[ccp4bb] Job posting - Sr. Technical Leader for Solution Biophysics

2016-10-27 Thread Bussiere, Dirksen 
The Structural and Biophysical Chemistry group at Novartis-Emeryville is 
seeking to recruit a B.S./M.S. level scientist with experience in solution 
biophysics and structural biology.  The description of the position can be 
found online at:



https://sjobs.brassring.com/tgwebhost/jobdetails.aspx?jobId=2446588=13617=5260=IND



Please apply online using the Brassring system and reference Job ID 198354BR 
when applying.  If you have any questions, please feel free to contact me.



-Dirk Bussiere


Dirksen Bussiere, Ph.D., M.B.A.
Director, Structural and Biophysical Chemistry / NLS
Novartis Insts. for BioMedical Research
5300 Chiron Way
Emeryville, CA 94608-2916
USA

Phone+1  510-879-9505
Fax +1  510-655-9910
dirksen.bussi...@novartis.com
www.novartis.com

[ccp4bb] AW: [ccp4bb] AW: [ccp4bb] intensity statistics and twinning

2016-10-27 Thread Hillen, Hauke 
Agreed, and this is ongoing work. Yet it is not trivial to get better 
resolution than this for small (in the world of EM) samples either.

Von: Mark van Raaij [mjvanra...@cnb.csic.es]
Gesendet: Donnerstag, 27. Oktober 2016 22:08
An: Hillen, Hauke
Betreff: Re: [ccp4bb] AW: [ccp4bb] intensity statistics and twinning

Another option might be to go full cryo-EM

Mark J van Raaij
CNB-CSIC
www.cnb.csic.es/~mjvanraaijOn 27 Oct 2016 21:37, "Hillen, Hauke" 
 wrote:
>
> Dear Mark,
>
> Thanks for your reply. Unfortunately, I have already spent a lot of time 
> trying to do exactly this. I do think some biologically relevant questions 
> can be answered by architecture at this resolution, so I would like to try to 
> get the most out of these datasets I can.
>
> Best wishes,
> Hauke
>
>
> 
> Von: Mark van Raaij [mjvanra...@cnb.csic.es]
> Gesendet: Donnerstag, 27. Oktober 2016 21:29
> An: Hillen, Hauke
> Betreff: Re: [ccp4bb] intensity statistics and twinning
>
> I'd say intensity statistics at this resolution at not reliable and your 
> crystal are most likely not twinned.
> Unless you think you can answer any interesting biological question at this 
> resolution, I'd forget about these datasets and spend all my efforts at 
> getting better diffracting ones. Even if this means going back to cloning or 
> working on a different species...although lysine methylation, limited 
> proteolysis etc. might also be tried if you haven't done so already.
> A slightly different crystal contact might make the difference and yield much 
> better diffraction.
>
> Mark J van Raaij
> CNB-CSIC
> www.cnb.csic.es/~mjvanraaij
>
> On 27 Oct 2016 21:11, "Hillen, Hauke"  wrote:
> Dear ccp4 community,
>
> I am currently working on some low resolution datasets (around 4.5A). The 
> space group seems to be P21, as suggested by XDS and pointless. I have 
> collected many datasets of these crystals, both native as well as 
> SeMet-labeled. Using MR-SAD I have been able to obtain a clearly 
> interpretable electron density map for all features I expect and heavy atom 
> sites that make sense for both the model used in MR and the yet unmodeled 
> components. So far, so good.
>
> While routinely analyzing my datasets with Phenix Xtriage, I have noticed 
> that the intensity statistics for all of these datasets look unusual. In 
> fact, Xtriage complains about this with the message: „The intensity 
> statistics look unusual, but twinning is not indicated or possible in the 
> given space group“ when processed in P21.
> The occurence of this message depends somewhat on the typ of input file I use 
> for the same dataset as well as the input parameters (high resolution 
> cut-off). If I use XDSCONV to convert the intensities to amplitudes for 
> phenix, this message appears. If I use the output of XSCALE directly as 
> intensities, this message does not appear, yet the actual statistics are 
> somewhat similar. I have attached the log file output for four scenarios at 
> the end of this message (P21 intensities, P21 amplitudes, P1 intensities, P1 
> amplitudes).
> These results got me questioning whether the true space group is really P21, 
> or whether it could be that it is P1 with some twinning issue. Since the 
> Xtriage output regarding the „normality“ of the intensity statistics varies 
> upon the input format, I assume that this case may be somewhat borderline. 
> Since I have very little experience both with low-resolution crystals as well 
> as with twinning, I am a bit unsure how to proceed with this data.
> How can I distinguish between a partially twinned P1 crystal and an untwinned 
> P21 crystal? It is my impression from previous discussions here that 
> distinguishing twinned from untwinned data simply by comparing refinement 
> results with and without twin laws is not always conclusive, as the R-factors 
> are not directly comparable. If the crystal is truly P21, could these issues 
> arise from intensity to amplitude conversion problems? (Xtriage also suggests 
> this as a possibility) If so, can these be overcome? Or could the deviation 
> from ideal intensities simply originate from the low quality (= resolution) 
> of the data and are within the range of tolerance for such a dataset? Could 
> this be some type of pseudosymmetry issue? And finally, what
>
> I would be very grateful for any advice on how to proceed with these data!
>
>
> Kind regards,
> Hauke
>
>
>
> Processed as P21, intensity input:
>
> === Diagnostic tests for twinning and pseudosymmetry 
> ==
>
> Using data between 10.00 to 3.50 Angstrom.
>
> --Patterson analyses--
>
> Largest Patterson peak with length larger than 15 Angstrom:
> Frac. coord.  :0.1640.000   -0.021
> Distance to origin:   17.720
> Height relative to origin :3.072 %
>

