ulletin board on behalf of David J.
Schuller
Sent: Wednesday, August 28, 2024 1:49 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] error in error message
I am attempting to install CCP4 9.0 from the launcher, downloaded 2024-08-28. I
get an error message about a missing dependency. One sente
I am attempting to install CCP4 9.0 from the launcher, downloaded 2024-08-28. I
get an error message about a missing dependency. One sentence is "Setup cannot
proceed further until these components are not installed..."
Clearly the "not" is erroneous.
==
e export mtz feature merge the individual 'mini' mtz files to the appropriate
file for deposition?
Kind regards,
Kyle
From: CCP4 bulletin board on behalf of Deborah Harrus
Sent: 05 February 2024 11:30
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb]
Hi
The simple answer is to estimate your own value (as we always used to do before
I coded this up about 20 years ago…) by overlaying a prediction over the images
and determining what value of mosaicity gives the best coverage. It may also be
worthwhile changing the “mosaic block size” in the “
Dear community,
I am trying to run panDDA. As first, I am simply trying to follow the
tutorial.
I have an issue with pandda.inspect:
"INFO:: There are 1 command line scripts to run
/storage/software/ccp4/ccp4-8.0/bin/../lib/python3.7/site-packages/pandda/inspect/__init__.py
calling run_script
Dear Maria,
Apologies for late reply. I'm not sure which version of
"adding_stats_to_mmcif" is in CCP4 at the moment, but if you're facing
the issue again in the future please could you try using the latest
version at https://github.com/wwPDB/py-adding_stats_to_mmcif ? If it
doesn't work, ple
Στις 2024-01-31 22:48, Nicholas Clark έγραψε:
Maria,
Apologies for the second email. I forgot that "Prepare files for
deposition" also merges the CCP4 formatted files into an MTZ. If I
recall correctly, I used "CONVERT2MTZ" in the command line to complete
the merging of the CCP4 files to generat
: [ccp4bb] Error in "Prepare and validate files for deposition" task"
Maria,
Apologies for the second email. I forgot that "Prepare files for deposition"
also merges the CCP4 formatted files into an MTZ. If I recall correctly, I used
"CONVERT2MTZ" in the command
Maria,
Apologies for the second email. I forgot that "Prepare files for
deposition" also merges the CCP4 formatted files into an MTZ. If I recall
correctly, I used "CONVERT2MTZ" in the command line to complete the merging
of the CCP4 files to generate the necessary MTZ for deposition.
Instructions
Hi Maria,
I'm not sure if anyone has replied to this chain. However, I had a similar
issue when I was trying to prepare files for deposition in the past. You
can use the PDB file and upload it to https://pdb-extract.wwpdb.org/ to
generate the CIF file for deposition.
Best,
Nick Clark
On Tue, Ja
Dear all,
I am trying to deposit 2 structures to the PDBe, solved and refined in
CCP4 (version 7), and checked in PRIVATEER as they have a lot of sugars
in. To this end, I used "Prepare and validate files for deposition"
task, as I had previously (and succesfully) done. However, and in spite
Greetings to all!
I am learning and trying to run a docking program using Schrodinger
Maestro. While identifying the binding site for the co-crystallized
ligand, I am facing an error that states "Ligand misidentified. No receptor
atoms left after masking the ligand." I am clueless how to proceed f
Hello,
I am trying to use pandda in order to locate potential ligands in my
structures...
pandda.analyse did run without error
However, at the pandda.analyse step, the coot window opens normally, but the
additional pandda window does not appear.
I do have an error message :
Hi
I am getting the following error while running the class ranker program for
automatically selecting the 2D classes. Can anybody please suggest where
the issue is ?
