Hi Martyn & Dirk,
On Thu, May 10, 2007 at 02:18:14PM +0200, Dirk Kostrewa wrote:
> I want to second Miguel: a switch between a "basic" GUI (could be with
> even less options) and an "advanced" and "expert" GUI that allows
> access to most and all options that can be used in scripts would be
>
On Thu, May 10, 2007 at 02:46:44PM +0100, Kolstoe S.E. wrote:
> The most useful aspect of the ccp4i GUI is its automatic generation of
> com files. However, I would prefer the GUI to output a .com file into my
> working directory (rather than the obscure location they are saved to
> now) every time
Hello Scott,
hmmm - it is quite difficult to do a good analysis of your problem,
remotely. You've tried the enantiomorphic space group I4(3), just to be
sure? In principle, the molecular replacement solution given by Phaser
sounds good, but this is no proof of whether it's correct. What sounds
Dear Coders,
Do I see this correctly that crossec.lib
is the XSECT.DAT file from Don Cromer's FPRIME
program? If so, has there ever been an update?
Mine is from some reel tape I got from him long ago
when I ported the code...seems to be the same.
Thx, br
-
Hi
> Maybe any parameter setting unchanged from the values in the
> $CCP4/ccp4i/tasks/*.def file should be internally flagged as being at
> the 'default value' - resulting in them _not_ being written to the
> com-file? This way any potential change in defaults inside the actual
> program would hav
Clemens Vonrhein wrote:
One thing I found very confusing though, is that the com-files created
by the CCP4i will often have (nearly) all possible keywords set, even
if I haven't changed any of the defaults in the gui. Often, a CCP4
program has defaults itself and only requires keywords if one wan
It is a bit clunky - you can use siperpose molecules - fit residues to
fit a selected range (1-40; 60-100 say) and write out a complete fitted
pdb file. Then you could use a VERY old program
compar xyzin1 original.pdb xyzin2 fitted.pdb (xyzin3 another.pdb)
and it will match all pairs with the
Dear CCP4bb,
The intention with CCP4i GUIs is that those folders which are open by
default (after you have chosen the mode of action from the top protocol
folder) are for everyone and those that are closed by default are for
experts OR difficult cases. Unfortunately that is an OR not an AND; t
I would agree with Clemens that the Scala GUI task generates far too
many keyworded commands, for things which have sensible defaults in
the program.
One problem conundrum for the GUI (because it works by generating a
script without actually running the program) is that the GUI has no
wa
Bernhard Rupp wrote:
Dear Coders,
Do I see this correctly that crossec.lib
is the XSECT.DAT file from Don Cromer's FPRIME
program? If so, has there ever been an update?
Mine is from some reel tape I got from him long ago
when I ported the code...seems to be the same.
Thx, br
-
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Hash: SHA1
Excellent!
Thank you Gerard,
Miguel
Gerard DVD Kleywegt escribió:
>> But my understanding is that Iain's procedure gives the rmsds of the
>> _aligned_ C-alphas, whereas Jenny actually seems to be more interested
>> in those that she excludes from th
Hi all
Apologies for the non-ccp4 question - hopefully some of you who use CNS can
help me - I have a problem with anneal.inp in CNS:
When I run the anneal script for my structure containing novel ligand, the
program fails before the start of the torsion dynamics with no error message
- exc
CCP4 bulletin board wrote on 05/10/2007 09:31:59
PM:
> Hello,
> I'm an undergraduate and recently crystallized and obtained 2.9A
> diffraction data for a protein which is predicted to fold into a WD40
> 7-bladed beta-propeller structure (which has been crudely verified by
> cryo-EM by another lab
Hi Emmanuel,
Perhaps a little more information ?
What was the Z-score and LLG in PHASER ? I take it the translation
function solution is fairly well separated from the rest ? Are you sure
the spacegroup is correct ? How complete is the model before refinement
?
Not to be paranoid, but Hexagona
I think the filament from one of our x-ray generators must be a record
breaker. Yesterday it clocked up its 6000th hour or 250th day on the
job, not counting down / holiday time.
