Re: [ccp4bb] Ramachandran outlier

[Tim Gruene]

Dear Rohit Kumar Singh,

you can remove a couple of residues before and after the outlier and
rebuild it. You can also switch on Ramachandran restraints in Coot and
run real-space refinement. If this does not help, I would delete a
single residue within the region in question, run real-space refinement
for both segments and reconnect.

Regards,
Tim

On 01/13/2015 08:35 AM, rohit kumar wrote:
> Hello all,
> 
> if outlier is in between 5 to 6 %, how someone can fix it.
> As the resolution is low (3.0-3.5 A).
> 
> On Mon, Jan 12, 2015 at 7:53 PM, Robbie P. Joosten  wrote:
> 
>> Hi Dialing,
>>
>> 86% favoured can actually be quite okay for an initial model. As long as
>> it doesn't have 14% in the disallowed region, the vast majority of residues
>> will be correct, or close enough to the correct answer that they can be
>> fixed easily. Of course, such a model will need tweaking, but this is more
>> or less the point of calling it an 'initial' model.
>>
>> Cheers,
>> Robbie
>>
>>
>> On 01/12/2015 01:18 PM, Dialing Pretty wrote:
>>
>>> Dear All，
>>>
>>> If an initial PDB has only 86% residues in the Ramachandran favored
>>> region, it
>>> would mean there is a significant error (for example significant length of
>>> protein fragment in the total protein assigned to the wrong electron
>>> density map
>>> position) , right?
>>>
>>> Dialing
>>>
>>>
> 
> 

-- 
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

GPG Key ID = A46BEE1A



signature.asc
Description: OpenPGP digital signature

Re: [ccp4bb] Ramachandran outlier

[rohit kumar]

Hello all,

if outlier is in between 5 to 6 %, how someone can fix it.
As the resolution is low (3.0-3.5 A).

On Mon, Jan 12, 2015 at 7:53 PM, Robbie P. Joosten  wrote:

> Hi Dialing,
>
> 86% favoured can actually be quite okay for an initial model. As long as
> it doesn't have 14% in the disallowed region, the vast majority of residues
> will be correct, or close enough to the correct answer that they can be
> fixed easily. Of course, such a model will need tweaking, but this is more
> or less the point of calling it an 'initial' model.
>
> Cheers,
> Robbie
>
>
> On 01/12/2015 01:18 PM, Dialing Pretty wrote:
>
>> Dear All，
>>
>> If an initial PDB has only 86% residues in the Ramachandran favored
>> region, it
>> would mean there is a significant error (for example significant length of
>> protein fragment in the total protein assigned to the wrong electron
>> density map
>> position) , right?
>>
>> Dialing
>>
>>


-- 
WITH REGARDS
Rohit Kumar Singh
Lab. no. 430,
P.I. Dr. S. Gourinath,
School of Life Sciences,
Jawaharlal Nehru University
New Delhi -110067

Re: [ccp4bb] export the x, y value from AKTA UNICORN

[Orru, Roberto]

Hello Bing,

It is possible to do it with the software version 5.01, but I guess that it 
should be available on all version.
Under the Evaluation software, open your result file. In the menu "file" go 
down to export, select the curve that you want to export and save it. It is an 
asci file that you can open with any text editor.

Best,
Roberto

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Wang, Bing
Sent: Monday, January 12, 2015 11:23 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] export the x, y value from AKTA UNICORN

Hi all,

Sorry for this off topic! I need you guys to help me to export the x/y value 
from AKTA UNICORN since I want to redraw it in EXCEL. Is it possible? How to do?

Also I don't need and like the software which can extract the data from the 
images or pdf files, because it is not precise.

Thank you very much!

Bing

[ccp4bb] export the x, y value from AKTA UNICORN

[Wang, Bing]

Hi all,

Sorry for this off topic! I need you guys to help me to export the x/y value 
from AKTA UNICORN since I want to redraw it in EXCEL. Is it possible? How to do?

Also I don't need and like the software which can extract the data from the 
images or pdf files, because it is not precise.

Thank you very much!

Bing

Re: [ccp4bb] X-ray Source Differences (WAS: RE: [ccp4bb] How far does rad dam travel?)

[Keller, Jacob]

>at the beginning of my experience of S-SAD about 10 years ago, it was not too 
>difficult to do S-SAD phasing with inhouse data provided the resolution was 
>better than 2.0A, while it did not always work with synchrotron data. Purely 
>personal experience.

I assume that the synchrotron data were collected at similarly-low energy?

>However, the inhouse machines I am familiar with have three circles, so that 
>you get much better real redundancy with equivalent reflections recorded at 
>different settings. This reduces systematic errors, I think.
The most sophisticated synchrotron beamline I have been to offered a mini-kappa 
with 30degree range - that's not much compared to 10-20 different settings with 
varying phi- omega- and distance settings.

Yes, I haven't seen much about people collecting multiple orientations of the 
same crystal, since I think people generally roast their crystals really fast 
to see higher-resolution spots. I am thinking recently that the best option 
might really be home sources with pixel-array detectors...

>The top-hat comes from a quote I received from Bruker, and I have no reason to 
>believe the person acted purely with a salesperson's intent.

Pretty interesting--wonder what's the best way to confirm this for our home 
source...?