PYTHON ERROR: The required python module 'torch' was not found.
in: /usr/local/relion-4.0-source/src/class_ranker.cpp, line 1954
on behalf of Kay Diederichs
>
> Sent: Sunday, June 4, 2023 8:43 AM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Error in xdsgui: you have to install generate_XDS.INP
> in your path
>
> Dear Zhen Gong,
>
> Installation of XDS and associated programs is doc
Dear Kay, Graeme and David,
Thank you very much for your reply and help! XDSwiki is always the first
reference that I will go to whenever having related questions. Since I am
really not a programming person, it was not that straightforward for me to
figure out how things work as it should be. A
University
schul...@cornell.edu
From: CCP4 bulletin board on behalf of Kay Diederichs
Sent: Sunday, June 4, 2023 8:43 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Error in xdsgui: you have to install generate_XDS.INP in
your
Dear Zhen Gong,
Installation of XDS and associated programs is documented in the "Installation"
article in XDSwiki.
If I google "XDSwiki installation article", it is the first hit.
Your PATH is probably different when you double-click XDSGUI to start it,
compared to what it is on the command li
Dear all,
I have encountered this problem in xdsgui: you have to install generate_XDS.INP
in your path. Generate_XDS.INP works fine in command line but not in the GUI. I
saw the same question was raised up by another user previously on CCP4bb but I
was not able to see Key's reply any more.
Th
Hi All,
When I use pymol pulgin, I have an issue with pvol.
I try to install pyvol based on instruction shown in here:
https://schlessinger-lab.github.io/pyvol/install.html#:~:text=Download%20the%20basic%20GUI%20installer,PyVOL%20and%20any%20missing%20dependencies.
Following the instu
Dear Pedro,
What a stupid error they have in Blend!
I also had the same problem when using Blend and I fixed it by just editing
that create_file_for_BLEND.py. That code just concentrates two strings into
one, so what you need is to change every string.join line e.g.
newname=string.join(["dat
Hi again Ian,
I will send the files to you in a private e-mail.
Best regards
Kristoffer
From: CCP4 bulletin board on behalf of Ian Tickle
Reply to: Ian Tickle
Date: Wednesday, 12 October 2022 at 14:06
To: "CCP4BB@JISCMAIL.AC.UK"
Subject: Re: [ccp4bb] Error while running ED
pl -xyzin bindividual1_fixed_refine_001.pdb -hklin hkl_ed.mtz
> -flabel FOBS -atomsf atomsf_neutron
>
>
>
> Best regards
>
> Kristoffer
>
>
>
>
>
> *From: *Ian Tickle
> *Date: *Tuesday, 11 October 2022 at 19:33
> *To: *Kristoffer Lundgren
> *Cc: *"CCP4BB
bindividual1_fixed_refine_001_map_coeffs.mtz hklout hkl_ed.mtz<
Date: Tuesday, 11 October 2022 at 19:33
To: Kristoffer Lundgren
Cc: "CCP4BB@jiscmail.ac.uk"
Subject: Re: [ccp4bb] Error while running EDSTATS
Hi Kristoffer
The deposited structure factor file is missing an FOM column wh
Hi Kristoffer
The deposited structure factor file is missing an FOM column which is
needed for MTZFIX to do its job of checking the veracity of the FWT and
DELFWT columns. The message I get with CCP4 7.1 is different, in fact it's
exactly what I expect:
mtzfix: ERROR: Labels not found - maybe
Hi Kristoffer
Thanks for the error report. I'll look into it and get back to you.
Cheers
-- Ian
On Tue, 11 Oct 2022 at 17:09, Kristoffer Lundgren <
8a31f470d88b-dmarc-requ...@jiscmail.ac.uk> wrote:
> Dear all,
>
>
>
> I am trying to run EDSTATS on a neutron structure containing a manganes
Dear all,
I am trying to run EDSTATS on a neutron structure containing a manganese ion
(https://www.rcsb.org/structure/7KKW), but either I am doing something wrong or
something is broken. When using EDSTATS supplied with CCP4 8.0 I end up with
the error message:
mtzfix: WARNING: Output file i
Hi Graeme,
I suspected as much. I think I still have a CCP4 7.x installed.
