Pointless is used before scaling, and this question is asked after scaling, ie
it belongs in Scala or [c]truncate in the CCP4 context (at present anyway)
Phil
On 15 Jul 2010, at 07:29, Tim Gruene wrote:
> On Thu, Jul 15, 2010 at 01:02:30AM -0400, Hailiang Zhang wrote:
>> Hi all:
>>
>> Does CCP4
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We are currently conducting study on a novel estrogenic compound secreted by
a Singapore phytoplankton isolate. Candidates are required to work in the
following research activities:
1. Large scale batch culture of chattonella marina
2. Bioassay-guided fra
If you were born before the Dutch lost their first World Cup final, you may
remember the days when "everybody" knew that PDB entry 1tim was the structure
of chicken triosephosphate isomerase, 1hhb was human haemoglobin, 1lyz was hen
egg-white lysozyme, etc. Unfortunately, life for a structural b
Gerard DVD Kleywegt wrote:
For a five-minute illustrated introduction to PDBprints (including
instructions on how to include them in your own webpages) point your
browser to:
http://pdbe.org/pdbprints
Good idea.
But the icons for published/unpublished, protein present/prote
Yep, its green-blue vs grey... Bad choice I guess? Perhaps you can
provide a set of examples that work for you?
Flip
On 7/15/2010 13:20, Kevin Cowtan wrote:
Gerard DVD Kleywegt wrote:
For a five-minute illustrated introduction to PDBprints (including
instructions on how to include them in you
On Thu, Jul 15, 2010 at 12:20:02PM +0100, Kevin Cowtan wrote:
> Gerard DVD Kleywegt wrote:
>> For a five-minute illustrated introduction to PDBprints (including
>> instructions on how to include them in your own webpages) point your
>> browser to:
>>
>> http://pdbe.org/pdbprint
Project leader positions at IECB – Bordeaux 2010
Dear Colleagues,
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Could you spread this information around and encourage talented young
researchers willing to develop innovative projects at the
biology-chemistry interface to apply ?
http://pdbe.org/pdbprints
Good idea.
But the icons for published/unpublished, protein present/protein absent,
nucleotide present/nucleotide absent and ligand present/ligand absent look
identical to me - I have to read the alt text.
Is there some colour thing going on here w
We are pleased to announce the 2010 Cryo-EM Modeling challenge and a PSB 2011
workshop, organized by Steven Ludtke, Wah Chiu, Helen Berman and Gerard
Kleywegt.
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* Modeling as a tool for interpretation of cryo-EM reconstructions *
Cryo-EM sing
I have trouble distinguishing the green and grey on
my MacBook. Herbert, who is colorblind, can just barely
distinguish that there are two different colors. Note
that 1 of 12 men are colorblind so this is actually quite
common. I would suggest using a pale transparent image
to suggest abse
Dear Pascal,
be aware that fos-choline detergents are extremely efficient solubilizers of
membrane proteins. We found that even partially aggregated membrane proteins
could be solubilized with fos-choline 12, while this fraction did sediment
using for example dodecylmaltoside (see e.g. fig5 and
Hi all,
Something wrong has happened when I install arp/warp7.1 in my CentOS
machine. What it told me during the installation is as below:
[r...@lenovo6 arp_warp_7.1]# ./install.sh
ARP/wARP installer is checking your c-shell...
c-shell is installed on your machine at /bin/csh
Your login shell is:
On Thu, 15 Jul 2010, Tim Gruene wrote:
Maybe icons which are crossed out might be a better solution for the negative
ones.
The problem with this is that "X-RAY" crossed out suggests "no X-rays", i.e.
a non X-ray experiment, not an X-ray experiment for which the structure
factors are unavaila
Better still, I can let you see them though my eyes. Here's what the
icons look like to me, and a link to Vizcheck, the tool I used to
generate them:
http://www.ysbl.york.ac.uk/~cowtan/colour/pdb/pdb.html
http://www.vischeck.com/vischeck/vischeckImage.php
Running this in various modes you sho
There are so many ways to address this issue. Perhaps the simplest would be to
use a combination of dimming and thick, solid borders vs. dashed borders to
distinguish the two states of the icons. Cheers! MM
On Jul 15, 2010, at 9:46 AM, Kevin Cowtan wrote:
> Better still, I can let you see them
What would be wrong with WORDS? They were such a clever
invention. I can tell the difference between colors, but it
takes a second step to figure out what they mean anyway. Why
not just write "no info" over the gray ones? And a 1-word
caption on all the little icons would help, IMHO.
