Hi Lisa,
Why are you so sure there are 4 molecules in the ASU? There may only be
3 and forcing a fourth molecule is causing lots of clashes. In a similar
case, I have seen phaser put two molecules right on top of each other
when I forced it to search for too many molecules.
In your case I woul
Bosch, Juergen wrote:
To pick a bit on George's point with MR & citation.
Here's how you can read it in the paper from your favourite competitor:
A homology model was generated using [fill in any program for ab initio
prediction] and subsequently used for molecular replacement with Molrep.
The
On Thu, Apr 19, 2012 at 4:28 PM, wtempel wrote:
> I went ahead and explicitly applied that +0.5*a translation. [...] It turns
> out that after the origin
> shift, some distances between equivalent atoms of the two structures
> exceeded 3A
I'd be interested to know if cphasematch would reach the
> I wouldn't claim 99.99% are honest reviewers (that would only be one black
> sheep out of 1 crystallographers).
Similarly to sexual orientation, honesty is not a two-state phenomenon, but the
one that varies from 0 to 100%. So, it is likely that a higher percentage of
referees (than 0.01%)
Hello Phil,
I went ahead and explicitly applied that +0.5*a translation. Worked like a
charm.
My excuse for not trying earlier? Within the project, I have dealt with
many additional complex crystals, and have gotten used to simply "hopping
crystals", i.e. refine the same structure in the highly iso
To pick a bit on George's point with MR & citation.
Here's how you can read it in the paper from your favourite competitor:
A homology model was generated using [fill in any program for ab initio
prediction] and subsequently used for molecular replacement with Molrep. The
structure was refined
El 19/04/12 18:42, Patrick Loll escribió:
>>
>> Well, it is clear from this comment that in different fields there are
>> different rules... . In macromolecular Xtallolgraphy, where some people deal
>> with biologists from biomedical sciences, the impact of journals is an
>> important aspect dur
I noticed this missing when I first installed v. 6.2 as well.
They noted this in the "problems page". You just need to replace the
phaser_MR.tcl file with the updated version in the updates page. I tried this
earlier and it created a new line in the GUI to specify the packing criterion
under
> Biology is obsessed with high impact, and I argue science is ill served by
> this preoccupation.
When two equally good scientists apply for a job, which one will be selected,
the one with N-C-S publications or the one with J-B-C publications?
Alex
On Apr 19, 2012, at 9:42 AM, Patrick Loll wro
On 4/19/2012 10:00 AM, Eleanor Dodson wrote:
1) Phaser is very prone to reject solutions because of packing clashes..
(PS How do you reset the packing limit in the current GUI?)
Good question! There used to be a box in CCP4-6.1.13 that allowed you to
change the number of allowed clashes, which
Dear Wolfram,
your a and c axes are very similar; and your beta is near 120°: It
sounds me a twinned crystal. Did you perform a twinning
analysis in P21 space group? Can you post any refined parametrs (R,
Rfree, Resolution, Wilson ADP)?-CCP4 bulletin board ha scritto: -Per: CCP4BB@JISCM
Wolfram,
Did you solve these structures independently by molecular replacement ?
It sounds like your two solutions might be related by alternative
origins (0,1/2 along a,c). If you translate the second example along
the a axis by -a/2 does it refine with similar R-factors ?
Phil Jeffrey
Pr
Hello all,
I am puzzled by this situation:
I have two different crystal of the same protein, in the presence, one in
the absence of a ligand.
Both structures refine nicely in space group P21.
Cell constants (a,b,c,beta) are (i) 61,124,61,119 (a
>
> Well, it is clear from this comment that in different fields there are
> different rules... . In macromolecular Xtallolgraphy, where some people deal
> with biologists from biomedical sciences, the impact of journals is an
> important aspect during evaluation and, unfortunately, pre-publica
Maria,
"But do "gel"-biologists, also with good criteria of quality, ask for
samples shown in a figure of a gel ? ", if the gel looks 'photoshoped',
then yes!!!
I personally think that in a situation where a referee asks for
coordinates, the responsibility and the accountability lie with the
Hi Tony, Tim, Victor and Saul,
Thank you very much for the help on Arp/wARP setup. I did it with one big pir
file last night without inserting the poly Ala, most of the terminal residues
at the "sequence junctions" were not fitted or removed as Tony mentioned. I am
amazed how well ArpwArp worke
There is a separate problem with Thomas' script, though. Many structures
do not have an "OXT" atom at the C-terminus of their polypeptide chains.