Thanks & best regards,
Pedro
On 11/10/2022 15:33, Winter, Graeme (DLSLtd,RAL,LSCI) wrote:
Hi Pedro
Problem here is that ccp4.python is Python 3 and BLEND is still written for
Python 2.7
This was one of the modernisa
Hi Pedro
Problem here is that ccp4.python is Python 3 and BLEND is still written for
Python 2.7
This was one of the modernisation things which changed from 2 -> 3
An older version of ccp4 would probably still work - version 7.something
Looks like BLEND needs to be updated…
Best wishes Graeme
Dear All,
I am trying to run BLEND on a series of XDS files in MTZ format.
However, I get the following error:
Traceback (most recent call last):
File
"/pxsoft/ccp4/ccp4-8.0/share/blend/python/create_file_for_BLEND.py",
line 74, in
newname=string.join(["dataset_",sfx],"")
AttributeE
Hi all,
I keep getting the following errors with my deposition jobs in i2 version
8.0.002:
"-ERROR- adding_stats_to_mmcif_i2_gui:19 Failed instantiating plugin object”
and
"-ERROR- adding_stats_to_mmcif_i2_gui:48 Error in wrapper
adding_stats_to_mmcif_i2 0.1:: Error in the plugin script startP
On 14/10/2020 13:38, Abhilasha Thakur wrote:
I have a query related to PyRx Virtual Screening Software, Some of my ligands files are not read by PyRx. I
downloaded the SDF format and then SDF to PDB conversion by Open Bable, then uploaded the ligand library
into the PyRx and then set as ligand
August 2020 13:42
An: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
Betreff: [EXTERNAL] [ccp4bb] Error in coot post-refine in Phenix
EXTERNAL : Real sender is
owner-ccp...@jiscmail.ac.uk<mailto:owner-ccp...@jiscmail.ac.uk>
Has anyone else run into this problem? Using Phenix (ni
Dear all,
I don't seem to be able to get a functional installation of ccp4i2 on Mac
Catalina. I have downloaded the latest ccp4i2 installer and reinstalled
XQuartz, but the application still doesn't open (no errors shown if I open the
application on finder)
I have then reinstalled in the comman
Dear Gihan,
The most likely thing I can think of is that the sequence contains a character
not recognised as a legitimate one-letter code. This could happen if you use a
special letter coding for an ambiguous residue, or if you say it’s a nucleic
acid sequence instead of a protein sequence.
S
Hi.
I get this "INPUT ERROR: Erro interpreting Composition sequence" message when I
try to MR in ccp4 Pherser MR. I've been using regular *.fasta file for the
sequence. First, I thought the error coming from the changes I made to the
*.fasta fill, but even when I'm using the original file stra
Dear Helen and Andrew,
Thank you very much for your suggestions and help. It is working now and
able to run the aimless successfully.
Your help is much appreciated
Mike
On Thu, Jul 11, 2019 at 7:53 PM Helen Ginn wrote:
> Dear Mike and Andrew,
>
> I've since updated to a later version of cc
Dear Mike and Andrew,
I've since updated to a later version of ccp4 (7.0.076) and now have the XMLOUT
tags specified automatically. Woops!
Thanks for that error log Andrew - I had a look at the aimless.script file to
see how that filename was generated, and looked up the command on the CCP4
de
Dear Mike and Helen,
As I understand it, the XML is only written when POINTLESS/AIMLESS are run
through the CCP4 GUI and the command comes from the GUI script, so there is no
way you can turn this off from POINTLESS itself.
However, if you use the “Run&View com file” option from CCP4i GUI, you
Dear Mike,
No problem! Happy to provide suggestions, though I'd prefer to be addressed
directly on here.
Here's another suggestion, no promises. If you can provide more detail on the
GUI input and the output log files, it would be easier to know why this is
happening in the first place. Howeve
Dear Andrew,
Thanks for your suggestion. Yes, you are right that the error is because
.xml file is not being written. but not able to find the reasons...I
checked...Disk space is free and have permission to write also. I could
able to run Pointless, but not Aimless.
Any other reason??
Thanks
Mi
I think Helen’s answer is absolutely right. I asked Phil Evans about this when
I saw him yesterday, and he said that error usually arises when it is not
possible to write the xml file, either because a disk is full, or because you
do not have permission to write to that area.
Andrew
> On 3 Jul
Hello Mike,
This is just a guess. From the error message it seems that it’s trying to write
to the root directory of your filesystem.