JPK




Best,
Tim

On 01/12/2015 09:05 PM, Keller, Jacob wrote:
>> the top-hat profile is one of the reasons why inhouse machines produce 
>> better quality data than synchrotrons. However, the often much increased 
>> resolution you achieve at the synchrotron is generally worth more than the 
>> quality of the data at restricted resolution.
>>
>> Cheers,
>> Tim
> 
> Several surprises to me:
> 
> -Data from in-house sources is better?
>   I have not heard of this--is there any systematic examination of this? 
> I saw nothing about this in a very brief Google foray.
> 
> -In-house beam profiles are top-hats?
>   Is there a place which shows such measurements? Does not pop out of 
> Google for me, but I would love to be shown that this is true.
> 
> -Resolution at the synchrotron is better?
>   This does not really seem right to me theoretically, although in 
> practice it does seem to happen. I think it is just a question of waiting for 
> enough exposure time, as the CCP4BB response quoted at bottom describes.
> 
> JPK
> 
> 
> 
> ===
> 
> 
> Date: Tue, 12 Oct 2010 09:04:05 -0700
> From: James Holton 
> Re: Re: Lousy diffraction at home but fantastic at the synchrotron?
> There are a few things that synchrotron beamlines generally do better than 
> "home sources", but the most important are flux, collimation and absorption.
> Flux is in photons/s and simply scales down the amount of time it takes to 
> get a given amount of photons onto the crystal. Contrary to popular belief, 
> there is nothing "magical" about having more photons/s: it does not somehow 
> make your protein molecules "behave" and line up in a more ordered way. 
> However, it does allow you to do the equivalent of a 24-hour exposure in a 
> few seconds (depending on which beamline and which home source you are 
> comparing), so it can be hard to get your brain around the comparison.
> Collimation, in a nutshell, is putting all the incident photons through the 
> crystal, preferably in a straight line. Illuminating anything that isn't the 
> crystal generates background, and background buries weak diffraction spots 
> (also known as high-resolution spots). Now, when I say "crystal" I mean the 
> thing you want to shoot, so this includes the "best part" of a bent, cracked 
> or otherwise inhomogeneous "crystal". The amount of background goes as the 
> square of the beam size, so a 0.5 mm beam can produce up to 25 times more 
> background than a 0.1 mm beam (for a fixed spot intensity).
> Also, if the beam has high "divergence" (the range of incidence angles onto 
> the crystal), then the spots on the detector will be more spread out than if 
> the beam had low divergence, and the more spread-out the spots are the easier 
> it is for them to fade into the background. Now, even at home sources, one 
> can cut down the beam to have very low divergence and a very small size at 
> the sample position, but this comes at the expense of flux.
> Another tenant of "collimation" (in my book) is the DEPTH of non-crystal 
> stuff in the primary x-ray beam that can be "seen" by the detector. This 
> includes the air space between the "collimator" and the beam stop. One 
> millimeter of air generates about as much background as 1 micron of crystal, 
> water, or plastic. Some home sources have ridiculously large air paths (like 
> putting the backstop on the detector surface), and that can give you a lot of 
> background. As a rule of thumb, you want you air path in mm to be less than 
> or equal to your crystal size in microns. In this situation, the crystal 
> itself is generating at least as much background as the air, and so further 
> reducing the air pa

Re: [ccp4bb] X-ray Source Differences (WAS: RE: [ccp4bb] How far does rad dam travel?)

[Tim Gruene]

Hi Jacob,

at the beginning of my experience of S-SAD about 10 years ago, it was
not too difficult to do S-SAD phasing with inhouse data provided the
resolution was better than 2.0A, while it did not always work with
synchrotron data. Purely personal experience.

However, the inhouse machines I am familiar with have three circles, so
that you get much better real redundancy with equivalent reflections
recorded at different settings. This reduces systematic errors, I think.
The most sophisticated synchrotron beamline I have been to offered a
mini-kappa with 30degree range - that's not much compared to 10-20
different settings with varying phi- omega- and distance settings.

The top-hat comes from a quote I received from Bruker, and I have no
reason to believe the person acted purely with a salesperson's intent.

Best,
Tim

On 01/12/2015 09:05 PM, Keller, Jacob wrote:
>> the top-hat profile is one of the reasons why inhouse machines produce 
>> better quality data than synchrotrons. However, the often much increased 
>> resolution you achieve at the synchrotron is generally worth more than the 
>> quality of the data at restricted resolution.
>>
>> Cheers,
>> Tim
> 
> Several surprises to me:
> 
> -Data from in-house sources is better?
>   I have not heard of this--is there any systematic examination of this? 
> I saw nothing about this in a very brief Google foray.
> 
> -In-house beam profiles are top-hats?
>   Is there a place which shows such measurements? Does not pop out of 
> Google for me, but I would love to be shown that this is true.
> 
> -Resolution at the synchrotron is better?
>   This does not really seem right to me theoretically, although in 
> practice it does seem to happen. I think it is just a question of waiting for 
> enough exposure time, as the CCP4BB response quoted at bottom describes.
> 
> JPK
> 
> 
> 
> ===
> 
> 
> Date: Tue, 12 Oct 2010 09:04:05 -0700
> From: James Holton 
> Re: Re: Lousy diffraction at home but fantastic at the synchrotron?
> There are a few things that synchrotron beamlines generally do better than 
> "home sources", but the most important are flux, collimation and absorption.
> Flux is in photons/s and simply scales down the amount of time it takes to 
> get a given amount of photons onto the crystal. Contrary to popular belief, 
> there is nothing "magical" about having more photons/s: it does not somehow 
> make your protein molecules "behave" and line up in a more ordered way. 
> However, it does allow you to do the equivalent of a 24-hour exposure in a 
> few seconds (depending on which beamline and which home source you are 
> comparing), so it can be hard to get your brain around the comparison.
> Collimation, in a nutshell, is putting all the incident photons through the 
> crystal, preferably in a straight line. Illuminating anything that isn't the 
> crystal generates background, and background buries weak diffraction spots 
> (also known as high-resolution spots). Now, when I say "crystal" I mean the 
> thing you want to shoot, so this includes the "best part" of a bent, cracked 
> or otherwise inhomogeneous "crystal". The amount of background goes as the 
> square of the beam size, so a 0.5 mm beam can produce up to 25 times more 
> background than a 0.1 mm beam (for a fixed spot intensity).
> Also, if the beam has high "divergence" (the range of incidence angles onto 
> the crystal), then the spots on the detector will be more spread out than if 
> the beam had low divergence, and the more spread-out the spots are the easier 
> it is for them to fade into the background. Now, even at home sources, one 
> can cut down the beam to have very low divergence and a very small size at 
> the sample position, but this comes at the expense of flux.
> Another tenant of "collimation" (in my book) is the DEPTH of non-crystal 
> stuff in the primary x-ray beam that can be "seen" by the detector. This 
> includes the air space between the "collimator" and the beam stop. One 
> millimeter of air generates about as much background as 1 micron of crystal, 
> water, or plastic. Some home sources have ridiculously large air paths (like 
> putting the backstop on the detector surface), and that can give you a lot of 
> background. As a rule of thumb, you want you air path in mm to be less than 
> or equal to your crystal size in microns. In this situation, the crystal 
> itself is generating at least as much background as the air, and so further 
> reducing the air path has diminishing returns. For example, going from 100 mm 
> air and 100 um crystal to completely eliminating air will only get you about 
> a 40% reduction in background noise (it goes as the square root).
> Now, this rule of thumb also goes for the "support" material around your 
> crystal: one micron of cryoprotectant generates about as much background as 
> one micron of crystal. So, if you have a 10 micron crystal mounted in a 1 mm 
> thick drop, and manage to hit

[ccp4bb] X-ray Source Differences (WAS: RE: [ccp4bb] How far does rad dam travel?)