[ccp4bb] AW: intensity statistics and twinning

2016-10-27 Thread Hillen, Hauke 
Dear Jacob,

So far, I have only built an inital model into the "experimental" MR-SAD map, 
which is not complete. I am now playing with different refinement strategies 
(mainly rigid body). Both R and Rfree have not dropped below 40 (43/44 current 
best).
These are the statistics XDS reports. This is not my very best dataset, but 
quite close and the described intensity statistics issue is the same for my 
slightly better dataset.

P21
 SUBSET OF INTENSITY DATA WITH SIGNAL/NOISE >= -3.0 AS FUNCTION OF RESOLUTION
 RESOLUTION NUMBER OF REFLECTIONSCOMPLETENESS R-FACTOR  R-FACTOR 
COMPARED I/SIGMA   R-meas  CC(1/2)  Anomal  SigAno   Nano
   LIMIT OBSERVED  UNIQUE  POSSIBLE OF DATA   observed  expected
  Corr

12.5498122798  2943   95.1%   2.8%  2.6% 
9774   41.98  3.3%99.8*16*   0.9931304
 9.01   183814956  4999   99.1%   3.2%  3.0%
18374   35.97  3.7%99.8* 20.8892396
 7.40   222926214  6373   97.5%   4.5%  4.3%
22234   22.38  5.3%99.8* 30.8413003
 6.42   270897515  7586   99.1%  12.2% 12.3%
270479.44 14.4%98.5*-10.7953648
 5.75   315418463  8510   99.4%  26.5% 26.9%
315294.83 30.9%94.9* 20.7924150
 5.26   350729393  9464   99.2%  45.0% 46.0%
350342.91 52.6%86.0* 10.7634601
 4.87   34621   10015 10282   97.4%  66.3% 68.0%
345071.86 78.7%69.8* 20.7304843
 4.56   39690   10874 10951   99.3% 102.7%106.4%
396451.27120.5%53.5* 20.7055328
 4.30   41043   11376 11671   97.5% 196.7%205.7%
408810.65230.8%26.2* 20.6405480
total  259541   71604 72779   98.4%   6.6%  6.6%   
2590258.57  7.8%99.8* 20.761   34753

P1
SUBSET OF INTENSITY DATA WITH SIGNAL/NOISE >= -3.0 AS FUNCTION OF RESOLUTION
 RESOLUTION NUMBER OF REFLECTIONSCOMPLETENESS R-FACTOR  R-FACTOR 
COMPARED I/SIGMA   R-meas  CC(1/2)  Anomal  SigAno   Nano
   LIMIT OBSERVED  UNIQUE  POSSIBLE OF DATA   observed  expected
  Corr