I am assuming you are using the old ccp4i interface. It might be because the
ccp4i project directory you’re running it under has been set to / or is empty.
If s
Hello everyone,
Data reduction with Aimless from (CCP4i) fails with error message as below
FILEIO: cannot open file /Processing1_8_pointless.xml
How can this error be fixed? Comment please...
Thanks
Mike
To unsubscribe
Dear all,
Sorry for asking for a very naive question that might be asked before.
After integration, I am trying to do "data reduction" through Aimless, but
task fails with an error message as
#CCP4I TERMINATION STATUS 0 "FILEIO: cannot open file
/Processing1_8_pointless.xml
I really appreciate
Dear all,
I got such kind of error information during opening ccp4 in mac. Can anyone
tell me how to fix it ? Thanks a lot!
Application initialization failed: couldn't connect to display
"/private/tmp/com.apple.launchd.hH7rs61iI7/org.macosforge.xquartz:0"
Error in startup script: can't read "tk_
Thank you Paul.
On 18/09/2017 16:18, Vikram Dalal wrote:
I am model building a protein in coot. I added Ala residues in coot. I used the real space refinement option
to fit in electron density but i got an error (attached in the picture).
Poor coot has become detached from the Refmac monomer library. This
> Hope this helps,
>> > Robbie
>> > Sent from my Windows 10 phone
>> > Van: r...@mrc-lmb.cam.ac.uk<mailto:r...@mrc-lmb.cam.ac.uk>
>> > Verzonden: dinsdag 20 juni 2017 16:14
>> > Aan: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
>&g
in.
> > Hope this helps,
> > Robbie
> > Sent from my Windows 10 phone
> > Van: r...@mrc-lmb.cam.ac.uk<mailto:r...@mrc-lmb.cam.ac.uk>
> > Verzonden: dinsdag 20 juni 2017 16:14
> > Aan: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
> > Onde
...@mrc-lmb.cam.ac.uk<mailto:r...@mrc-lmb.cam.ac.uk>
> Verzonden: dinsdag 20 juni 2017 16:14
> Aan: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
> Onderwerp: [ccp4bb] Error in assignment of symmetry operators
> Dear All,
> Apologies for posting a Buster-related que
mrc-lmb.cam.ac.uk>
Verzonden: dinsdag 20 juni 2017 16:14
Aan: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
Onderwerp: [ccp4bb] Error in assignment of symmetry operators
Dear All,
Apologies for posting a Buster-related question to this list, the
buster-discuss one seems less act
Dear All,
Apologies for posting a Buster-related question to this list, the
buster-discuss one seems less active :-) I am trying to run a refinement job,
and hit the following problem:
ERROR : [run_buster-0046] unable to create initial SCREEN
output with gelly - see
refine/01-BUST
Hi
It looks like you've got the Windows environment variable "MOSDIR" set to "E:\"
when running CCP4i - I have no idea how that would happen; it's normally set to
something like C:\MOSDIR. If you haven't got an E:\ drive that would be the
root of your problem...
Have a look in the list of Wind
Hi, Mr/Ms,
I am a user of CCP4i. I recently discovered that imosflm cannot be used
on my win7. the error message is shown below.
[image: Inline image 1]
However, when I go to 'bin' folder and double click the imosflm.bat, the
program can be start up successfully. I don't know what's the pro
I am very thankful to all.
>
-Ursprüngliche Nachricht-
Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Paul
Emsley
Gesendet: Dienstag, 3. Januar 2017 15:30
An: CCP4BB@JISCMAIL.AC.UK
Betreff: Re: [ccp4bb] error in phenix refinement
On 03/01/2017 14:10, Vikram Dalal wrote:
> Hi all,
>
>
> I ha
Your PDB file contains atoms that are less than 0.001 A apart. This doesn't
look like a good model. Please consider fixing it first.
Pavel
P.S.: There is Phenix mailing list for Phenix related questions.