It is probably safer to select the C-terminus with:
sele_c = 'last (chain %s and name O and polymer) % chain
I'm aware of that. But I think the more
Hi all,
With respect to C. Groom,
"The sense I get from the small-molecule community is that they (we) have a
great degree of well placed trust and see real value in pre-publication
review of structures, not just papers - I'm sure this is true for the
overwhelming majority of the macromolecular w
Hi all,
With respect to C. Groom,
"The sense I get from the small-molecule community is that they (we) have a
great degree of well placed trust and see real value in pre-publication
review of structures, not just papers - I'm sure this is true for the
overwhelming majority of the macromolecular w
Thanks Victor - for giving a rational and detailed explanation. I obviously got
carried away with the number of alanines to intersperse!
With regards,
Tony.
On 19 Apr 2012, at 16:52, "Victor Lamzin" wrote:
> Dear Tony, Tongqing, Tim,
>
> Adding some alanine spacer is good for a simple rea
Dear Tony, Tongqing, Tim,
Adding some alanine spacer is good for a simple reason - during
sequence docking ARP/wARP checks the distance between the ends of the
fragments.
Imagine you have two chains, 10 residues each. If you concatenate them
together, terminal residues belonging to differ
Tom, that's indeed true. But, the file can be encrypted, and it doesn't
necessarily have to be in strict PDB format.
Getting out of my comfort and knowledge zone here... But with the advent of
HTML5 is a "plugin" strictly necessary?
Tony.
Plus if you're only looking at a chunk of structure -
Hi
I would just like to note that a web-browser plug in is on the client
machine - to
view a PDB file in any viewer like this (ie Astex-viewer, jmol) requires
that file to be physically
downloaded onto the client computer - and put into the TEMP folder of
that machine.
As such, the act of vi
Thanks Ian,
Of course it'd have to be "something else" :-) but the capability of
displaying models and maps via a web-browser is at least within current
capabilities.
Perhaps the "whole" model or electron density doesn't need to be presented -
perhaps just a representative chunk or chunks w
Randy,
This is somewhat of a "thought" experiment at best...but to think on whilst I
commute home after a great BCA meeting...
You don't necessarily need a password-protected server - just a way of making a
particularly cryptic URL - which the author is (at first) the only person to
receive -
Dear CCP4BBers,
I'd like to bring to your attention a post-doctoral research assistant
opportunity available in the Banfield Laboratory at the John Innes Centre in
Norwich, UK.
We primarily study protein structure/function relationships important in the
co-evolutionary arms race between plan
> Crucially this does *not* allow the coordinates or maps to be downloaded, but
> visually inspected online - via some form of web-browser plugin; Aztex Viewer
> or similar.
Anthony, it would have to be something other than AstexViewer since
the distributed version at least allows you to do a "S
The idea of referees being given a link to the structure at the PDB came up in
discussions with PDB people, when we were preparing our X-ray validation
report. Among other potential issues, it would be a lot of work for them to
set up a secure password-protected system, and the growth in the PD
Arp/Warp server?
JPK
On Thu, Apr 19, 2012 at 9:00 AM, Eleanor Dodson
wrote:
> Several possibilities.
>
> 1) Phaser is very prone to reject solutions because of packing clashes..
> (PS How do you reset the packing limit in the current GUI?)
> Running chainsaw before you begin the search can help
This subject raised (and keeps raising) its head above the parapet not all that
long ago on this bulletin board. Maybe it's time to bite the bullet and try
and do something about it?
I would like to see and can imagine the following scenario... something I have
tentatively suggested before...
Hi Tim,
On Thu, 2012-04-19 10:07 EDT, Tim Gruene wrote:
> Hi Thomas,
>
> your script requires to download the entire PDB first into one
> directory, doesn't it? While technically feasible, this might take a
> while and a little bit of disk space.
I keep a mirror of the 8+ pdb files and w
Several possibilities.
1) Phaser is very prone to reject solutions because of packing clashes..
(PS How do you reset the packing limit in the current GUI?)
Running chainsaw before you begin the search can help - it prunes out
patches where the sequences don't match and gives a sensibly truncated
Colin,
Speaking as someone who has one foot in small molecule crystallography
and the other in macromolecular, I have to say that attitudes are
completely different, and that there are good reasons for this. A PhD
student or junior postdoc in a macromolecular lab may have spent the
last three (or
As Randy pointed out, you should check Patterson map for off-origin
peaks. There is also a small chance that you actually have P2 -
systematic absences may result from tNCS nearly colinear with
crystallographic axis.