12.5398982654  2942   90.2%   2.8%  2.7% 
9886   43.31  3.3%99.7*   -140.7872174
 9.01   183864772  4996   95.5%   3.1%  3.1%
18381   36.63  3.6%99.8*   -110.7884283
 7.40   223045799  6365   91.1%   4.5%  4.4%
22271   23.38  5.2%99.8*-60.7965259
 6.42   270657035  7570   92.9%  12.3% 12.3%
270219.82 14.2%98.7*-20.7916428
 5.75   315378135  8518   95.5%  26.6% 26.9%
314994.93 30.9%95.1*-10.7717557
 5.26   350949053  9464   95.7%  45.1% 45.6%
350452.97 52.4%86.9*-10.7478411
 4.87   345949050 10259   88.2%  67.4% 68.7%
344821.97 78.4%73.2*-10.7138170
 4.56   39744   10256 10966   93.5% 103.8%106.6%
396651.31120.5%56.4*-10.6779516
 4.30   41123   10884 11658   93.4% 197.8%205.3%
409630.67230.1%27.0*-10.6179596
total  259745   67638 72738   93.0%   6.6%  6.6%   
2592138.87  7.7%99.8*-20.727   61394


Best wishes,
Hauke



Von: Keller, Jacob [kell...@janelia.hhmi.org]
Gesendet: Donnerstag, 27. Oktober 2016 21:36
An: Hillen, Hauke; CCP4BB@JISCMAIL.AC.UK
Betreff: RE: intensity statistics and twinning

It would be helpful to know what your current R values are in modelling, and 
also the merging statistics. It looks like you might have a twinned p1 crystal.

JPK

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Hillen, 
Hauke
Sent: Thursday, October 27, 2016 3:11 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] intensity statistics and twinning

Dear ccp4 community,

I am currently working on some low resolution datasets (around 4.5A). The space 
group seems to be P21, as suggested by XDS and pointless. I have collected many 
datasets of these crystals, both native as well as SeMet-labeled. Using MR-SAD 
I have been able to obtain a clearly interpretable electron density map for all 
features I expect and heavy atom sites that make sense for both the model used 
in MR and the yet unmodeled components. So far, so good.

While routinely analyzing my datasets with Phenix Xtriage, I have noticed that 
the intensity statistics for all of these datasets look unusual.

[ccp4bb] AW: [ccp4bb] intensity statistics and twinning

2016-10-27 Thread Hillen, Hauke 
Dear Mark,

Thanks for your reply. Unfortunately, I have already spent a lot of time trying 
to do exactly this. I do think some biologically relevant questions can be 
answered by architecture at this resolution, so I would like to try to get the 
most out of these datasets I can.

Best wishes,
Hauke



Von: Mark van Raaij [mjvanra...@cnb.csic.es]
Gesendet: Donnerstag, 27. Oktober 2016 21:29
An: Hillen, Hauke
Betreff: Re: [ccp4bb] intensity statistics and twinning

I'd say intensity statistics at this resolution at not reliable and your 
crystal are most likely not twinned.
Unless you think you can answer any interesting biological question at this 
resolution, I'd forget about these datasets and spend all my efforts at getting 
better diffracting ones. Even if this means going back to cloning or working on 
a different species...although lysine methylation, limited proteolysis etc. 
might also be tried if you haven't done so already.
A slightly different crystal contact might make the difference and yield much 
better diffraction.

Mark J van Raaij
CNB-CSIC
www.cnb.csic.es/~mjvanraaij

On 27 Oct 2016 21:11, "Hillen, Hauke"  wrote:
Dear ccp4 community,

I am currently working on some low resolution datasets (around 4.5A). The space 
group seems to be P21, as suggested by XDS and pointless. I have collected many 
datasets of these crystals, both native as well as SeMet-labeled. Using MR-SAD 
I have been able to obtain a clearly interpretable electron density map for all 
features I expect and heavy atom sites that make sense for both the model used 
in MR and the yet unmodeled components. So far, so good.