[Keller, Jacob]

>the top-hat profile is one of the reasons why inhouse machines produce better 
>quality data than synchrotrons. However, the often much increased resolution 
>you achieve at the synchrotron is generally worth more than the quality of the 
>data at restricted resolution.
>
>Cheers,
>Tim

Several surprises to me:

-Data from in-house sources is better?
I have not heard of this--is there any systematic examination of this? 
I saw nothing about this in a very brief Google foray.

-In-house beam profiles are top-hats?
Is there a place which shows such measurements? Does not pop out of 
Google for me, but I would love to be shown that this is true.

-Resolution at the synchrotron is better?
This does not really seem right to me theoretically, although in 
practice it does seem to happen. I think it is just a question of waiting for 
enough exposure time, as the CCP4BB response quoted at bottom describes.

JPK



===


Date: Tue, 12 Oct 2010 09:04:05 -0700
From: James Holton 
Re: Re: Lousy diffraction at home but fantastic at the synchrotron?
There are a few things that synchrotron beamlines generally do better than 
"home sources", but the most important are flux, collimation and absorption.
Flux is in photons/s and simply scales down the amount of time it takes to get 
a given amount of photons onto the crystal. Contrary to popular belief, there 
is nothing "magical" about having more photons/s: it does not somehow make your 
protein molecules "behave" and line up in a more ordered way. However, it does 
allow you to do the equivalent of a 24-hour exposure in a few seconds 
(depending on which beamline and which home source you are comparing), so it 
can be hard to get your brain around the comparison.
Collimation, in a nutshell, is putting all the incident photons through the 
crystal, preferably in a straight line. Illuminating anything that isn't the 
crystal generates background, and background buries weak diffraction spots 
(also known as high-resolution spots). Now, when I say "crystal" I mean the 
thing you want to shoot, so this includes the "best part" of a bent, cracked or 
otherwise inhomogeneous "crystal". The amount of background goes as the square 
of the beam size, so a 0.5 mm beam can produce up to 25 times more background 
than a 0.1 mm beam (for a fixed spot intensity).
Also, if the beam has high "divergence" (the range of incidence angles onto the 
crystal), then the spots on the detector will be more spread out than if the 
beam had low divergence, and the more spread-out the spots are the easier it is 
for them to fade into the background. Now, even at home sources, one can cut 
down the beam to have very low divergence and a very small size at the sample 
position, but this comes at the expense of flux.
Another tenant of "collimation" (in my book) is the DEPTH of non-crystal stuff 
in the primary x-ray beam that can be "seen" by the detector. This includes the 
air space between the "collimator" and the beam stop. One millimeter of air 
generates about as much background as 1 micron of crystal, water, or plastic. 
Some home sources have ridiculously large air paths (like putting the backstop 
on the detector surface), and that can give you a lot of background. As a rule 
of thumb, you want you air path in mm to be less than or equal to your crystal 
size in microns. In this situation, the crystal itself is generating at least 
as much background as the air, and so further reducing the air path has 
diminishing returns. For example, going from 100 mm air and 100 um crystal to 
completely eliminating air will only get you about a 40% reduction in 
background noise (it goes as the square root).
Now, this rule of thumb also goes for the "support" material around your 
crystal: one micron of cryoprotectant generates about as much background as one 
micron of crystal. So, if you have a 10 micron crystal mounted in a 1 mm thick 
drop, and manage to hit the crystal with a 10 micron beam, you still have 100 
times more background coming from the drop than you do from the crystal. This 
is why in-situ diffraction is so difficult: it is hard to come by a crystal 
tray that is the same thickness as the crystals.
Absorption differences between home and beamline are generally because 
beamlines operate at around 1 A, where a 200 um thick crystal or a 200 mm air 
path absorbs only about 4% of the x-rays, and home sources generally operate at 
CuKa, where the same amount of crystal or air absorbs ~20%. The "absorption 
correction" due to different paths taken through the sample must always be less 
than the total absorption, so you can imagine the relative difficulty of trying 
to measure a ~3% anomalous difference.
Lower absorption also accentuates the benefits of putting the detector further 
away. By the way, there IS a good reason why we spend so much money on 
large-area detectors. Background falls off with the square of distance, but the 
spots don't 

Re: [ccp4bb] Off-topic - PyMol map sampling at unit cell boundary

[Shane Caldwell]

Hi all,

To follow up on my question from last week, Dr. Emsley's work-around worked
great for me. Increase map sampling in coot, export, and then proceed in
pymol without using the map_double command. I end up with gigantic map file
sizes (~160MB), and it's more work to make all my maps this way, but it
gets me past the problem.

For the curious, images of the same map sampled at 2.5 and 5.0 are linked
below, along with the default-sampled map and its map_doubled children:

2.5:  http://imgur.com/WpBDNvw
5.0:  http://imgur.com/Ryw3X0T

Default (1.5 sampled) map: http://imgur.com/i46YH6r
Doubled once: http://imgur.com/Vy8oJfx
Doubled twice: http://imgur.com/q3gO0cI

Cheers,

Shane Caldwell
McGill University


On Fri, Jan 9, 2015 at 4:57 PM, Paul Emsley 
wrote:

> On 09/01/15 21:08, Shane Caldwell wrote:
>
>> Hi ccp4bb,
>>
>> Apologies for a cross-post. I previously asked this question on the
>> pymol-users mailing list, but I thought I'd ask here as well, in case
>> someone who doesn't follow that bb might have run into my problem rendering
>> maps in PyMol. I'm starting to think it's a non-trival problem to solve.
>>
>> I'm drawing a mesh based on a ccp4 map exported from coot. To get finer
>> sampling, I use the map_double command (twice sequentially, but the problem
>> is visible after the first). Doubling the map introduces a discontinuity.
>> The second doubling introduces a gap, but even even the first has a visible
>> distortion. (see linked images below)
>>
>> This discontinuity lines up with the unit cell boundary, so it has
>> something to do with sampling at the unit cell edge (the cell boundary is
>> faintly visible in the background of the linked images). Not sure if
>> there's a simple fix I'm overlooking or if it's a fundamental limitation of
>> the sampling algorithm. Any help you can provide would be great!
>>
>> I've linked images of the same map at all 3 samplings below:
>> Parent map: http://imgur.com/i46YH6r
>> Doubled once: http://imgur.com/Vy8oJfx
>> Doubled twice: http://imgur.com/q3gO0cI
>>
>
> That's amusing.  Looks like a pymol bug (but of course, given the source
> of this comment, you should take that with a pinch of salt).
>
> As a work-around, I'd advise that you turn up the map sampling rate to 2.8
> or so in Coot (before you read in your mtz file and subsequently export the
> map (fragment)) - then you won't need pymol map doubling.
>
> Paul.
>
>

Re: [ccp4bb] Privateer fails to run

[Marcin Wojdyr]

While most (all?) CCP4 programs use the MMDB library for reading
PDB files, handling of incorrect PDBs is not consistent.
Default settings in MMDB (and in clipper) are strict, but most of the
programs use a combination of options that make it more liberal (SetFlag()).