On Tue, Jan 3, 2017 at 6:10 AM, Vikram Dalal
wrote:
> Hi all,
>
>
> I have added the water
On 03/01/2017 14:10, Vikram Dalal wrote:
Hi all,
I have added the water, EDO and GOL in coot in a protein structure. I got this
error message
(Fig 1) after running the phenix refinement.
Hello Vikram,
A flicker of confusion crosses my brow as I contemplate the on-going thought process tha
@jiscmail.ac.uk]
Sent: 07 December 2016 08:59
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] error with AMPLE on CCP4 7.0 installed as precompiled binary
Hello,
I downloaded ccp4 7.0 linux binary on SUSE Linux Enterprise Server 11 machine
(which has no monitor). AMPLE program when run through com
Hello,
I downloaded ccp4 7.0 linux binary on SUSE Linux Enterprise Server 11 machine
(which has no monitor). AMPLE program when run through command line gives
following error
Traceback (most recent call last): File
"/home1/nkumar/software/ccp4-7.0/bin/ample.py", line 1039, in
main() File
Hi
It looks like Dimitris has been bitten by something that is all too common,
unfortunately (so common that the next release of iMosflm will try to trap this
issue).
This error occurs when the user tries to open an image in iMosflm by using the
"open session" function - which is actually th
Hi Dimitris
Can you send me *one* of the CBF files directly so that I can see it?
On 5 Mar 2015, at 15:42, dladakis wrote:
> Hello
> I recently collected data from ESRF, trying to read data on imosflm and i
> keep getting an error message "could not parse file". The images are .cbf
> format an
Hello
I recently collected data from ESRF, trying to read data on imosflm and i keep
getting an error message "could not parse file". The images are .cbf format and
I have downloaded the latest version of ccp4 on linux.
Anyone who could give an insight into that problem?
Thanks
Dimitris
Postdoc,
972-8-646-1710
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of jeorgemarley thomas [kirtswab...@gmail.com]
Sent: Tuesday, February 24, 2015 9:50 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] error message in xds
Dear All,
I am getting an error me
Dear All,
I am getting an error message after indexing the data in XDS as " !!! ERROR
!!! DIMENSION OF DIFFERENCE VECTOR SET < 2" , please suggest what wrong has
happened and what could be done for this, initially the message was
insufficient number of spots accepted was there, then I change the
r
Not very easily without more information..
The conversion does two steps - the first is scalepack2mtz which is meant
to generate an mtz file ( "/tmp/gouri/tvpsat_akg_1_1_mtz.tmp"). Can you see
if that ran correctly?
Ekleanor Dodson
On 17 November 2014 07:10, rohit kumar wrote:
> Dear all,
>
>
Dear all,
during conversion of .sca file to mtz in ccp4, i got this message (see
below).
***
* Information from CCP4Interface script
***
The program
Hello, I'm evaluating changes in crystal packing between different forms of my
protein. I use NCONT to calculate the number of atoms within a distance of 10 A
from each CA atom of the protein chain. My protein is also a crystallographic
dimer, then I want to list contacts between the two monomer
Hi Ian,
Improving the CCP4 tests is a priority. We (the core team) have a project
looking into that. If developers have their own tests for components of the
suite that have not made it into the distribution, then we'd be happy to
collect them for the new test set.
Best wishes
-- David
On 29 A
Hi Marcin
It was obviously added originally because there was a limit to the length
of the PATH variable (presumably there still is), so repeated invocations
of setup scripts could take you over the limit. Ideally the script should
remove old versions from the PATH, not just prepend the new one,
On Mon, Apr 28, 2014 at 03:51:57PM +0100, Ian Tickle wrote:
> Harry,
>
> I've run into this problem before with other programs when I switch between
> v6.3 & v6.4. I think the problem is this code in ccp4.setup-sh:
>
> if [ `expr ":${PATH}:" : ".*:${dir}:"` -eq 0 ]; then
We can remove this co
Hi Felix
You're very trusting! Bugs in new versions of software are not unknown!
The bug may not manifest itself in a program crash (though it makes life
easier if it does), rather it may simply give different numerical results
that you may not spot for some after. This is why CCP4 distributes t
Hi Tim,
What can be a reason to work with an obsolete version of CCP4?