While routinely analyzing my datasets with Phenix Xtriage, I have noticed that 
the intensity statistics for all of these datasets look unusual. In fact, 
Xtriage complains about this with the message: „The intensity statistics look 
unusual, but twinning is not indicated or possible in the given space group“ 
when processed in P21.
The occurence of this message depends somewhat on the typ of input file I use 
for the same dataset as well as the input parameters (high resolution cut-off). 
If I use XDSCONV to convert the intensities to amplitudes for phenix, this 
message appears. If I use the output of XSCALE directly as intensities, this 
message does not appear, yet the actual statistics are somewhat similar. I have 
attached the log file output for four scenarios at the end of this message (P21 
intensities, P21 amplitudes, P1 intensities, P1 amplitudes).
These results got me questioning whether the true space group is really P21, or 
whether it could be that it is P1 with some twinning issue. Since the Xtriage 
output regarding the „normality“ of the intensity statistics varies upon the 
input format, I assume that this case may be somewhat borderline. Since I have 
very little experience both with low-resolution crystals as well as with 
twinning, I am a bit unsure how to proceed with this data.
How can I distinguish between a partially twinned P1 crystal and an untwinned 
P21 crystal? It is my impression from previous discussions here that 
distinguishing twinned from untwinned data simply by comparing refinement 
results with and without twin laws is not always conclusive, as the R-factors 
are not directly comparable. If the crystal is truly P21, could these issues 
arise from intensity to amplitude conversion problems? (Xtriage also suggests 
this as a possibility) If so, can these be overcome? Or could the deviation 
from ideal intensities simply originate from the low quality (= resolution) of 
the data and are within the range of tolerance for such a dataset? Could this 
be some type of pseudosymmetry issue? And finally, what

I would be very grateful for any advice on how to proceed with these data!


Kind regards,
Hauke



Processed as P21, intensity input:

=== Diagnostic tests for twinning and pseudosymmetry ==

Using data between 10.00 to 3.50 Angstrom.

--Patterson analyses--

Largest Patterson peak with length larger than 15 Angstrom:
Frac. coord.  :0.1640.000   -0.021
Distance to origin:   17.720
Height relative to origin :3.072 %
p_value(height)   :1.000e+00

Explanation
The p-value, the probability that a peak of the specified height or larger
is found in a Patterson function of a macromolecule that does not have any
translational pseudo-symmetry, is equal to 1.000e+00.  p_values smaller than
0.05 might indicate weak translational pseudo symmetry, or the self vector of
a large anomalous scatterer such as Hg, whereas values smaller than 1e-3 are
a very strong indication for the presence of translational pseudo symmetry.


 --Wilson ratio and moments--

Acentric reflections:


  /^2:1.935   (untwinned: 2.000; perfect twin 1.500)
  ^2/:0.805   (untwinned: 0.785;

Re: [ccp4bb] intensity statistics and twinning

2016-10-27 Thread Keller, Jacob 
It would be helpful to know what your current R values are in modelling, and 
also the merging statistics. It looks like you might have a twinned p1 crystal.

JPK

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Hillen, 
Hauke
Sent: Thursday, October 27, 2016 3:11 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] intensity statistics and twinning

Dear ccp4 community,

I am currently working on some low resolution datasets (around 4.5A). The space 
group seems to be P21, as suggested by XDS and pointless. I have collected many 
datasets of these crystals, both native as well as SeMet-labeled. Using MR-SAD 
I have been able to obtain a clearly interpretable electron density map for all 
features I expect and heavy atom sites that make sense for both the model used 
in MR and the yet unmodeled components. So far, so good.

While routinely analyzing my datasets with Phenix Xtriage, I have noticed that 
the intensity statistics for all of these datasets look unusual. In fact, 
Xtriage complains about this with the message: „The intensity statistics look 
unusual, but twinning is not indicated or possible in the given space group“ 
when processed in P21.
The occurence of this message depends somewhat on the typ of input file I use 
for the same dataset as well as the input parameters (high resolution cut-off). 
If I use XDSCONV to convert the intensities to amplitudes for phenix, this 
message appears. If I use the output of XSCALE directly as intensities, this 
message does not appear, yet the actual statistics are somewhat similar. I have 
attached the log file output for four scenarios at the end of this message (P21 
intensities, P21 amplitudes, P1 intensities, P1 amplitudes).
These results got me questioning whether the true space group is really P21, or 
whether it could be that it is P1 with some twinning issue. Since the Xtriage 
output regarding the „normality“ of the intensity statistics varies upon the 
input format, I assume that this case may be somewhat borderline. Since I have 
very little experience both with low-resolution crystals as well as with 
twinning, I am a bit unsure how to proceed with this data.
How can I distinguish between a partially twinned P1 crystal and an untwinned 
P21 crystal? It is my impression from previous discussions here that 
distinguishing twinned from untwinned data simply by comparing refinement 
results with and without twin laws is not always conclusive, as the R-factors 
are not directly comparable. If the crystal is truly P21, could these issues 
arise from intensity to amplitude conversion problems? (Xtriage also suggests 
this as a possibility) If so, can these be overcome? Or could the deviation 
from ideal intensities simply originate from the low quality (= resolution) of 
the data and are within the range of tolerance for such a dataset? Could this 
be some type of pseudosymmetry issue? And finally, what