Marcin

On Mon, Jan 12, 2015 at 04:28:07PM +, Jon Agirre wrote:
> Hi Jan,
> 
> Privateer relies on Clipper-minimol, which in turn uses MMDB. According to
> MMDB's error code description list (
> https://www.ebi.ac.uk/pdbe/docs/cldoc/object/cl_obj_irets.html) :
> 
> Error_WrongEntryID 3 A PDB or mmCIF record that ought to display
> this entry's ID, shows an ID contradicting to that in header.
> 
> I've been able to replicate the error by opening a PDB file downloaded from
> PDBe and changing the HEADER line to show a different PDB ID. Is that your
> case?
> 
> Thanks for your interest,
> 
> Jon
> 
> On 12 January 2015 at 15:59, Jan Stransky 
> wrote:
> 
> > Dear all,
> > I am experiencing some troubles with running Privateer. It seems to fail
> > to read a PDB file. The Error message:
> >
> > Reading xxx.pdb... MMDBfile: read_file error: xxx.pdb :3
> > terminate called after throwing an instance of 'clipper::Message_fatal'
> > Aborted
> >
> > Any ideas?
> > Best regards,
> > Jan
> >
> 
> 
> 
> -- 
> Dr Jon Agirre
> York Structural Biology Laboratory / Department of Chemistry
> University of York, Heslington, YO10 5DD, York, England
> http://www.york.ac.uk/chemistry/research/ysbl/people/research/jagirre/
> +44 (0) 1904 32 8253

-- 
This e-mail and any attachments may contain confidential, copyright and or 
privileged material, and are for the use of the intended addressee only. If you 
are not the intended addressee or an authorised recipient of the addressee 
please notify us of receipt by returning the e-mail and do not use, copy, 
retain, distribute or disclose the information in or attached to the e-mail.
Any opinions expressed within this e-mail are those of the individual and not 
necessarily of Diamond Light Source Ltd. 
Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments 
are free from viruses and we cannot accept liability for any damage which you 
may sustain as a result of software viruses which may be transmitted in or with 
the message.
Diamond Light Source Limited (company no. 4375679). Registered in England and 
Wales with its registered office at Diamond House, Harwell Science and 
Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom

Re: [ccp4bb] Bulk solvent

[James Holton]

Yes, you can provide your own bulk solvent model as a "partial 
structure" to REFMAC.

http://www.ysbl.york.ac.uk/~garib/refmac/docs/keywords/xray-principal.html#labin_fparti_phiparti
http://www.ysbl.york.ac.uk/~garib/refmac/docs/keywords/xray-general.html#scpa
http://www.ysbl.york.ac.uk/~garib/refmac/docs/keywords/xray-principal.html#solv

Once you have an electron density map for the bulk solvent that you are 
happy with, use the CCP4 program SFALL to convert that map into 
structure factors:


sfall mapin my_better_solvent.map hklout my_better_solvent.mtz << EOF
mode sfcalc mapin
EOF

 SFALL will output FC and PHIC, but since these names are sort of 
"taken" inside of REFMAC, you may want to re-name them to be Fsolv and 
PHIsolv using CAD.  While you are at it, you might as well combine Fsolv 
PHIsolv with your input MTZ file (the one that contains your observed 
data.  REFMAC only takes one input MTZ file.  For example:


cad hklin1 old_refme.mtz hklin2 my_better_solvent.mtz hklout 
new_refme.mtz << EOF

labin file 1 E1=FP E2=SIGFP E3=FreeR_flag
labin file 2 E1=FC E2=PHIC
labou file 2 E1=Fsolv E2=PHIsolv
scale file 2 1 0
EOF

Next, you want to alert REFMAC to the "partial structure" you are 
providing.  Do this by assigning them to FPART1 and PHIP1.  My input 
usually looks like this:


refmac5 hklin new_Refme.mtz xyzin best_model_yet.pdb hklout 
refmacout.mtz xyzout refmacout.pdb <<  EOF

LABIN FP=FP SIGFP=SIGFP FREE=FreeR_flag FPART1=Fsolv PHIP1=PHIsolv
SCPART 1
SOLVENT NO
EOF

The "SCPART 1" is required if you want REFMAC to refine a scale and B 
factor for your bulk solvent like it does with the bulk solvent it makes 
automatically.  If the map you input into SFALL used "1" to define a 
"solvent" map voxel and "0" to define vacuum, then the "scale factor" 
you will find under "Partial structure 1: scale" in the refmac output 
log will be your refined bulk solvent electron density (k_sol), which 
has units of electrons/Angstrom^3.


Note that I am using "SOLVENT NO" in the above example to turn off the 
"built-in" bulk solvent model.  If you don't do this, REFMAC will make 
its own bulk solvent as usual, but refine it as an additional partial 
structure.  Then you will have two bulk solvent masks!   REFMAC actually 
supports multiple partial structures (up to four, I think), but my 
experience with this is that it gets unstable rather quickly.


That's the mechanics of it anyway.  It is a pity that phenix.refine 
doesn't support external partial structures like this, but perhaps it 
will soon.


One thing to beware is that MSKOUT may or may not be on any particular 
scale.  If you want to actually recover the "refined" bulk solvent map, 
you need to first re-scale the mskout.map so that it ranges from 0 to 1 
in value (check this with MAPDUMP), before you feed it to SFALL.  Then, 
during the CAD step above apply an appropriate scale and B factor to 
Fsolv using "SCALE FILE 1":

http://www.ccp4.ac.uk/html/cad.html#scale
You will find appropriate scale and B factor values printed out on the 
last "Partial structure   1:" entry in your last refmac log.



Now, of course, you have the finer detail problem of what, exactly, to 
do to the "default" bulk solvent mask to make it better.   Simply adding 
the Fo-Fc map is not only cheating; it doesn't work!  By default, the 
Fo-Fc map does not contain structure factors flagged as part of the FREE 
set.  So, if you "edit" your bulk solvent by adding Fo-Fc, you will 
immediately get an Rwork of zero, but will see no change to Rfree.  This 
is because all the "free" structure factors used to make the Fo-Fc map 
were zero.