I remember reading somewhere that 6.3.0 version is obsolete.
FF
Dr Felix Frolow
Professor of Structural Biology and Biotechnology, Department of Molecular
Microbiology and Biotechnology
Tel Aviv University 69978, Israel
A
Dear all,
For experiments that involve switching between different versions of CCP4
you might like to try the CCP4Dispatchers scripts (see
http://www.ccp4.ac.uk/html/CCP4Dispatchers.html). On a binary install of
ccp4 6.4.0 these will have been generated automatically. For example, on my
Linux mach
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Dear Sreetama, dear Ian,
I avoid sourcing both version 6.3 and 6.4 in the same terminal. If I
need to work with 6.3 I modify my .bashrc from 6.4 to 6.3 and then
open a new terminal to make sure everything refers to v6.3 and vice versa.
Best,
Tim
On
Harry,
I've run into this problem before with other programs when I switch between
v6.3 & v6.4. I think the problem is this code in ccp4.setup-sh:
if [ `expr ":${PATH}:" : ".*:${dir}:"` -eq 0 ]; then
if test $ccp4_first_in_path -eq 1; then
PATH=${dir}:${PATH}
else
PATH=${PA
Hi Sreetama
That's the problem - sourcing the old ccp4 6.3 distro has set up MOSFLM_EXEC to
point to an old copy of ipmosflm that will not run with the latest iMosflm.
> Mosflm version 7.0.9 for Image plate and CCD data 14th May 2012
which cannot be used with iMosflm 7.1.0.
So it looks
Dear Sir,
If I sorce ccp4-6.3, and then change in the bashrc file & source
ccp4-6.4, (and source the modified .bashrc file in either case) but don't close
the previous terminal, then opening imosflm gives the aforementioned error.
After closing the imosflm GUI, if I type at the ter
Hi
When you get this error, and "everything" has been closed, what do you get if
you type (in the same terminal window that you tried to start iMosflm) -
$MOSFLM_EXEC
?
It's plain from the message that
"ipmosflm" is not compatible'
that iMosflm is trying to run with an inco
Dear All,
Whenever I open up imosflm GUI from the terminal, I get the
following error:
iMosflm version 7.1.1, 24th March 2014
"ipmosflm" is not compatible.
Please configure iMosflm with the correct executable.
clicking the Configure button at the bottom of the error message panel
On Tue, 1 Apr 2014 17:28:48 +0200, Almudena Ponce Salvatierra
wrote:
>sorry, I missed this part of the error message:
>
>!!! ERROR !!! AUTOMATIC DETERMINATION OF SPOT SIZE PARAMETERS HAS FAILED.
> YOU MAY RESTART THIS STEP AFTER SPECIFYING VALUES IN XDS.INP
>FOR:
> RE
It means that there exists a technical problem that probably has nothing
directly to do with your data and XDS: the program tried to read data that
could not be read.
I would guess that the disk is full, or your quota exceeded.
Hope this helps,
Kay
Dear Almudena,
You can try to run XDS with 300 frames. At the end, you have to open the
file called INTEGRATE.LP and copy the refined value of
REFLECTING_RANGE= REFLECTING_RANGE_E.S.D.=
BEAM_DIVERGENCE=BEAM_DIVERGENCE_E.S.D.=
at the end of your XDS.INP.
Now, you can re-run XDS with all
sorry, I missed this part of the error message:
!!! ERROR !!! AUTOMATIC DETERMINATION OF SPOT SIZE PARAMETERS HAS FAILED.
YOU MAY RESTART THIS STEP AFTER SPECIFYING VALUES IN XDS.INP
FOR:
REFLECTING_RANGE=REFLECTING_RANGE_E.S.D.=
BEAM_DIVERGENCE=
Dear CCP4 users,
while I am running CORRECT within XDS, the program suddenly stops, and
gives the following message:
forrtl: severe (24): end-of-file during read, unit 2, file
/data/almudena/160314SLS/dts2/bin1_01.tmp
I actually don't know what it means. I could run it with no problems with
300
Centrosymmetric reflections typically have C=0 and D=0, although non-zero values
should not matter, as they do not modify phase probabilities for centrosymmetric
reflections.
