Re: [ccp4bb] Mr. Bump and adding FASTA to CCP4 6.3 installation?
Hi Nate, The fasta licencing doesn't allow us to distribute it with the suite so it needs to be downloaded separately. For MrBUMP to find it you should have it somewhere in your system PATH. The easiest thing to do is to put the fasta3? .exe executable into your $CCP4/bin directory. However, to avoid having to do this every time you install a new version of CCP4 you should add the path to where you've installed the fasta executables to your system PATH environment variable. On windows this can be done by right mouse clicking on My Computer, select Properties , select Advanced tab and then select Environment Variables. Here you can edit the PATH variable and add the fasta bin directory location. In your case I guess that this will be C:\CCP4\fasta\bin. You'll need to restart your ccp4i for the new settings to take effect. If you need any more help with installation or running MrBUMP please let me know. Best wishes, Ronan From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Nathan Pollock Sent: 16 August 2012 05:47 To: ccp4bb Subject: [ccp4bb] Mr. Bump and adding FASTA to CCP4 6.3 installation? Hello, Mr. Bump requires Fasta to be installed. Could someone tell me what needs to be done to install Fasta so that it is seen and used by CCP4 6.3 programs? Installers for previous versions, 6.1 and 6.2, also installed Fasta, for 6.3 we are supposed to download and install manually. OK, I downloaded and unpacked into C:\CCP4\fasta\ - now what? The download site, http://fasta.bioch.virginia.edu/fasta_www2/fasta_down.shtml , says not a word about installation in Windows, nor it is mentioned in the Readme file. Thanks! - Nate -- Scanned by iCritical.
Re: [ccp4bb] Improvement in crystal quality
Dear Nishant, are you sure your crystals are protein ? The condition contains 1 M of different salts and PEG as well - I wouldn't exclude that you are having salt crystals. You can easy check this with Izit dye or simply by trying to destroy the crystal with a microtool. If it is salt you can not crush ist. Best wishes, Ulrike
[ccp4bb] Attached error messages when creating directories in ccp4i - home/.CCP4/unix/configure.def in use?
Dear CCP4 users,
One user on our network got many error messages (attached) when creating ccp4i
directories (CCP4_DATABASE) in the recently installed 6.3.0 however the
directories is getting created and jobs can be run in them as well!
The unfortunate user have a very old configure.def in /home/.CCP4/unix and also
a configure.def.LOCK file in /home/.CCP4/unix
How can I help him get rid of this error messages when creating directories in
ccp4i-6.3.0?
Maybe I should simply delete the home/.CCP4/unix/configure.def.LOCK file? or
should I rename it into configure.def that currently is six months old and in
edit by some other software due to error messages below...?
Thanks,
Martin
###
#
# More extensive problem description below
#
###
I installed ccp4-6.3.0 using my regular user (not root) using a fedora 10
client where the ccp4 files are stored at a redhat server (fileserver)
accessible from all fedora 10 client computers.
One of my users got the following message when first starting ccp4-6.3.0
## Error message first time start
Running auto-configure for configure
You are the first person to run this version of CCP4i and
it is trying to automatically configure and save information
to the file:
/net/fileserver/xtal/ccp4-6.3.0/ccp4-6.3.0/share/ccp4i/etc/unix/configure.def
but you do not have write permission for this directory.
Please get the person who installed CCP4i to run it and
do the configure.
It is OK to continue running CCP4i.
problem 1 #
The problem user get a lot of error messages when creating new CCP4 directories
When pressing ApplyExit the attached error message appear
Despite this the new directory (CCP4_DATABASE) was created at the correct
position and jobs can be run in this directory as well!
# ccp4i startup error message - start
Now when starting ccp4i the problem user got this message:
There is a lock on the file
/net/fileserver/users/quises/.CCP4/unix/directories.def
You may be editing this file in another program
Delete the lock and continue?
If I continue Problem 1 remains
Myself installing ccp4-6.3.0 and other recently created users does not have the
directory creation problem...
Questions:
Q1: How should I configure ccp4i for the problem user or on the server and
client computers to avoid the attached error message when creating directories
in ccp4i?
Q2: Why do the problem user want to write in
/net/fileserver/xtal/ccp4-6.3.0/ccp4-6.3.0/share/ccp4i/etc/unix/ when my own
user prefer home/.CCP4/unix?