Finding some way to "transfer" information from the differences in the 
working set into the free set is challenging, and indeed this is the 
central problem of model building.


-James Holton
MAD Scientist

On 1/11/2015 11:05 AM, Alastair Fyfe wrote:

A related/follow-on question, hopefully on the same topic:

When mask-based solvent modeling leads to problems caused by 
calculation of an inappropriate mask (eg inclusion of disordered loops 
or inaccessible pockets as bulk-solvent volume) it seems that a 
feasible workaround is to (a) output the calculated mask via MSKOUT 
(b) edit it to remove spurious regions (c) calculate partial structure 
factors for the new solvent region using refmac's previous kSol, bSol 
estimates (d)  include the partial structure factors in a second round 
of refinement by specifying "SOLVENT NO", FPART and SCPART.


However, this does not re-calculate kSol and bSol to reflect the 
modified mask. Is there a way to simply supply the mask to be used 
rather than have refmac calculate it ?

Thanks,
Alastair Fyfe


On 01/11/2015 08:04 AM, Eleanor Dodson wrote:

Yes. If the model is incomplete it is obviously not sensible to use the
mask based solvent - you will tend to lose the unmodelled features. 
It also

gives unrealistically low R factors for a crystal with high solvent
content. However the best test would be to 

Re: [ccp4bb] Queries regarding bead beater and french press.

[Munson, Mary]

We are huge fans of the Retsch Planetary Ball Mill grinder. Grinds yeast cells 
(different volumes) at liquid N2 temp. Minimal proteolysis will high efficiency 
lysis. Made an enormous difference to obtaining a higher yield of intact, 
functional protein complexes.

-Mary Munson
UMass Medical School

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Johnson 
Luwang
Sent: Monday, January 12, 2015 10:45 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Queries regarding bead beater and french press.

Dear All,
I am looking for an equipment that can do Saccharomyces cerevisiae cells lysis 
(say about 100-200ml lysate volume). I have used the Constant Systems cell 
disruptor TS 0.75kW model (at another facility)  that can go up to 40kpsi.  It 
works perfect for my yeast cell lysis experiment.   We were planning to set up 
similar facility at our place, but some of my colleagues suggested me about 
"bead beater"  for the same purpose.  Quite frankly I don't have much idea 
about bead beater. And I need the suggestions from the experts who have used 
these two systems (french press and bead beater). Is the bead beater better 
than the french press for yeast cell lysis? If so can you suggest me a bead 
beater model which is the best for our purpose?
Many thanks.
Best Regards,
Johnson L.W.

Re: [ccp4bb] Queries regarding bead beater and french press.

[Roger Rowlett]

The Bead Beater has a 15, 40, and 350 mL chambers. I haven't used mine 
to homogenize yeast, but I suspect it is similar in performance to E. 
coli disruption. (Different bead sizes are used for yeast than 
bacteria.) We get excellent, gentle disruption of E. coli in 8 minutes 
total. A French Press takes a loong time for more than 40-50 mL 
of lysate, and often requires multiple passes for complete disruption. 
Beads and cell wall debris can be easily removed by centrifugation for 
direct application on your FPLC.


We moved to Bead Beaters from a French Press more than a decade ago and 
haven't looked back. We can do one liter overexpression preps (20-30 g 
wet packed cells) in the 40 mL chamber.


Cheers,

___
Roger S. Rowlett
Gordon & Dorothy Kline Professor
Department of Chemistry
Colgate University
13 Oak Drive
Hamilton, NY 13346

tel: (315)-228-7245
ofc: (315)-228-7395
fax: (315)-228-7935
email: rrowl...@colgate.edu

On 1/12/2015 10:44 AM, Johnson Luwang wrote:

Dear All,
I am looking for an equipment that can do /Saccharomyces 
cerevisiae/ cells lysis (say about 100-200ml lysate volume). I have 
used the Constant Systems cell disruptor TS 0.75kW model (at another 
facility)  that can go up to 40kpsi.  It works perfect for my yeast 
cell lysis experiment.   We were planning to set up similar facility 
at our place, but some of my colleagues suggested me about "bead 
beater"  for the same purpose.  Quite frankly I don't have much idea 
about bead beater. And I need the suggestions from the experts who 
have used these two systems (french press and bead beater). Is the 
bead beater better than the french press for yeast cell lysis? If so 
can you suggest me a bead beater model which is the best for our purpose?


Many thanks.

Best Regards,
Johnson L.W.

[ccp4bb] 6th workshop on Neutron Scattering Applications in Structural Biology

[Meilleur, Flora]

Firth announcement

6th Workshop on Neutron Scattering Applications in Structural Biology
Oak Ridge, TN. June 1 - June 5, 2015

Application deadline: April 10, 2015

The workshop on Neutron Scattering Applications in Structural Biology aims at 
enabling structural biologists to fully exploit the latest instrumentation and 
software development at the SNS and HFIR facilities at Oak Ridge National 
Laboratory. Attendees will participate in lectures and tutorials focusing 
exclusively on neutron techniques applied in structural biology. The workshop 
is designed for graduate students, post-doctoral fellows and faculty new to or 
with limited experience of neutron scattering.

Travel and accommodation expenses are supported for selected participants from 
the United States. International applications are welcome. However the course 
organization is not able to support travel or accommodation.

The number of participants will be limited to 15. There is no registration fee 
for all selected participants.

The application package consisting of 1) Information form, 2) CV, 3) Applicant 
motivation letter (1/2 to 1 page), 4) Principal Investigator letter of support 
(for graduate students only; 1/2 to 1 page), should be sent electronically to 
meille...@ornl.gov before April 10, 2015.

Detailed information can be found on the workshop web page: 
https://public.ornl.gov/neutrons/conf/gcnb2015.

Flora Meilleur, Ph. D
Assistant Professor, Molecular and Structural Biochemistry
North Carolina State University
Neutron Sciences Directorate
Oak Ridge National Laboratory
Phone: 865-242-5747

Re: [ccp4bb] Privateer fails to run

[Jon Agirre]

Hi Jan,

Privateer relies on Clipper-minimol, which in turn uses MMDB. According to
MMDB's error code description list (
https://www.ebi.ac.uk/pdbe/docs/cldoc/object/cl_obj_irets.html) :

Error_WrongEntryID 3 A PDB or mmCIF record that ought to display
this entry's ID, shows an ID contradicting to that in header.

I've been able to replicate the error by opening a PDB file downloaded from
PDBe and changing the HEADER line to show a different PDB ID. Is that your
case?

