script for mtzdump.
The 'run and view command file' will not work with the way that ARP/
wARP Classic (ab)
Hello,
on two recently installed Linux boxes (PC, i7) with Debian testing
(squeeze),
arp warp classic does not run but produces the following log-file:
--- 8< snip -
#CCP4I VERSION CCP4Interface 2.0.5
#CCP4I SCRIPT LOG arp_warp
#CCP4I DATE 20 Nov 2009 10
Dear Yuan,
Most likely your ARP/wARP settings are not sourced.
1. Quit CCP4i
2. Modify your ./cshrc (or .bashrc) so that it sources CCP4 first and
ARP/wARP then. Below is one example of .cshrc:
#
# Setup CCP4
source /Users/victor/xtal/ccp4/ccp4-6.0.2/include/ccp4.setup
#
# Setup ARP/wARP
sour
Hi,
Does anyone know how to Plugging ARP/wARP GUI into CCP4i interface? I
followed http://www.embl-hamburg.de/arp-cgi-bin/FAQ7.0_1.pl, but always
get a warning "Can not get environment variable for wardoc" with a
subsequent Application Error "Error:bad window path name \".warning..."
Under Ubun
Indeed it did! It is kind of funny that Arpwarp Classic would be fine
without a restart, but Expert System wouldn't, after installing the
arpwarp interface in ccp4i. What was that joke about the computer
scientists' solution to broken cars being 'Get out of the car, and get
back in'?
Thank yo
Hi everybody,
I was messing around with Arp/warp in ccp4 recently, and got stuck with
the version that uses the new autotracing algorithm. The same run using
the "Classic" algorithm runs without a problem, but the "Expert System"
using flex-wARP 1.0 dies with "PHIB is not assigned to an mtz la
Dear Sangeetha,
what you noticed is a bug that appears under particular circumstances.
Sorry for your inconvenience. From your logfile excerpt I think that
this bug has been observed before and been fixed. The next release will
include the fixed version, however useless this might sound to you
Hi all,
I am trying to fit a ligand into density using ARP/wARP 7.0.1 in CCP4 suite
6.0.2 on CCP4interface 1.4.4.2.
I get an error message telling me to look for the error in a
"##_warp_ligand_details.log".
_
Running Refmac5 to refine
Please make sure you source arpwarp_setup.csh (or .bash) after you
source CCP4, this should cure the problem. Instructions on how to source
arpwarp_setup are printed when you install ARP/wARP with the install.sh
script.
Best regards,
Victor
Sridhar Prasad wrote:
I installed CPP4 version 6.1
I installed CPP4 version 6.1.1 on a Linux laptop which is running ubuntu.
Following which I also installed ARP/WARP 7.0.1 version.However, when I attempt
to launch ARP/WARP using the CCP4I GUI interface, I get the following message
Can not get environment variable for warpdoc.
Could someone ple
Interesting that these questionaire responses are very different from
the numbers obained from looking at downloads counts for other cross-platform
crystallography software. I wonder if they are more reflective of the currently
available ARP-wARP platforms and perhaps the role of administrator-
pr
We were collecting information on computer platforms that people would
like ARP/wARP to run on.
126 people responded with 296 platform choices. The latter grouped as
follows:
Linux i686 26%
Linux x86_64 24%
Linux ia644%
total Linux54%
Mac powerpc 9%
Mac Intel 10.
We are collecting information on computer platforms that people would
like ARP/wARP to run on. To access the questionnaire please go to
http://www.embl-hamburg.de/ARP/platinf_new.shtml
Thank you for your cooperation.
With best regards,
Victor
Hello all,
While testing a newly installed ARP/wARP interface (ver. 7.0.1) in ccp4i
(ver. 6.1.0) on Ubuntu (8.10) I noticed that the Fobs and Sigma pull-down
menus are missing from the ARP/wARP Quick Fold window. This is accompanied
by the following error message, which is output in stderr by
Thanks, Anastassis, "Solvent" is working now after installing the fixed
file.
Cheers,
Matt
2009/1/8 Anastassis Perrakis
> Hi -
> Its a bug in version 7.0.1 that went (almost) unnoticed ... there was one
> more complaint a year ago and I had fixed it but there was no release in
> between. Sorr
Hi -
Its a bug in version 7.0.1 that went (almost) unnoticed ... there was
one more complaint a year ago and I had fixed it but there was no
release in between. Sorry.
Apart from simply doing the solvent building from the REFMAC interface
instead (either with arp_warp as since now or wit
Thanks Damian, but I have been using my library file for refmac refinement
and it works fine. And I can't find the line "Unrecognized atom type", but
presumably, if it works in refmac refinement, why not in Arp/wArp?
