I've found that predator is one of the best services of this sort:
Ref: PROTEINS: Structure, Function, and Genetics 27:329–335 (1997)
Server: http://mobyle.pasteur.fr/cgi-bin/portal.py?#forms::predator
The server is slow but the service is good.
James
On Jul 18, 2011, at 10:47 PM,
Hello,
version 6.2.0 of ccp4 has strange permissions set to several
setup/configuration scripts which are read while sourcing ccp4.setup.
For a long time, ccp4 packages have been distributed with some arbitrary file
and directory ownerships which users are obviously supposed to edit to meet
Dear all,
I am now writing a script for phenix.phaser.
In the input file params.eff there is a keyword labin which corresponds to
the labels inside input mtz files. The important columns in my ccp4 mtz file
are FP, SIGFP.
I edit the line of labin as:
labin F=FP SIGF=SIGFP
when running the
Dear Oliver and others,
an alternative way of installing system-wide third party software is
with a non-root account that is in the same group as all the users. Use
that account to install software centrally and initialize in each user's
.bashrc. (Root is used only for administrative tasks
We are working to relax the permissions on the files to rwx r-x r-x
Charles Ballard
CCP4
On 19 Jul 2011, at 11:25, Weiergräber, Oliver H. wrote:
Hello,
version 6.2.0 of ccp4 has strange permissions set to several
setup/configuration scripts which are read while sourcing ccp4.setup.
For
Could you please unsuscribe me from this mailing list?
My e-mail address is : a...@novalix-pharma.com
Thanks,
Regards,
Aurélie Martinez.
- Message d'origine -
De: CCP4BB automatic digest system lists...@jiscmail.ac.uk
Date: Tue, 19 Jul 2011 00:04:10 +0100
Sujet:
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
While we're on the subject of issues with the ccp4 6.20 distribution, I've had
a problem with the Mac OS X package installer.
It seems to be missing the ccp4i executable. Launching the application gives
the following error:
19/07/2011 13:04:02 [0x0-0x269269].com.yourcompany.ccp4[17160]
Dear all,
ideally, permissions should be either
rw-r--r-- (0644)
or (for files that need to be executed as well as directories)
rwxr-xr-x (0755)
One quick fix:
find . -type d -exec chmod -v 0755 {} ;
find . -type f -exec chmod -v 0755 {} ;
but that last command makes every single
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:
Dear all,
or use a modified version of Clemens's commands for that:
find . -perm 700 -exec chmod 755 {} \;
find . -perm 750 -exec chmod 755 {} \;
find . -perm 600 -exec chmod 644 {} \;
find . -perm 640 -exec chmod 644 {} \;
Best regards,
Dirk.
Am 19.07.11 14:34, schrieb Clemens Vonrhein:
Just a general curiosity - did I miss the release announcement for the
6.2.0 version on the bb or is it the CCP4 policy not to make such
announcements? Perhaps the idea is to prevent people rushing to
download the latest release and crushing the server :)
--
I'd jump in myself, if I weren't so
Thanks for all the suggestions.
I forgot to mention that I had tried microseeding and it was partially
successful. I am trying this while also pursuing other venues. At Florian's
suggestion I have set up a free interface diffusion method and it looks very
promising. I have a few free floating
You don't mention many other details about your stereo setup, so I will
asssume you have/plan to get a nVidia 3D Vision setup.
If those are the only 3 choices, I would cross off the Samsung. It is a
year older technology, with lower resolution and significant crosstalk.
The ASUS and the
Another option is to use the recursive feature of chmod to
change the permissions on the files. E.g.
chmod -R a+rX .
which will recursively add read for all users to files (and directories) and
will
also add execute if the file is a directory or if it already has at least one
execute
bit
My $0.02.
My old lab had the Samsung and an Acer. The Samsung was small and worked well
in a dedicated graphics room. The Acer died just after the warrantee period.
I now have a 23in Zalman attached to my macbook pro. Outside of stereo viewing
the text is alright, but not as clear as my
Dear all,
Recently I crystallized and solved the structure of a protein using molecular
replacement. The crystal diffracts to 1.8A and has the R free of 0.21.
During refmac and phenix refinement, I found that the N-terminal (~25 amino
acids) electron density wasn't quite good, especially a
but that last command makes every single file executable, which is
rather ugly (but doing a selective chmod 0755/0644 is a bit tricky
I was wondering about having every file executable in the source
distributions a while back, and came up with an quick way to make it
less ugly (inline due to
did you try looking if there is a company offering data recovery services from
these kind of tapes?
if there is, there may not be a need to buy a tape drive yourself.Mark
Quoting Min, Xiaoshan:
Dear CCP4 community,
We have a few datasets that reside in tapes (Sony QG-112M 8 mm tape
and
Dear Padmaja,
I have use Samsung 2233RZ for stereo running on Linux and Windows
systems. Perfomance is great.
HTH
Guenter
Pardon the off-topic query, but I would like to get some feedback
about any personal preference for 3D LCD monitors. I am trying to
decide between the following 3
Hi Obayed,
even though there is 20% sequence identity you may be able to get a very good
homology model, especially if there is more than one protein structure in the
PDB with 20% homology. Then you can overlap the pdbs and find out what
structurally needs to be preserved as opposed to what is
Homer is one of the best services for homology modeling:
http://protein.cribi.unipd.it/Homer/
James
On Jul 19, 2011, at 2:06 PM, Paul Kraft wrote:
Hi Obayed,
even though there is 20% sequence identity you may be able to get a very good
homology model, especially if there is more than
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