Thanks for your interest,

Jon

On 12 January 2015 at 15:59, Jan Stransky 
wrote:

> Dear all,
> I am experiencing some troubles with running Privateer. It seems to fail
> to read a PDB file. The Error message:
>
> Reading xxx.pdb... MMDBfile: read_file error: xxx.pdb :3
> terminate called after throwing an instance of 'clipper::Message_fatal'
> Aborted
>
> Any ideas?
> Best regards,
> Jan
>



-- 
Dr Jon Agirre
York Structural Biology Laboratory / Department of Chemistry
University of York, Heslington, YO10 5DD, York, England
http://www.york.ac.uk/chemistry/research/ysbl/people/research/jagirre/
+44 (0) 1904 32 8253

Re: [ccp4bb] Queries regarding bead beater and french press.

[Jurgen Bosch]

[Advertisement on] Avestin Emulsiflex C5 [/Advrtisement off]
Google is your friend.

Jürgen
..
Jürgen Bosch
Johns Hopkins University
Bloomberg School of Public Health
Department of Biochemistry & Molecular Biology
Johns Hopkins Malaria Research Institute
615 North Wolfe Street, W8708
Baltimore, MD 21205
Office: +1-410-614-4742
Lab:  +1-410-614-4894
Fax:  +1-410-955-2926
http://lupo.jhsph.edu

On Jan 12, 2015, at 10:44 AM, Johnson Luwang 
mailto:jlw_...@iisertvm.ac.in>> wrote:

Dear All,
I am looking for an equipment that can do Saccharomyces cerevisiae cells lysis 
(say about 100-200ml lysate volume). I have used the Constant Systems cell 
disruptor TS 0.75kW model (at another facility)  that can go up to 40kpsi.  It 
works perfect for my yeast cell lysis experiment.   We were planning to set up 
similar facility at our place, but some of my colleagues suggested me about 
"bead beater"  for the same purpose.  Quite frankly I don't have much idea 
about bead beater. And I need the suggestions from the experts who have used 
these two systems (french press and bead beater). Is the bead beater better 
than the french press for yeast cell lysis? If so can you suggest me a bead 
beater model which is the best for our purpose?

Many thanks.

Best Regards,
Johnson L.W.

[ccp4bb] Privateer fails to run

[Jan Stransky]

Dear all,
I am experiencing some troubles with running Privateer. It seems to fail 
to read a PDB file. The Error message:


Reading xxx.pdb... MMDBfile: read_file error: xxx.pdb :3
terminate called after throwing an instance of 'clipper::Message_fatal'
Aborted

Any ideas?
Best regards,
Jan

[ccp4bb] Queries regarding bead beater and french press.

[Johnson Luwang]

Dear All,
I am looking for an equipment that can do *Saccharomyces cerevisiae* cells
lysis (say about 100-200ml lysate volume). I have used the Constant Systems
cell disruptor TS 0.75kW model (at another facility)  that can go up to
40kpsi.  It works perfect for my yeast cell lysis experiment.   We were
planning to set up similar facility at our place, but some of my colleagues
suggested me about "bead beater"  for the same purpose.  Quite frankly I
don't have much idea about bead beater. And I need the suggestions from the
experts who have used these two systems (french press and bead beater). Is
the bead beater better than the french press for yeast cell lysis? If so
can you suggest me a bead beater model which is the best for our purpose?

Many thanks.

Best Regards,
Johnson L.W.

Re: [ccp4bb] Bulk solvent

[Dirk Kostrewa]

Dear Bernhard,

further thinking about the Babinet scaling effects, I have to correct my 
conclusion in the last sentence:


On 12.01.2015 14:21, Dirk Kostrewa wrote:
If, however, the unmodelled part is less well ordered (which is the 
more common case), it's contribution will mainly affect the model's 
Fcalc at low resolution. If the overall scaling is dominated by the 
high resolution terms (which is usually the case), the unmodelled part 
will not have an effect on the overall scale factor of the model's 
Fcalc, leaving only the Fcalc at low resolution somewhat too low. 
Since lowering the model's Fcalc scale factor at low resolution is the 
main purpose of the Babinet solvent correction, this will lead to an 
_underestimation_ (!) of the Babinet bulk solvent contribution scale 
factor (ksol). This, in principle, should increase, or overestimate, 
the signal of the difference densities at low resolution, which might 
also help with interpretation of the unmodelled part.


The underestimation of the Babinet bulk solvent scale factor is 
equivalent to an overestimation of the contrast between protein and 
solvent and should therefore lead to an overestimation of the Fcalc at 
low resolution. If scaling is still dominated by the high resolution 
terms, this should lead to a decrease, or underestimation, of the 
structure factor differences at low resolution, which would reduce the 
overall signal of the difference densities. But still, this will be an 
overall effect and not restricted to the location of the unmodelled part.


Best regards,

Dirk.

--

***
Dirk Kostrewa
Gene Center Munich, A5.07
Department of Biochemistry
Ludwig-Maximilians-Universität München
Feodor-Lynen-Str. 25
D-81377 Munich
Germany
Phone:  +49-89-2180-76845
Fax:+49-89-2180-76999
E-mail: kostr...@genzentrum.lmu.de
WWW:www.genzentrum.lmu.de
***

Re: [ccp4bb] Ramachandran outlier

[Robbie P. Joosten]

Hi Dialing,

86% favoured can actually be quite okay for an initial model. As long as 
it doesn't have 14% in the disallowed region, the vast majority of 
residues will be correct, or close enough to the correct answer that 
they can be fixed easily. Of course, such a model will need tweaking, 
but this is more or less the point of calling it an 'initial' model.


Cheers,
Robbie

On 01/12/2015 01:18 PM, Dialing Pretty wrote:

Dear All，

If an initial PDB has only 86% residues in the Ramachandran favored region, it
would mean there is a significant error (for example significant length of
protein fragment in the total protein assigned to the wrong electron density map
position) , right?

Dialing

Re: [ccp4bb] Bulk solvent

[Dirk Kostrewa]

Dear Bernhard,

I think, the main difference of an unmodelled part between the mask bulk 
solvent correction and the Babinet bulk solvent correction is, that the 
mask approach can use quite detailed structural information, whereas the 
Babinet approach uses only two additional scale factors. Let's 
illustrate this for a model with an unmodelled part:


In the mask bulk solvent correction, the solvent mask fills the region 
outside the modelled part and thus lowers the local contrast of the 
unmodelled part. For the unmodelled part, it would be better if there 
wouldn't be any bulk solvent density (BUSTER allows this). Then, the 
superior scaling of the mask bulk solvent approach without reducing the 
local contrast should really help with the interpretation of the 
unmodelled part.
However, masking out the unmodelled part shouldn't be too detailed, 
since the hole left in the bulk solvent mask will return as positive 
difference density and can be heavily biased towards the atoms that were 
used to exclude the solvent mask. I've seen this in the very old X-Plor, 
where setting the occupany to "0" of a part of the model took it out 
from the model's Fcalc but not from the solvent mask calculation, 
leading to positive difference density exactly around the "omitted" 
atoms + mask radius.


