Dear Engin,
Yep, I can reproduce this using a binary installation myself - that
would be a bug. We (CCP4) will look into it and get a fix to you as soon
as possible.
Thanks for the report,
Graeme
CCP4 Support Team
-Original Message-
From: CCP4 bulletin board
Dear Victor,
The CCP4mg package is just about to be updated to version 2 built around
Qt rather than the old Python/Tcl/Tk version. The former version was
highly platform specific and would have required rather a large number
of system permutations - this would make the load on the server as you
Strange ... I just updated to OS 10.5.6, and fully expected to have to
reinstall X11 yet again, but I still have 2.3.1 on my machine after
the update. Odd that it should be inconsistent from one machine to
another.
Randy Read
On 17 Dec 2008, at 22:54, William G. Scott wrote:
Please, we
This doesn't seem to be a general phenomenon. My xquartz is still 2.3.1
after installing the latest service pack (Leopard 6).
Andreas
William G. Scott wrote:
Please, we all need to mention this to the Apple people. This is
totally unacceptable.
On Dec 17, 2008, at 2:54 PM, Engin Ozkan
Hi Randy and Andreas,
I wouldn't rely on the reported XQuartz version after updating to
10.5.6, but rather re-install the most recent version of Xquartz
again, to be on the safe side.
Best regards,
Dirk.
P.S.: This version allows to overwrite the X11 resolution with the
command
I have a theory. Automated software updates did not update many
computers correctly, macs in our lab hung at configuring installation
and had to be restarted. This phenomenon is observed by many, and
consider yourself lucky, if you haven't (Apple might have fixed it by now).
Hi all,
I have just installed the new CCP4I package for Windows, and refined a
structure I was working on using an older version (CCP4I 6.0.2), and the
refinement statistics are significantly worse when using the same input files.
Under Refmac 5.2 the details were:
$$
Ncyc Rfact
Dear Sean,
I have noticed this and more to the point the geometry as assessed
by MOLPROBITY is much worse for
the latest version of REFMAC (3.0068).
I have tested a few other versions of REFMAC and the results vary
quite a lot.
For exactly the same run, I get the best results with an
Jon,
Riding hydrogens are *not* part of your model, they are part of the
algorithm used to predict observations. Thus, the information is
automatically included when you report the software used for refinement.
There are definitely some (many) parameters that are never included in
the deposited
As a follow-up to the question posted by Jon Winger regarding riding
hydrogens, do we all agree that the current PDB format does not allow
complete reconstruction of the final stage refinement? For instance,
the geometry weight factor is never reported.
Second question: is it important to make
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Dear all,
I have just installed ccp4 v6.1 on a linux box running centos 5.1. Most things
seem to be working fine, but when I attempt to launch imosflm from the gui I
get the following message:
Error in startup script: can't create directory : no such file or directory
while executing
file
On 12/18/2008 7:23 AM, Ed Pozharski wrote:
Riding hydrogens are *not* part of your model,
The fact that you don't see H in your fo-fc map due to limited
resolution and high level of noise does not mean that H atoms are not
present in actual real structure -:)
There are definitely some
Hi Stephen,
Have you a project set up in CCP4i? Make sure that your CCP4i project
directory is set before you try to start Imosflm. When run through
CCP4i, Imosflm uses this directory to write it's output files.
You can set the project directory by clicking on the
DirectoriesProjectsDir
Dear Ed,
Riding hydrogens are *not* part of your model, they are part of the
algorithm used to predict observations.
snip
As a diversion from PDB-ology I would point out that, according to
Bayesian statistics, of which the maximum-likelihood method is a
Riding hydrogens are *not* part of your model,
The fact that you don't see H in your fo-fc map due to limited
resolution and high level of noise does not mean that H atoms are not
present in actual real structure -:)
Let me ask you this - are bond length restraints part of the *model*?
Dear All,
I wonder whether someone has a quick authoritative answer (admitting a
little
rtfm or rtfc on my side might help) how refinement programs read and
understand the charged symbols MG2+ for example and whether
they properly use the corresponding scattering factor curves.
Does everyone
On 12/18/2008 8:23 AM, Ed Pozharski wrote:
Riding hydrogens are *not* part of your model,
The fact that you don't see H in your fo-fc map due to limited
resolution and high level of noise does not mean that H atoms are not
present in actual real structure -:)
Let me ask you
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Hi All,
I have been in the habit of transferring my initial free R assignments
to any new data sets or to isomorphous data sets such as substrate
complexes. Although theoretically this is necessary to obtain a valid
free R many of my colleagues maintain that this is completely
unnecessary
- bond length restraints do not contribute to the scattering and
hence do not affect the R-factors, while H atoms do contribute to
scattering and therefore R-factors computed from the model with or
without hydrogens can be different (I spent a couple of months
implementing it in PHENIX and I
On Thu, 2008-12-18 at 10:15 -0800, Ethan A Merritt wrote:
The riding-hydrogen treatment is definitely part of the model.
But the number of parameters associated with it is not derived from the
number of individual hydrogen atoms and their coordinates, it is
limited to the number of parameters
Alun R. Coker schrieb:
Hi All,
I have been in the habit of transferring my initial free R assignments
to any new data sets or to isomorphous data sets such as substrate
complexes. Although theoretically this is necessary to obtain a valid
free R many of my colleagues maintain that this is
Hi Alun,
If it's necessary in theory, and it's little effort, why not do it?
Even if in practise it may be not necessary, I think not doing it is
a sign of sloppy science - on a par with not sequencing your inserts
to confirm absence of unwanted PCR mutations, checking by Edman
Hi Ed,
I didn't really open a can of worms... Sorry if I did!
But there are many things affecting R-factors not
being reported. Do I have to deposit the bulk solvent mask?
Not that many and most of them are reported (at least those that may
affect the R-factor significantly). The model
Alun,
Kay is right on target; I think there is no debate about that you must
use one FreeR set for all (even marginally*) isomorphous crystals. Your
colleagues who are not following this practice are not doing themselves
any favors.
If you don't keep the same FreeR set, R Rfree for that 2nd
Alun,
I agree completely with previously stated opinions (and your practice)
that preservation of a single test set is very important for the
refinement of similar structures. One complication that for spacegroups
in which there is a potential axis-indexing ambiguity (e.g. certain
trigonal
Alun R. Coker wrote:
Hi All,
I have been in the habit of transferring my initial free R assignments
to any new data sets or to isomorphous data sets such as substrate
complexes. Although theoretically this is necessary to obtain a valid
free R many of my colleagues maintain that this is
Hi Alun
I've never seen a soaked ligand-bound structure that's truly isomorphous
with the native - simply soaking freezing the crystal is virtually
guaranteed to introduce very serious non-isomorphism, e.g. up to 5%
change in one or more cell parameters. At least, we always have a MR
step to
a few öre's worth from sweden ...
there is a surprising number of deposited ligand structures where
re-refinement shows that the ligand is built into noise.
nope, not surprised at all:
- http://xray.bmc.uu.se/cgi-bin/gerard/reprint_mailer.pl?pref=89
-
Hi All,
Apologies for a non-CCP4 question. I want to clone a couple of proteins of
human and mouse origin. Can anyone tell me where from I can order Human and
mouse (brain/liver) cDNA library? Any suggestions are welcome.
Thanks,
Rajan
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