On Thu, 2012-04-19 at 14:20 +0800, LISA wrote:
> Hi all,
>
> I am trying to sol
It has always struck me as something of a surprise that pre-publication review
of structures in protein-land differs so significantly from small
molecule-land. One of the activities of the CCDC is to supply pre-release CSD
structures to referees, using a simple, automated system to establish tha
This is off course a valid point. A desperate graduate student faking a
structure risks his or hers career and reputation, while an anonymous
referee, "borrowing" someone else's results gets away without any risk
of being caught. Besides making the name of the reviewer public, I see
other options:
Dear Marc,
I would release the PDB coordinates at the RCSB. The release will protect
you from
use of the coordinates since you have now acquired a release date prior to
referee viewing.
Assuming that an honest referee would request the coordinates only to
verify that all is well
before fina
Dear All,
Here comes the problem of blind reveiw, the authors are always at the
receving end to share all there data, results and now the full
cordinates to an unknown person, just trusting the journal editor. Why
don't the journals think about making the name of the reviewer also
public.
Eventhou
Thanks a lot to everyone for their insightful comments I certainly had
an interesting day trying to digest all that was said! Although my initial
reaction to the request was to turn it down since I had never heard of
such a request before, I decided in the end to accede to the request,
since not
Posted on behalf of Sylvie Nessler (CNRS):
Postdoctoral Fellowship in Structural Biology: Bacterial tyrosine kinases and
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A post-doctoral position is available for highly motivated candidates to join
the research group of Prof. Sylvie Nessler at University Paris-sud 11. W
Hi,
There is the exact same problem when releasing a software,
possibly open source, before the corresponding article is accepted.
And I don't know a correct solution to this problem.
Regards,
F.
On 04/19/2012 05:34 PM, Yu Wai Chen wrote:
Dear Marc,
As a reviewer I find it difficult to “vis
Hi,
Just to add on Joel's remarks: I had a case where I reviewed a paper for which the coordinates and SF's have already been released. By looking at the e.d. map (from the EDS server) I could spot a mistake in the tracing of one important spot (which happened
to be near the active site - no I
Hi,
My first guess would be that this crystal possesses translational NCS, and that
you're using the "old" (distributed with current old CCP4) version of Phaser
that can't handle tNCS. You can tell if this is the case by looking at whether
there's a large off-origin peak in the native Patterso
I vaguely recalled reading a paper from Janet Thornton's group showing that
there was a non-random distribution of N-terminus to C-terminus distances in
proteins, with the distance being less on average than you would expect if the
C-terminus were at a random position on the surface relative to
Dear Marc,
As a reviewer I find it difficult to “visualise” a structure based on
a static 2D figure.
I echo Joel's comments. If the (unreleased) coordinates are not
supplied by the authors on request, I would simply refuse to review the
paper on that ground. I suppose one can trust a repu
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Hash: SHA1
Hi Thomas,
your script requires to download the entire PDB first into one
directory, doesn't it? While technically feasible, this might take a
while and a little bit of disk space.
Tim
On 04/19/12 09:52, Thomas Holder wrote:
> Hi Sam,
>
> you could
Dear Tongqing,
On Apr 19, 2012, at 5:26 AM, Zhou, Tongqing (NIH/VRC) [E] wrote:
> I am trying to use Arp/wArp to build an antibody-antigen complex with 1.65 A
> data, there are three chains (heavy, light chains of antibody and the
> antigen) in the complex, my question is how to put the sequenc
Hi Sam,
you could do this with PyMOL in batch mode with a python script.
Something like this:
---
out = open('out.txt', 'w')
def check_nc_distance(pdbfile):
from pymol import cmd
cmd.delete('*')
cmd.load(pdbfile)
for chain in cmd.get_chains():
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Hash: SHA1
Dear Tony, dear Tongqing,
the way I understand the working mechanism of arp/warp works I do not
see the point introducing the polyALA spacer into the sequence. Just
concatenate all sequences into one file as though it was one molecule.
Cheers,
Tim
O
Dear Marc,
The only way a reviewer can really judge the quality ofa structure and
verify the claims made in a structural biology manuscript is by having
access to the pdb files and x-ray data. I have myself as a reviewer
requested co-ordinates and data for this purpose, and the results can be
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