Something like this could not happen with the Babinet approach, since it 
only affects overall scale factors. But here, the effect is quite 
counter-intuitive!
If the unmodelled part is well ordered (but just missing), it's 
contribution will be missing from the model's Fcalc at all resolutions 
and thus will affect the overall scale factor of the model Fcalc, only, 
but not the additional Babinet scale factors. If the missing atoms are 
not accounted for in the overall scaling, this could decrease, or 
underestimate, the signal of the difference density everywhere, which is 
a general problem, but not specifically related to the Babinet solvent 
correction.
If, however, the unmodelled part is less well ordered (which is the more 
common case), it's contribution will mainly affect the model's Fcalc at 
low resolution. If the overall scaling is dominated by the high 
resolution terms (which is usually the case), the unmodelled part will 
not have an effect on the overall scale factor of the model's Fcalc, 
leaving only the Fcalc at low resolution somewhat too low. Since 
lowering the model's Fcalc scale factor at low resolution is the main 
purpose of the Babinet solvent correction, this will lead to an 
_underestimation_ (!) of the Babinet bulk solvent contribution scale 
factor (ksol). This, in principle, should increase, or overestimate, the 
signal of the difference densities at low resolution, which might also 
help with interpretation of the unmodelled part.


But all these scaling effects should be small, unless a substantial part 
of the model is missing.


Best regards,

Dirk.

On 12.01.2015 11:09, Bernhard Rupp wrote:


What still evades me is, why exactly is the Babinet immune to these 
effects of excluding/masking-out unmodelled parts?


The Babinet correction is also a function of the MODELLED part, just 
the opposite sign. So an incomplete model


de facto equals an over-estimated solvent. Is it just the high 
effective dampening of this correction (B ~200) as


Pavel said that makes it less susceptible because the higher 
resolution reflections are less affected and


therefore have a chance to correct/overcome the inadequate (implicit) 
masking?


Best, BR

*From:*CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf 
Of *Eleanor Dodson

*Sent:* Sonntag, 11. Januar 2015 17:05
*To:* CCP4BB@JISCMAIL.AC.UK
*Subject:* Re: [ccp4bb] Bulk solvent

Yes. If the model is incomplete it is obviously not sensible to use 
the mask based solvent - you will tend to lose the unmodelled 
features. It also gives unrealistically low R factors for a crystal 
with high solvent content. However the best test would be to analyse 
maps and try to decide if & when the different procedures work best.. 
A project for a student dissertation perhaps??


  Eleanor

On 9 January 2015 at 20:13, Roberts, Sue A - (suer) 
mailto:s...@email.arizona.edu>> wrote:


I always try both methods - usually there is little difference.  However,

For CueO (multicopper oxidase) where there are about  25 disordered 
(unseen) residues in a loop,  using Babinet scaling instead of the 
default refmac scaling reduced the R factors by about 2% (both R and 
Rfree) and improved the quality of the maps substantially.


From Dirk's comment, I'd guess this is because the mask-based solvent 
model is putting solvent where there is (disordered) protein, which is 
different from real bulk solvent.


Sue

Dr. Sue A. Roberts
Dept. of Chemistry and Biochemistry
University of Arizona
1306 E. University Blvd,  Tucson, AZ 85721
Phone: 520 621 4168 
s...@email.arizona.edu 




-Original Message-
From: CCP4 bulletin board [mailt

[ccp4bb] Ramachandran outlier

[Dialing Pretty]

Dear All，
If an initial PDB has only 86% residues in the Ramachandran favored region, it 
would mean there is a significant error (for example significant length of 
protein fragment in the total protein assigned to the wrong electron density 
map position) , right?
Dialing

[ccp4bb] Postdoctoral Position at the Max Planck in Tübingen, Germany

[Fulvia Bono]

Postdoctoral position in Structural Characterization of mRNA Transport Complexes

Asymmetric mRNA localization is widely used to control the spatial distribution 
of proteins within the cell, but the underlying molecular mechanisms remain 
unclear. 
A fully funded ERC Postdoctoral position is available immediately to 
investigate the mRNA localization pathway at the molecular level by means of 
biochemistry and X-ray crystallography and to gain insights into its function 
in development. 
The structural work will be complemented by biochemical, biophysical and in 
vivo data.
Our group is located in an excellent scientific environment on the Max Planck 
Campus in Tübingen. 
http://www.eb.tuebingen.mpg.de/research/research-groups/fulvia-bono.html

Qualifications:
High motivation and a strong background in biochemistry and crystallography are 
essential. A keen interest in RNA biology is desirable. 

Applications:
Applications should include a CV and list of publications, summary of work 
experience, a one-page motivation letter and contact information of three 
referees. Please send applications to fulvia.b...@tuebingen.mpg.de.

The Max Planck Society is an equal opportunity employer. It seeks to increase 
the percentage of female employees in areas where they are underrepresented. 
The Max Planck Society is also committed to employing more individuals with 
disabilities, and disabled applicants are preferred if qualification is equal.

With best wishes,
Fulvia

***
Dr. Fulvia Bono
Max Planck Institute for Developmental Biology
Spemannstrasse 35
D-72076 Tübingen
Germany
Phone: +49 7071 6011367
E-mail: fulvia.b...@tuebingen.mpg.de

Re: [ccp4bb] Bulk solvent

[Steiner, Roberto]

On 12 Jan 2015, at 10:09, Bernhard Rupp 
mailto:b...@ruppweb.org>> wrote:

What still evades me is, why exactly is the Babinet immune to these effects of 
excluding/masking-out unmodelled parts?
The Babinet correction is also a function of the MODELLED part, just the 
opposite sign. So an incomplete model
de facto equals an over-estimated solvent. Is it just the high effective 
dampening of this correction (B ~200) as
Pavel said that makes it less susceptible because the higher resolution 
reflections are less affected and
therefore have a chance to correct/overcome the inadequate (implicit) masking?