I would be very grateful for any advice on how to proceed with these data!


Kind regards,
Hauke



Processed as P21, intensity input:

=== Diagnostic tests for twinning and pseudosymmetry ==

Using data between 10.00 to 3.50 Angstrom.

--Patterson analyses--

Largest Patterson peak with length larger than 15 Angstrom:
Frac. coord.  :0.1640.000   -0.021
Distance to origin:   17.720
Height relative to origin :3.072 %
p_value(height)   :1.000e+00

Explanation
The p-value, the probability that a peak of the specified height or larger
is found in a Patterson function of a macromolecule that does not have any
translational pseudo-symmetry, is equal to 1.000e+00.  p_values smaller than
0.05 might indicate weak translational pseudo symmetry, or the self vector of
a large anomalous scatterer such as Hg, whereas values smaller than 1e-3 are
a very strong indication for the presence of translational pseudo symmetry.


 --Wilson ratio and moments--

Acentric reflections:


  /^2:1.935   (untwinned: 2.000; perfect twin 1.500)
  ^2/:0.805   (untwinned: 0.785; perfect twin 0.885)
  <|E^2 - 1|>:0.696   (untwinned: 0.736; perfect twin 0.541)

Centric reflections:


  /^2:2.431   (untwinned: 3.000; perfect twin 2.000)
  ^2/:0.733   (untwinned: 0.637; perfect twin 0.785)
  <|E^2 - 1|>:0.812   (untwinned: 0.968; perfect twin 0.736)


  --NZ test for twinning and TNCS--


The NZ test is diagnostic for both twinning and translational NCS.  Note
however that if both are present, the effects may cancel each other out,
therefore the results of the Patterson analysis and L-test also need to be
considered.


 Maximum deviation acentric  :  0.028
 Maximum deviation centric   :  0.103

 _acentric  : -0.009
 _centric   : -0.061


 --L test for acentric data--

Using difference

[ccp4bb] intensity statistics and twinning

2016-10-27 Thread Hillen, Hauke 
Dear ccp4 community,

I am currently working on some low resolution datasets (around 4.5A). The space 
group seems to be P21, as suggested by XDS and pointless. I have collected many 
datasets of these crystals, both native as well as SeMet-labeled. Using MR-SAD 
I have been able to obtain a clearly interpretable electron density map for all 
features I expect and heavy atom sites that make sense for both the model used 
in MR and the yet unmodeled components. So far, so good.

While routinely analyzing my datasets with Phenix Xtriage, I have noticed that 
the intensity statistics for all of these datasets look unusual. In fact, 
Xtriage complains about this with the message: „The intensity statistics look 
unusual, but twinning is not indicated or possible in the given space group“ 
when processed in P21.
The occurence of this message depends somewhat on the typ of input file I use 
for the same dataset as well as the input parameters (high resolution cut-off). 
If I use XDSCONV to convert the intensities to amplitudes for phenix, this 
message appears. If I use the output of XSCALE directly as intensities, this 
message does not appear, yet the actual statistics are somewhat similar. I have 
attached the log file output for four scenarios at the end of this message (P21 
intensities, P21 amplitudes, P1 intensities, P1 amplitudes).
These results got me questioning whether the true space group is really P21, or 
whether it could be that it is P1 with some twinning issue. Since the Xtriage 
output regarding the „normality“ of the intensity statistics varies upon the 
input format, I assume that this case may be somewhat borderline. Since I have 
very little experience both with low-resolution crystals as well as with 
twinning, I am a bit unsure how to proceed with this data.
How can I distinguish between a partially twinned P1 crystal and an untwinned 
P21 crystal? It is my impression from previous discussions here that 
distinguishing twinned from untwinned data simply by comparing refinement 
results with and without twin laws is not always conclusive, as the R-factors 
are not directly comparable. If the crystal is truly P21, could these issues 
arise from intensity to amplitude conversion problems? (Xtriage also suggests 
this as a possibility) If so, can these be overcome? Or could the deviation 
from ideal intensities simply originate from the low quality (= resolution) of 
the data and are within the range of tolerance for such a dataset? Could this 
be some type of pseudosymmetry issue? And finally, what