The intensity had only dropped by around 25 % of the value it was when I
put it in, eight-and-a-half months ago...
R
Forwarded from Jane Richardson:
Yuan Lin,
The sources you've been given (esp. the reduced-variable ones)
are excellent for identifying RNA structural motifs but not very good
for crystallographic validation, and the PDB tools are still primitive
for nucleic acids. Fortunately, a suitable system
Dear all,
I have a structure (with 6 dissulphide bridges) at fairly low
resolution (3A) that I am trying to refine with Refmac. I've used
phaser with a template with 72% sequence identity. RFZ was 3.4 and TFZ
6.6, without clashes, with 80.7% of completeness. Space group was
p3121 (pointless) and
On Friday 11 May 2007 00:57, Bernhard Rupp wrote:
> Dear Coders,
>
> Do I see this correctly that crossec.lib
> is the XSECT.DAT file from Don Cromer's FPRIME
> program? If so, has there ever been an update?
I do not know the history of crossec.lib, but the X-ray scattering
server
http://sku
Hi Jim,
MAPMAN from the Uppsala software factory will do this.
> re m1 ccp4.map
(FORMAT) CCP4
> wr m1 xplor.map
(FORMAT) X-PLOR
Check the new map is written out on the same scale, just talking to a
colleague I can't recall if any additional commands are required...
Best,
Iain
-Original
Good day all,
First off, thank you all so much for your help a
couple days ago! I just have a quick question
regarding the use of CCP4 to generate density maps.
Is there a way to generate a map(s) that can be read
into PyMol? I understand that PyMol can only read CNS
or XPLOR maps, is this corr
Jim,
i actually think you can read in CCP4 maps, at least i have been doing it for
some time now.
load *.map, format=ccp4
hope this helps. best of luck.
cheers,
nick
-Original Message-
From: James Pauff <[EMAIL PROTECTED]>
To: CCP4BB@JISCMAIL.AC.UK
Date: Fri, 11 May 2007 09:06:21
Thank you all, that was much easier than I expected.
Best,
Jim
Boardwalk
for $500? In 2007? Ha! Play Monopoly Here and Now (it's updated for today's
economy) at Yahoo! Games.
http://get.games.yahoo.com/
You dont say how close your sequence ID is for your new protein and the
model. It is often very hard to kick start refinement with low homology
And what about internal symmetry
Is there a Non crystallographic translation?
Does the self rotation function show a relationship between the two
mole
Eleanor Dodson wrote:
> It is a bit clunky - you can use siperpose molecules - fit residues to
> fit a selected range (1-40; 60-100 say) and write out a complete fitted
> pdb file. Then you could use a VERY old program
> compar xyzin1 original.pdb xyzin2 fitted.pdb (xyzin3 another.pdb)
> and it w
I would highly recommend Doug Theobald's program Theseus for this -
the pictures at www.theseus3d.org say it all. Theseus does maximum
likely hood superimpositions of multiple structures (i.e. NOT
pairwise against a "master" copy), and the real beauty of it is that
you don't have to pick w
Jenny,
I of course would suggest that you follow Olve's advice, and use
theseus to do a maximum likelihood, simultaneous superposition of all
your structures ( http://www.theseus3d.org ). The variable bits,
like your loop, will be naturally down-weighted in a rigorous
statistical manner.
does anyone know of any reports where heavy atom positions were identified
by any method (or mol. rep.) in a Laue data set (or sets)?
also - i thought there was some Laue work out there on watching virus
nucleic acids move around in a crystal, so again, if anyone knows any
references (or names
WOW. There are so many ways to do it. Thank you all for replying.
Nian Huang
Department of Biochemistry
Univ of Texas Southwestern Medical Center
On 5/10/07, Charlie Bond <[EMAIL PROTECTED]> wrote:
Just to complete the set, in pdb-mode for emacs, if you do
pdb-increment-centroid 0 0 0 (e.g. to
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