Somehow, entering non-zero values for C and D for centrosymmetric reflection
creates strange results during transformatio
You don't say how you are doing the transformation?
I would simply input the file to cad
cad hklin1 thisfile.mtz hklout newfile.mtz
labi file 1 allin
end
I think (and hope) that the data and phases will be converted correctly to the
CCP4 asymmetric unit.
Eleanor
On 25 Mar 2014, at 09:16, Zbys
I am reading an external file, which contains phases and ABCDs in the space
group P43212. My file has an asymmetric unit with k>= h.
Since CCP4 uses a different asymmetric unit with h>=k, this requires phase and
ABCD coefficients transformation. The transformation seems to be correct for
reflect
Dear CCP4 / Coot community,
I am trying to use LIDIA from Coot 0.7.2 - as supplied with CCP4-6.4.0 - to
look at a protein / ligand complex.
However, when trying to launch LIDIA from the Extensions menu of Coot - I get
the following error.
I guess this suggests some form of fortran compile erro
Dear All
the soon to be released update (via the update mechanism) will address this by
applying the patch to imosflm.tcl.
Charles Ballard
CCP4
On 23 Oct 2013, at 23:35, Andreas Förster wrote:
> Hi David,
>
> I've just renamed the ipmosflm in $CCP4/bin to ipmosflm_new and then defined
>
>
Hi David,
I've just renamed the ipmosflm in $CCP4/bin to ipmosflm_new and then
defined
MOSFLM_EXEC as /path/to/ccp4-6.3.0/bin/ipmosflm.
CCP4 6.3 needs to be installed for this to work.
Andreas
On 23/10/2013 5:39, David Schuller wrote:
iMosflm developers:
I have installed CCP4 6.4.0, wh
Hi David
Nothing to do with the iMosflm developers. CCP4 has made some changes
that have caused this error to arise in 6.4.0 on Linux (this is not
to say that the iMosflm code didn't have the bug, just that it
doesn't appear with either our own version or with the same version
distributed
Hi Phil,
On Mon, 2013-08-12 at 11:31 +0100, Phil Evans wrote:
> I do have problems building static executables on OSX: the CCP4 guys seem to
> be better at it.
>
> Specifically, when I build with a "static" flag, fatal error messages from
> program exceptions get lost, making it hard to underst
I do have problems building static executables on OSX: the CCP4 guys seem to be
better at it.
Specifically, when I build with a "static" flag, fatal error messages from
program exceptions get lost, making it hard to understand some serious errors.
However I have put on our ftp site
ftp://ftp.
Hi
I noticed last week that, although the CCP4 updater for OSX requires 64-bit
(see CCP4 discussions passim), all the executables are 32-bit (or at least in
my current copy, updated a few weeks ago). So there is an inconsistency - no
doubt this will be sorted out shortly.
If you want a 64-bit
Hi Sheena,
simple quickfix to your problem:
a) Run CAD and limit the output resolution on that mtz file so you don't run
into the memory allocation error of pointless.
b) try phenix.xtriage also if it is not a CCP4 program
Jürgen
..
Jürgen Bosch
Johns Hopkins University
Bloo
Dear all
We have been trying to run pointless on a large mtz file which seems to be
allocating more than 1.5Gb of memory resulting in the following error:
The program run with command: /Applications/ccp4-6.3.0/bin/pointless
has failed with error message
pointless(507) malloc: *** mmap(size=1577
Dear Masaki,
I have just checked installation of CCP4-6.3.0 32 bit with Package Manager, and
found no problems with it.
Two suggestions:
1) there are residual files from previous CCP4 installation in your temporary
directory, which you gave to the Package Manager. Please make sure that that
d
Hi all
I installed Ubuntu 12.10 on my PC, today. Then I tried installing CCP4-6.3.0
on my system using Package Manager (32 bit) downloaded from CCP4 HP, but I
failed.
On the CCP4 setup, step 5 out of 5, I received the error message as follows;
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