Hi Christian, we use openbabel for this kind of thing, I'm sure you'll find
the file formats you want to interconvert among the long list it supports:
http://openbabel.org/wiki/Category:Formats
Cheers
-- Ian
On Wed, Aug 17, 2011 at 9:20 AM, Christian Roth
christian.r...@bbz.uni-leipzig.de
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Hash: SHA1
Hi Phil,
'wish' works on Debian (stable upwards) (and therefore probably also on
Ubuntu) where blt is hidden in a library, and it works greatly - I used
to do the opposite, i.e. changing bltwish into wish but e.g. loggraph
did not work properly that
It doesn't seem to work out of the box on Centos5.6, nor on Scientific Linux 6.
On SL6 I think we had to install yet another TCLTK from somewhere (can't
remember) to get BLT, and with that one using wish does work
Roll on the loggraph replacement!
Phil
On 17 Aug 2011, at 10:38, Tim Gruene
On 17/08/11 10:49, Phil Evans wrote:
Roll on the loggraph replacement!
Next month ?
Dear Phil,
for me (RHEL 6.1, 64-bit, ccp4 6.2), loggraph works with wish but
requires bltwish. The command is
exec $CCP4I_TCLTK/wish $0 -- ${1+$@}
but if I set
export CCP4I_TCLTK=/sharedSoftware/ActiveTcl-8.5/bin
I get the same error that you report because ActiveTcl-8.5 doesn't
contain
Dear Christian,
Sometime ago, I ran into the same problems as you describe. I think I
used an iUCR program to do the conversion. However, extensive manual
editing was still necessary. The problem was that the cif file had long
atoms names (5 characters), which got truncated upon conversion,
Dear all,
Is there a way to make COOT use it's own libraries and not the ones from ccp4
which is the default? I've tried using the command export
COOT_REFMAC_LIB_DIR=//path/to/coot//share/coot/lib (mentioned elsewhere) but it
doesn't work.
Thanks
Eric
On 17/08/11 16:18, Eric Karg wrote:
Dear all,
Is there a way to make COOT use it's own libraries and not the ones from ccp4
which is the default? I've tried using the command export
COOT_REFMAC_LIB_DIR=//path/to/coot//share/coot/lib (mentioned elsewhere) but
it doesn't work.
Thanks
Eric,
That IS the way to do it. Please make sure you have the dictionaries in
the path and check your coot startup script in case it sets
COOT_REFMAC_LIB_DIR back to nothing (and hence falls back to the ccp4
one). Do you get any message in your start up console? BTW which
version of Coot
This wrapper works for me
Phil
#!/bin/csh -f
#
# LMB wrapper script for Coot
#
if ($MACHTYPE == 'x86_64') then
set COOT_TOP = $COOT_HOME/Coot64
else
set COOT_TOP = $COOT_HOME/Coot32
endif
if (! $?COOT_REFMAC_LIB_DIR) then
# Dictionary location not set, use the Coot dictionaries
setenv
Thanks all for the comments. I was thinking of crosslinking a protein that
hasn't crystallized. Cystein engineering seems a good idea but depends on the
availability of a good model. We'll be trying mild crosslinking using
bifunctional reagents of various lengths (I suspect glutaraldehyde will
There are 2 rogue reflections in a data set I have here. How can I
eliminate them?
I thought sftools did this but i cant seem to get the syntax right.
Short of dumping the whole file, using an editor, then reconstructing it
I am stuck..
Eleanor
Hi Eleanor,
Depends on what makes them rogues. If, say, they have very large amplitudes
then you could do something like:
sftools
read rogue.mtz
select col 1 1
write norogue.mtz
end
Or if it's easier to select just the rogue reflections by some combination of
select commands, you can do
Thanks for the suggestions. I could solve the problem by using the setenv
command to the coot directory,but I still cannot use the Real Space Refine Zone
in Coot because the names are not compatible. I'm trying to build an RNA
molecule by the way.
Any suggestions?
Eric
Am Mittwoch 17 August 2011 17:55:59 schrieb Eleanor Dodson:
There are 2 rogue reflections in a data set I have here. How can I
eliminate them?
I thought sftools did this but i cant seem to get the syntax right.