Yes Gerrit, the "[" and "]" should not be there.so auto_solvent.sh can
recogn
Dear Matt,
have you tried the 'input a user-defined library file' check box under
'refmac parameters' in the gui? Else try the keyword 'extralibrary' when
using the 'auto_solvent.sh' script from the command line. Both options
define a string 'LIB_IN mylib.cif' that is passed on to refmac.
Wh
Dear all,
I tried to use ARP/wARP 7.0.1 GUI for solvent building, however it couldn't
recognize my ligand library file (.cif), which works fine in refmac
refinement.
Apparently, the error message is:
===> Error: New ligand has been encountered. Stopping now
Refmac_5.2.0019: New ligand has been
Dear Victor
I'm glad that you see the desirability of updating Arp/warp to allow
any setting. I'm a recent convert to this idea myself
Best wishes
Phil
On 11 Jun 2008, at 09:17, [EMAIL PROTECTED] wrote:
Thanks very much to everybody for useful discussion on space groups,
axes and
ARP/
Thanks very much to everybody for useful discussion on space groups, axes and
ARP/wARP. I would particularly refer to the argument on space group uncertainty
in data processing and a need to have convenient means to screen various space
groups and axes settings for, e.g. automated molecular replace
sed
conventions could save us a lot of work!
-- Ian
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Victor Lamzin
Sent: 10 June 2008 16:45
To: PhilEvans
Cc: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Arp/warp space group P 21 2 21
Dear Phil,
One rea
Among very many other great things
Dr Felix Frolow
Professor of Structural Biology and Biotechnology
Department of Molecular Microbiology
and Biotechnology
Tel Aviv University 69978, Israel
Acta Crystallographica D, co-editor
e-mail: [EMAIL PROTECTED]
Tel: ++972-3640-8723
Fax: ++972-3640-9407
SHELX has been able to handle P 21 2 21 and other such space groups
without any problems for the last 38 years!
George
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-3021 or -3068
Fax. +49-551-39-2582
I think in refmac it has already been fixed (since October or so).
refmac 5.4 and later version should handle all available space groups
with their various disguises.
Garib
On 10 Jun 2008, at 16:11, Clemens Grimm wrote:
seems to be a 'non-standard' setting. Refmac also has problems with
th
same problem,
unless of course they anticipated this eventuality in the database
design.
So yes, making all software accept the internationally recognised
conventions could save us a lot of work!
-- Ian
> -Original Message-
> From: [EMAIL PROTECTED]
> [mailto:[EMAIL PROTECTED] On Behalf O
I should expand a bit: on this BB last year Ian Tickle pointed out
that the IUCr "standard" for primitive orthorhombic space groups is to
have a <= b <= c, irrespective of which axes are 2s or 2(1)s. Thus eg
space group 18 in its "standard" setting may be P 2 21 21, P 21 2 21
or P21 21 2:
Dear Phil,
One reason has been simplicity - many ARP/wARP modules operate with
space group number only. For space group 18 this would mean P21212.
Using space group name might be less robust - I remember some
compatibility problems when CCP4 introduced spaces into space group
names, this brok
Probably because it's not a standard notation.
The standard notation is P21212.
I would reindex and run again.
Klaus
PhilEvans wrote:
Is there a reason why Arp/warp doesn't like space group P 21 2 21?
Phil
--
Dr. Klaus Piontek
Albert-Ludwigs-University Freiburg
Institute of Organic Chemi
seems to be a 'non-standard' setting. Refmac also has problems with this
spacegroup, reindexing to P21 21 2 fixed the problem for me.
Clemens
Quoting PhilEvans <[EMAIL PROTECTED]>:
Is there a reason why Arp/warp doesn't like space group P 21 2 21?
Phil
Is there a reason why Arp/warp doesn't like space group P 21 2 21?
Phil
Thanks for a very quick answer, it indeed solved the problem.
Cheers,
Ronnie
On Apr 24, 2008, at 4:55 PM, Chris Richardson wrote:
On 24 Apr 2008, at 3:38 PM, Ronnie Berntsson wrote:
I've got a rather weird problem when trying to run arp/warp. When
trying to run arp/warp (latest version 7.0.
in arp/warp classic the script does not call refmac5 (the first thing
in your path) but $CBIN/refmac5 (refmac from the CBIN place)
I suspect that you still kept refmac 5.2 in the official CBIN
directory and put refmac5 in another location but earlier in your
path, so its picked up first ...