Phoebe
Hi,
I am currently refining some reasonably high (1.4-1.6 Å) resolution protein:RNA
complex structures and was trying the approach described in Schwartz et al.
Nat. Struct. Biol. 8 (2001) 761-765 where they divided each nucleotide into
three TLS groups – the ribose, the phosphorus atom plus bo
STOP
Hi Pranjal,
you can use POLYGON tool for this:
Crystallographic model quality at a glance.
L. Urzhumtseva, P. V. Afonine, P. D. Adams, A. Urzhumtsev
Acta Cryst. D65, 297-300 (2009)
Essentially, what it does is it compares your structure with all similar
structures in PDB and gives your the re
Sorry for a non-ccp4 question.
We have determined a structure which is mainly a coiled coil motif. The
two helices are from the same protein chain linked by a short turn.
However, the SAXS data indicates that "this protein is probably natively
unfolded or may have very flexible domains and lin
Hello Huw,
what happens when you remove the period '.' in the residue range description,
i.e., replace
RANGE 'B 3.' 'B 3.' P
with
RANGE 'B 3' 'B 3' P
?
Tim
On Thu, Jul 15, 2010 at 03:54:45PM +0100, Huw Jenkins wrote:
> Hi,
>
> I am currently refining some reasonably high (
Hammer time?
On Jul 15, 2010 4:06 PM, "Badyal, Sandip K. (Dr.)"
wrote:
STOP
Hi,
Yes, zero origin is a sure sign that it hasn't identified the atoms in
the TLS group.
There is presumably some problem matching atom names, but am not sure
what. If you send me the files, I can have a play.
However, you might have problems with the group definitions anyway. I
seem to remembe
On 15 Jul 2010, at 16:24, Tim Gruene wrote:
>
> what happens when you remove the period '.' in the residue range description,
> i.e., replace
>RANGE 'B 3.' 'B 3.' P
> with
>RANGE 'B 3' 'B 3' P
No difference unfortunately.
Thanks,
Huw
--
Dr Huw Jenkins
Astbury Centre for Stru
Rongjin,
With regards to the SAXS part of post: I'm guessing your collaborators are
making this determination from the SAXS data based on a Kratky plot
analysis? Given the inherently low resolution of this technique, it may be
difficult to assign the profile observed to a specific secondary struc
On 15 Jul 2010, at 16:28, Martyn Winn wrote:
> Yes, zero origin is a sure sign that it hasn't identified the atoms in
> the TLS group.
>
> There is presumably some problem matching atom names, but am not sure
> what. If you send me the files, I can have a play.
I thought that too but if I change
Hi Rongjin,
During the SAXS experiment, have you noticed X-ray induced damage on your
samples that could explain this?
If you are characterizing your protein in solution you may also be able to
pinpoint conformational flexibility using other techniques.
- analytical sedimentation. since you have
On Thursday 15 July 2010, Huw Jenkins wrote:
> Hi,
>
> I am currently refining some reasonably high (1.4-1.6 Å) resolution
> protein:RNA complex structures and was trying the approach described in
> Schwartz et al. Nat. Struct. Biol. 8 (2001) 761-765 where they divided each
> nucleotide into th
On 15 Jul 2010, at 17:06, Ethan Merritt wrote:
> My gut feeling is that the best TLS description would be each base
> (or base pair) in its own group, the use TLSMD to analyse and assign groups
> for the backbone atoms. But again I have no actual experience with this,
> so it's only a suggestion.
Dear Huw,
at 1.4-1.6A resolution I would actually try anisotropic refinement and tighten
the restraints a little in case the resolution is not quite high enough. You
can do this with refmac5, phenix.refine, and shelxl and you would not have to
worry about TLS groups anymore.