Short of dumping the whole file, using an editor, then reconstructing it
I am
Hi Eric,
Once you merge the ligand coordinates to your model and do one round of
refinement, the next time you open up coot and try using the real space
refinement it never works (even if you import cif dictionary of your ligand)
so not sure if its a problem with coot. Did anyone else had similar
Welcome to the quirks of RNA crystallography. It is a small community in a sea
of protein crystallographers so expect to get used to work arounds to get
things to work.
Your answers are at the coot mailing list archives (we recently had a
discussion regarding coot 0.6.2 ver 3562) .
On 17 Aug 2011, at 17:10, Eric Karg wrote:
Thanks for the suggestions. I could solve the problem by using the setenv
command to the coot directory,but I still cannot use the Real Space Refine
Zone in Coot because the names are not compatible. I'm trying to build an RNA
molecule by the way.
I usually dump the whole file into text. Even wrote a little jiffy
script for doing the converting back and forth:
http://bl831.als.lbl.gov/~jamesh/pickup/mtz2txt
Specifically, the text version of the MTZ file is actually an f2mtz
script that will use itself as an input file to re-generate
Dear Eleanore,
Ooops - the ccp4bb rejects attachements with *.sh ending? Let's try it
again with *.sh.txt ...
The attached script works for me - fantastic what one can do with
SFTOOLS :-)
Cheers
Clemens
On Wed, Aug 17, 2011 at 04:55:59PM +0100, Eleanor Dodson wrote:
There are 2 rogue
Dear Colleagues,
My institution is introducing concerted measures for improved security via
encryption of files. A laudable plan in case of loss or theft of a computer
with official files eg exams or student records type of information stored on
it.
Files, folders or a whole disk drive can be
Hi,
HIPAA and other regulations require systems which house patient
identifiable data to have encrypted disks at our uni. Systems which
house student data (e.g. SSN #'s, grades, etc) are also encrypted.
Since we are doing mostly basic research or using de-identified data
in structural biology, we
Thanks Clemens - I knew it should be possible! Documentation didnt exactly
help..
Eleanor
On Wed, 17 Aug 2011 19:20:21 +0100, Clemens Vonrhein
vonrh...@globalphasing.com wrote:
Dear Eleanore,
Ooops - the ccp4bb rejects attachements with *.sh ending? Let's try it
again with *.sh.txt ...
Yeah, it was a totally delightful interaction. So much for the Ubuntu spread
the love of humanity theme.
They have successfully migrated from figure 3 to figure 2:
http://bandcamp.tv/linux-demotivators/
As for BLT, my sense (being the unfortunate maintainer for it on fink) is that
it is dead
Hi John
My Mac laptop has been encrypted according to MRC rules for several
years and has caused no problems. Windows or Linux may behave
differently, but I have no reason to think they might (until a
ccp4bber tells me differently)!
On 17 Aug 2011, at 20:13, Jrh wrote:
Dear
Upon release of the newest MBA's from Apple there was this test on Ars
http://arstechnica.com/apple/reviews/2011/08/thunder-in-the-air-ars-reviews-the-mid-2011-macbook-air.ars/3
So if you are concerned in terms of speed I would say don't worry.
However never forget your password.
Jürgen
P.S. the
On Aug 17, 2011, at 3:25 PM, Harry wrote:
Hi Bill
I don't think this includes BLT, does it?
No. That was what I was trying to say (apparently not very well, sorry!):
On 17 Aug 2011, at 22:33, William Scott wrote:
if CCP4 could free itself of this dependency...
…then it could make
We have no problem with encryption on Windows 7 here at NIH
- Original Message -
From: Harry ha...@mrc-lmb.cam.ac.uk
To: CCP4BB@JISCMAIL.AC.UK CCP4BB@JISCMAIL.AC.UK
Sent: Wed Aug 17 18:23:21 2011
Subject: Re: [ccp4bb] Computer encryption matters
Hi John
My Mac laptop has been encrypted
On 08/18/2011 04:13 AM, Jrh wrote:
Dear Colleagues,
My institution is introducing concerted measures for improved security via
encryption of files. A laudable plan in case of loss or theft of a computer
with official files eg exams or student records type of information stored on
it.
Files,
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