On 24 Apr 2008, at 3:38 PM, Ronnie Berntsson wrote:
I've got a rather weird problem when trying to run arp/warp. When
trying to run arp/warp (latest version 7.0.1) it complains that I
should install a newer version of Refmac (5.4.0045). The version of
Refmac I have installed is 5.4.0066, an
Hi,
I've got a rather weird problem when trying to run arp/warp. When
trying to run arp/warp (latest version 7.0.1) it complains that I
should install a newer version of Refmac (5.4.0045). The version of
Refmac I have installed is 5.4.0066, and thats what is being used if I
run Refmac bot
Dear all,
May I ask you, if you had cases at low resolution (lets say at least
below 2.5 to be generous) that ARP/wARP produced a useful result for
you, to send me (... not to the list) a very short email, also
mentioning a publication that refers to that result?
Thanks in advance, Tassos
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Dear Francisco;
This looks like a disk access problem. Are you by any chance running
this process from a NFS mounted volume ?
Is this crash reproducible, that is if you "just re-run" the task (in
the CCP4i) will it produce a crash at the exact sa
Dear All :
When I run the new version of arp-warp in the ccp4i interface I got the
following error. Any ideas that what I am doing wrong ??
Thanks for the help.
Francisco
-
ERROR ('IOError', '', [' File
"/usr/local/arp_warp_7.0/flex-wARP-src-214/CArc.py", line 78, in
ch
: CCP4 bulletin board on behalf of Phil Evans
Sent: Mon 24/09/2007 6:18 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] arp/warp in p22121: what to do in Pointless
OK I'll try to change the default behaviour, after I've fixed the
current round of bugs!
Sometimes reindexing is require
se Mosflm and always specify SG
P222
for all oP cases (which I always do anyway), you would have to re-
index
anyway.
-- Ian
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Phil Evans
Sent: 24 September 2007 16:58
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re:
-index
anyway.
-- Ian
> -Original Message-
> From: [EMAIL PROTECTED]
> [mailto:[EMAIL PROTECTED] On Behalf Of Phil Evans
> Sent: 24 September 2007 16:58
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] arp/warp in p22121: what to do in Pointless
>
> I think this is o
rdinate format is used as long as
> > all programs use the same one, then I'll never need to reformat). So
> > Mosflm uses the IUCr convention (i.e. a<=b<=c for primitive
> > orthorhombic), and therefore any program which doesn't support that
> > convention for any space gr
;t support the
convention that you are forced to permute the axes?
Besides I did solve a structure in P22121 with Phaser so
I'm even more
confused!
-- Ian
-----Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Airlie McCoy
Sent: 19 September 2007 15:09
To:
So I vote for a default of preserving the input convention whatever it
is, and I definitely vote against all axis permutations unless a) it's
absolutely necessary (e.g. for consistency with other datasets), and b)
the user specifically requests it (and really really means it!).
Phew! It makes
15:09
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] arp/warp in p22121
>
> >The problem is specifically that ARP/wARP *doesn't* support the IUCr
> >convention as given in IT (Vol. A, >= 1983 edition, Table
> 9.3.4.1, p.758
> >in 5th ed.) regarding
rthorhombic), and therefore any program which doesn't support that
convention for any space group forces you to permute the axes completely
unnecessarily.
-- Ian
> -Original Message-
> From: Sue Roberts [mailto:[EMAIL PROTECTED]
> Sent: 19 September 2007 16:38
> To: Ia
a structure in P22121 with Phaser so I'm even more
confused!
-- Ian
> -Original Message-
> From: [EMAIL PROTECTED]
> [mailto:[EMAIL PROTECTED] On Behalf Of Airlie McCoy
> Sent: 19 September 2007 15:09
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] arp/warp in p2
The problem is specifically that ARP/wARP *doesn't* support the IUCr
convention as given in IT (Vol. A, >= 1983 edition, Table 9.3.4.1, p.758
in 5th ed.) regarding choice of cell in primitive orthorhombic space
groups, and I suspect in centred monoclinic ones also. AFAIK ARP/wARP
and pointless ar
> -Original Message-
> From: [EMAIL PROTECTED]
> [mailto:[EMAIL PROTECTED] On Behalf Of Victor Lamzin
> Sent: 18 September 2007 12:48
> To: [EMAIL PROTECTED]; CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] arp/warp in p22121
>
> Dear Florian,
>
> ARP/wARP
Dear Florian,
ARP/wARP supports 65 space groups where proteins crystallise and it
indeed uses the Hermann-Mauguin convention as given in the International
Tables. The space group P22121 (number 3018 in the CCP4 symop.lib) is
not supported by ARP/wARP. The standard for it would be number 18,
P
Hi -
ARP/wARP only likes standard space groups, like P21212,
P22121 is not-standard ... oh well ...
(Eleanor is complaining about it for about 13 years ... but never
mind that she is right)
Just re-index your sg to be P21212 (refl. utilities, reindex, in ccp4i).
Choose 'Entering reflection tr
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