Cheers, Tim
On Thu
Refinement with rigid-base TLS parameterization has been previously
explored:
Holbrook, Dickerson, Kim (1985) Acta Cryst B41, 255-262.
(the photocopy is located in the pile of dust that I maintain adjacent
to my desk)
Ethan Merritt wrote:
On Thursday 15 July 2010, Huw Jenkins wrote:
Hi,
Dear CCP4bb,
Can I refine anisotropic ADPs for macromolecule only, while isotropic ADPs
for water, simultaneously in ccp4? I have a 1.1.5 Angs data and when I
refine anisotropically the rfactor/rfree difference is 6. Is it true that if
I could refine the macromolecule anisotropically and the water
On Thursday 15 July 2010 09:18:33 am Huw Jenkins wrote:
>
> On 15 Jul 2010, at 17:06, Ethan Merritt wrote:
>
> > My gut feeling is that the best TLS description would be each base
> > (or base pair) in its own group, then use TLSMD to analyse and assign groups
> > for the backbone atoms. But aga
But of course. This is what mixed refinement is for - the easiest was
to get it to work is probably somehow generating anisou records for all
the atoms and then doing something like "egrep -v 'ANISOU|HOH'" on the
pdb file. Mixed refinement will then refine only the atoms with
pre-existing anisou
Dear Jian,
This bug (ARP/wARP not being able on some computer platforms to
recognise version number if it starts from zero) was fixed about half a
year ago. Please go to www.arp-warp.org and download the 7.1.1 patch.
After installing the patch the problem should go.
With best regards,
Victor
Thank you guys. I will try and let you know if there is a problem. I realy
appreciate your suggestions.
Ivan
On Thu, Jul 15, 2010 at 10:16 AM, Ed Pozharski wrote:
> But of course. This is what mixed refinement is for - the easiest was
> to get it to work is probably somehow generating anisou re
I like the species icon for 2cbr, human crabp in your list
http://xray.bmc.uu.se/gerard/structures_pdbprints.html.
Is it something from Greek mythology?
From: CCP4 bulletin board [ccp...@jiscmail.ac.uk] On Behalf Of Gerard DVD
Kleywegt [ger...@xray.bmc.uu.
On Thursday 15 July 2010 11:33:30 am Dunten, Pete W. wrote:
> I like the species icon for 2cbr, human crabp in your list
> http://xray.bmc.uu.se/gerard/structures_pdbprints.html.
>
> Is it something from Greek mythology?
Ah yes, the minotaur genome project.
I like the species icons to some exten
Does anyone know how to disassemble a P-1 peristaltic pump from
Pharmacia/Amersham/GE?
We have a couple that need simple repairs to either a switch or a rheostat on
the control panel, but I'm stumped as to how to actually get the damn thing
open.
If you've succeeded in doing this, I'd be grate
Also road signs can be cleverly replaced
<><>
On 15/07/2010, at 16.40, Phoebe Rice wrote:
> What would be wrong with WORDS? They were such a clever
> invention. I can tell the difference between colors, but it
> takes a second step to figure out what they mean anyway. Why
> not just write "no
Fully funded postdoctoral positions at Yale University School of Medicine are
available immediately from highly motivated, enthusiastic individuals with a
strong interest in the structure, function, and pharmacology of signaling
proteins implicated in neurological and neuropsychiatric diseases.
On 7/13/10 11:05 AM, Daniel Lietha wrote:
Does anyone know if the ZM-M215W and ZM-M240W Zalman monitors work in
3D with Coot and Pymol (would use them on Mac OS10.6)? If so, does the
increased resolution improve things compared to the ZM-M220W?
Thanks,
Daniel
Let me bring back to life the thre
I find the 22" sufficient if run at highest resolution 1680x1050. If you really
need more space get a second one and run the machine in dual mode. I'm waiting
for Apple to announce finally the new MacPro's to get one of them. It will be
connected to a 24" Cinema Display and a 22" Zalman.
Jürgen
I think the origin of this thread is that the original Zalman Monitors are no
longer sold and Zalman only announces these new ones now.
We are waiting for their availability (in Germany) and we have no doubt that
they are going to work like the previous models did - the technology (which is
about
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