My guess would be that each user would have all configure.def settings in
home/.CCP4/unix and NOT in
/net/fileserver/xtal/ccp4-6.3.0/ccp4-6.3.0/share/ccp4i/etc/unix/
I tried to change permissions
chmod 777 /net/fileserver/xtal/ccp4-6.3.0/ccp4-6.3.0/share/ccp4i/etc/unix/
and the problem user now got a configure.def in
/net/fileserver/xtal/ccp4-6.3.0/ccp4-6.3.0/share/ccp4i/etc/unix/
howewer this is not required for other users?
so I set permissions of
/net/fileserver/xtal/ccp4-6.3.0/ccp4-6.3.0/share/ccp4i/etc/unix/
back to 755 ...
The problem user have a quite old configure.def in home/.CCP4/unix...that is in
use by another program according to error messages???
The problem user also have a configure.def.LOCK file there that I do not have
in my own .CCP4/unix
Should I delete configure.def.LOCK that is up to date of should I rename
configure.def.LOCK into configure.def in home/.CCP4/unix/?
I do not want to corrupt the user database...problem 1 remain...
Thanks,
Martin
What to do about this?
Best regards,
Martin
Martin Moche, Ph.D.
Head of Protein Crystallography
Karolinska Institutet
MBB/PSF
Scheeles väg 2
171 77 Stockholm
Sweden
phone: +46-8-524 868 43
mobile: +46-73-322 93 27
fax:+46-8-524 868 68
email:martin.mo...@ki.semailto:martin.mo...@ki.se
can't read array(/CCP4_DATABASE): no such element in array
can't read array(/CCP4_DATABASE): no such element in array
while executing
set value $array($var)
(default arm line 2)
invoked from within
switch -regexp -- $type menu {
set value [GetMenuValue $arrayname $var ]
} default {
set value $array($var)
}
(procedure SaveArray line 104)
invoked from within
SaveArray $taskname $filename $arrayname -save_types
(procedure SavePreferences line 29)
invoked from within
SavePreferences directories directories -lock
(eval body line 1)
invoked from within
eval SavePreferences directories directories $args
(procedure SaveDirectories line 16)
invoked from within
SaveDirectories -lock
(procedure SwitchProject line 11)
invoked from within
SwitchProject $project $system(SWITCH_MENU)
(procedure apply_directories line 261)
invoked from within
apply_directories save edit_directories .edit_directories
[ccp4bb] Re-processing HKL3000 reduced data using Mosfilm to obtain Rmeas
I am working with CCP4 6.1.13 and want to re-process my raw image files to obtain the multiplicity-weighed Rmeas/Rrim from SCALA. The .x files were previously processed using HKL3000 at the Advanced Photon Source at Argonne National Lab. The university I am at does not have the license for HKL3000, and I want to re-process the images using Mosflm. I have the matrix for the orientation in each .x file, but I am having trouble creating a matrix file from the .x files. I am also unfamiliar with programs that output the matrix file. I would greatly appreciate any assistance in creating the matrix file.
Re: [ccp4bb] Re-processing HKL3000 reduced data using Mosfilm to obtain Rmeas
Why don't you try Imosflm that's self explanatory point and block type of GUI Jürgen .. Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Phone: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-3655 http://lupo.jhsph.edu On Aug 16, 2012, at 11:22, Ryan Bauer rba...@email.uark.edumailto:rba...@email.uark.edu wrote: I am working with CCP4 6.1.13 and want to re-process my raw image files to obtain the multiplicity-weighed Rmeas/Rrim from SCALA. The .x files were previously processed using HKL3000 at the Advanced Photon Source at Argonne National Lab. The university I am at does not have the license for HKL3000, and I want to re-process the images using Mosflm. I have the matrix for the orientation in each .x file, but I am having trouble creating a matrix file from the .x files. I am also unfamiliar with programs that output the matrix file. I would greatly appreciate any assistance in creating the matrix file.
Re: [ccp4bb] Re-processing HKL3000 reduced data using Mosfilm to obtain Rmeas
As Jürgen says why not use imosflm? Incidentally CCP4 6.1.13 is pretty old - I would recommend updating to 6.3.0 If you REALLY want to convert denzo orientation to the Mosflm convention, there's an old Fortran program of mine at ftp://ftp.mrc-lmb.cam.ac.uk/pub/pre/denzo2mosflm.f but I wouldn't recommend it Phil On 16 Aug 2012, at 16:12, Ryan Bauer wrote: I am working with CCP4 6.1.13 and want to re-process my raw image files to obtain the multiplicity-weighed Rmeas/Rrim from SCALA. The .x files were previously processed using HKL3000 at the Advanced Photon Source at Argonne National Lab. The university I am at does not have the license for HKL3000, and I want to re-process the images using Mosflm. I have the matrix for the orientation in each .x file, but I am having trouble creating a matrix file from the .x files. I am also unfamiliar with programs that output the matrix file. I would greatly appreciate any assistance in creating the matrix file.