I would be very grateful for any advice on how to proceed with these data!


Kind regards,
Hauke



Processed as P21, intensity input:

=== Diagnostic tests for twinning and pseudosymmetry ==

Using data between 10.00 to 3.50 Angstrom.

--Patterson analyses--

Largest Patterson peak with length larger than 15 Angstrom:
Frac. coord.  :0.1640.000   -0.021
Distance to origin:   17.720
Height relative to origin :3.072 %
p_value(height)   :1.000e+00

Explanation
The p-value, the probability that a peak of the specified height or larger
is found in a Patterson function of a macromolecule that does not have any
translational pseudo-symmetry, is equal to 1.000e+00.  p_values smaller than
0.05 might indicate weak translational pseudo symmetry, or the self vector of
a large anomalous scatterer such as Hg, whereas values smaller than 1e-3 are
a very strong indication for the presence of translational pseudo symmetry.


 --Wilson ratio and moments--

Acentric reflections:


  /^2:1.935   (untwinned: 2.000; perfect twin 1.500)
  ^2/:0.805   (untwinned: 0.785; perfect twin 0.885)
  <|E^2 - 1|>:0.696   (untwinned: 0.736; perfect twin 0.541)

Centric reflections:


  /^2:2.431   (untwinned: 3.000; perfect twin 2.000)
  ^2/:0.733   (untwinned: 0.637; perfect twin 0.785)
  <|E^2 - 1|>:0.812   (untwinned: 0.968; perfect twin 0.736)


  --NZ test for twinning and TNCS--


The NZ test is diagnostic for both twinning and translational NCS.  Note
however that if both are present, the effects may cancel each other out,
therefore the results of the Patterson analysis and L-test also need to be
considered.


 Maximum deviation acentric  :  0.028
 Maximum deviation centric   :  0.103

 _acentric  : -0.009
 _centric   : -0.061


 --L test for acentric data--

Using difference vectors (dh,dk,dl) of the form:
   (2hp, 2kp, 2lp)
where hp, kp, and lp are random signed integers such that
   2 <= |dh| + |dk| + |dl| <= 8
 Mean |L|   :0.471  (untwinned: 0.500; perfect twin: 0.375)
 Mean  L^2  :0.301  (untwinned: 0.333; perfect twin: 0.200)

The distribution of |L| values indicates a twin fraction of
0.00. Note that this estimate is not as reliable

Re: [ccp4bb] Good 3D Monitor for Molecular Modelling

2016-10-27 Thread Folmer Fredslund 

Hi Matt,

Have you tried looking at these pages:
http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Stereo
https://pymolwiki.org/index.php/Stereo_3D_Display_Options

HTH,
Folmer Fredslund

On 2016-10-27 17:20, Matthew Graf wrote:

Hello All,
 I am looking for suggestions on a good, but not too costly, 3D 
monitor for visualizing pdb structures and looking at outputs of 
modelling programs. I am not personally a structural biologist, but am 
on the hunt for someone who is. All help appreciated.


Kind regards,
Matt

Re: [ccp4bb] Good 3D Monitor for Molecular Modelling

2016-10-27 Thread Gert Vriend 

Hai Matt,

If you are not interested in hard-core crystallography stuff like 
interpreting electron-density maps or couplings to Coot or Refmac, then 
I can certainly recommend that you look at Yasara. We use it for 15 
years already for modelling and many different visualizations (and much 
more). I am especially happy with the fact that my entire WHAT IF 
software is included in Yasara. Yasara is one of the best modelling 
softwares available (Proteins. 2009;77 Suppl 9:114-22 
). Yasara is commercial, 
but very cheap, especially for academics. There is a limited version 
that is fully free of cost for everybody; called Yasara_view it does 
just enough to be very useful for education purposes. Yasara comes fully 
maintained and provides its customers a well-working help-desk.