I have the feeling that this might be the case.
More details on the two bulk-solvent correction methods available in Refmac 
(with formulae) are in Murshudov et al (2011) Acta Cryst D67, 355-367 - Section 
2.4

Best wishes
Roberto



Best, BR

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Eleanor 
Dodson
Sent: Sonntag, 11. Januar 2015 17:05
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Bulk solvent

Yes. If the model is incomplete it is obviously not sensible to use the mask 
based solvent - you will tend to lose the unmodelled features. It also gives 
unrealistically low R factors for a crystal with high solvent content. However 
the best test would be to analyse maps and try to decide if & when the 
different procedures work best.. A project for a student dissertation perhaps??
  Eleanor

On 9 January 2015 at 20:13, Roberts, Sue A - (suer) 
mailto:s...@email.arizona.edu>> wrote:
I always try both methods - usually there is little difference.  However,

For CueO (multicopper oxidase) where there are about  25 disordered (unseen) 
residues in a loop,  using Babinet scaling instead of the default refmac 
scaling reduced the R factors by about 2% (both R and Rfree) and improved the 
quality of the maps substantially.

>From Dirk's comment, I'd guess this is because the mask-based solvent model is 
>putting solvent where there is (disordered) protein, which is different from 
>real bulk solvent.

Sue

Dr. Sue A. Roberts
Dept. of Chemistry and Biochemistry
University of Arizona
1306 E. University Blvd,  Tucson, AZ 85721
Phone: 520 621 4168
s...@email.arizona.edu



-Original Message-
From: CCP4 bulletin board 
[mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of 
Armando Albert
Sent: Friday, January 09, 2015 12:56 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Bulk solvent

Dear all,
Is there any reason for using Babinet scaling for bulk solvent correction 
instead of mask based scaling?
Armando



Roberto A. Steiner, PhD
Randall Division of Cell and Molecular Biophysics
Faculty of Life Sciences and Medicine
King's College London

roberto.stei...@kcl.ac.uk
Phone 0044 20 78488216
Fax0044 20 78486435

Room 3.10A
New Hunt's House
Guy's Campus
SE1 1UL
London

Re: [ccp4bb] Bulk solvent

[Bernhard Rupp]

What still evades me is, why exactly is the Babinet immune to these effects of 
excluding/masking-out unmodelled parts? 

The Babinet correction is also a function of the MODELLED part, just the 
opposite sign. So an incomplete model

de facto equals an over-estimated solvent. Is it just the high effective 
dampening of this correction (B ~200) as

Pavel said that makes it less susceptible because the higher resolution 
reflections are less affected and

therefore have a chance to correct/overcome the inadequate (implicit) masking?

 

Best, BR

 

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Eleanor 
Dodson
Sent: Sonntag, 11. Januar 2015 17:05
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Bulk solvent

 

Yes. If the model is incomplete it is obviously not sensible to use the mask 
based solvent - you will tend to lose the unmodelled features. It also gives 
unrealistically low R factors for a crystal with high solvent content. However 
the best test would be to analyse maps and try to decide if & when the 
different procedures work best.. A project for a student dissertation perhaps??

  Eleanor

 

On 9 January 2015 at 20:13, Roberts, Sue A - (suer)  
wrote:

I always try both methods - usually there is little difference.  However,

For CueO (multicopper oxidase) where there are about  25 disordered (unseen) 
residues in a loop,  using Babinet scaling instead of the default refmac 
scaling reduced the R factors by about 2% (both R and Rfree) and improved the 
quality of the maps substantially.

>From Dirk's comment, I'd guess this is because the mask-based solvent model is 
>putting solvent where there is (disordered) protein, which is different from 
>real bulk solvent.

Sue

Dr. Sue A. Roberts
Dept. of Chemistry and Biochemistry
University of Arizona
1306 E. University Blvd,  Tucson, AZ 85721
Phone: 520 621 4168  
s...@email.arizona.edu




-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Armando 
Albert
Sent: Friday, January 09, 2015 12:56 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Bulk solvent

Dear all,
Is there any reason for using Babinet scaling for bulk solvent correction 
instead of mask based scaling?
Armando

 

[ccp4bb] early-stage postdoc Spanish call

[Maria Sola i Vilarrubias]

The call for early-stage PostDoc *Juan de la Cierva - Formación* 2-year
contract from the Spanish Ministry of Economy and Competitiveness (BOE 5
Diciembre de 2014 Sec III pág. 100556) is now open. We seek for an
early-stage postdoc to carry out a project in Structural Biology related to
mitochondrial DNA (mtDNA) transactions and regulatory proteins in the
Structural MitoLab (
http://www.ibmb.csic.es/index.php?pg=laboratorio&tab=lab_home&idLaboratorio=13
) of the Institute of Molecular Biology Barcelona, CSIC, located at the
premises of Barcelona Science Park, www.pcb.ub.edu.



The mtDNA sequence is known since 1981. Mitochondria are at the crossroads
of ageing and major health problems such as cancer, diabetes,
neurodegenerative disorders such as Parkinson’s and Alzheimer’s diseases,
and mtDNA is altered in all these conditions. The goal of the work is the
characterization of variable segments of this DNA, alone or in complexes
with binding proteins. In addition, crystallization of protein/DNA
complexes, small-angle X-ray scattering and atomic-force microscopy
analysis will be considered as additional goals.



For the *Juan de la Cierva-Formación* application, the candidate should:

- have obtained her/his Doctor title between January 1, 2013 and December
31, 2014.

- have a strong background in experimental sciences with expertise in
cloning and protein purification since the project is essentially wet-lab
oriented; experience in macromolecular crystallography is an advantage.

- have at least one first-author paper published in a high-impact journal
due to the intrinsic highly competitive nature of the call.

- be fluent use of English language and exhibit a very positive, highly
motivated attitude towards research.


Candidates who do not accomplish these conditions cannot be further
considered.



The outcome of the call is expected for summer 2015 and thereafter the
successful candidates will have up to 6-months to join the group.



Interested candidates may get more information about our projects, which
are basically related to mitochondrial proteins and mitochondrial DNA
regulation, at
http://www.ibmb.csic.es/index.php?pg=laboratorio&tab=lab_home&idLaboratorio=13



Interested candidates should send as soon as possible and before *January
2o, 2015* an e-mail with their CV together with a motivation letter and
contact details of two referees to



maria.s...@ibmb.csic.es


-- 
Maria Solà
Dep. Structural Biology
IBMB-CSIC
Baldiri Reixach 10-12
08028 BARCELONA
Spain
Tel: (+34) 93 403 4950
Fax: (+34) 93 403 4979
e-mail: maria.s...@ibmb.csic.es