(I do not benefit from Yasara sales...).

Look at www.yasara.org

Greetings

Gert


On 27-10-2016 17:20, Matthew Graf wrote:

Hello All,
 I am looking for suggestions on a good, but not too costly, 3D 
monitor for visualizing pdb structures and looking at outputs of 
modelling programs. I am not personally a structural biologist, but am 
on the hunt for someone who is. All help appreciated.


Kind regards,
Matt

[ccp4bb] GUP deadline approaching for APS Beamtime at NE-CAT

2016-10-27 Thread Salbego, Cyndi 
NE-CAT is accepting GUP proposals for the 2017-1 run cycle.  Please choose 
24-ID-C or 24-ID-E as your first choice to be scheduled with NE-CAT!


The 24-ID-C beamline can deliver X-rays in the range of 6 to 21 keV or ~2.1 to 
0.5 Å. This covers most of the popular elemental edges for phasing. This wide 
energy-range also makes the beamline well suited for ultra high-resolution data 
collection and soft X-ray sulfur SAD phasing. The beamline is equipped with an 
optional kappa goniometer for optimal alignment of crystals. A Pixel Array 
Detector (PAD), Pilatus-6MF, installed on the 24-ID-C beamline helps measure 
very weak Bragg reflection intensities due to its noise-less readout technology 
and also provides a very fast data collection capability in shutter-less data 
collection mode.

The 24-ID-E beamline is a fixed energy microdiffraction beamline delivering 
X-rays at 12.66 keV, optimized for Se-SAD experiments. It is equipped with a 
CCD-based ADSC Quantum 315 detector.

Both beamlines are equipped with state-of-the-art instrumentation to handle 
advanced data collection methods. MD2 microdiffractometers installed at both 
beamlines provide very clean beams from 5 microns to 100 microns in diameter 
and have exceptional sample visualization systems capable of visualizing 
micron-sized crystals with extreme clarity.

Deadline Friday, October 28, 2016 for:
   - New General User Proposals (GUPs)
   - New Beam Time Requests for APS run 2017-1  (1/31/2017 - 4/24/2017) on 
existing active proposals
   - Partner user proposals (PUPs)
   - CAT Member Proposals
   - APS Beamline Staff Proposals
   - CAT Beamline Staff Proposals

The GUP system (https://beam.aps.anl.gov/pls/apsweb/gup0005.start_page)  will 
accept proposals and beam time requests until 11:59 pm (Chicago time) on 
October 28, 2016. However, User Office support will not be available after 5:00 
pm that day. If you feel you may need help during the submission process, 
please create your proposal as early as possible.

For questions about the GUP system or the proposal submission process, please 
contact gu_prog...@aps.anl.gov.
For guidance on the Proposal System, see 
https://www1.aps.anl.gov/Users-Information/About-Proposals/Concepts-Definitions-and-Help.
For general inquiries, please feel free to contact the User Office 
(630-252-9090, apsu...@aps.anl.gov)


Cyndi Salbego
Administrator, NE-CAT
630.252.0689

[ccp4bb] Good 3D Monitor for Molecular Modelling

2016-10-27 Thread Matthew Graf 
Hello All, I am looking for suggestions on a good, but not too costly, 3D monitor for visualizing pdb structures and looking at outputs of modelling programs. I am not personally a structural biologist, but am on the hunt for someone who is. All help appreciated.Kind regards,Matt

[ccp4bb] Postdoctoral position in membrane protein structural biology

2016-10-27 Thread Ieva Vasiliauskaite 
Labex Epigenmed Postdoctoral Scientist -Membrane Protein Structural Biology- 
Montpellier, France 



A two years post-doctoral position, funded by the Labex Epigenmed 
(https://www.epigenmed.fr/index.php/accueil/labex-overview), is available in 
the Granier lab at the “Institut de Génomique Fonctionnelle” (UMR 5203 CNRS, 
U1191 INSERM, Montpellier 
University,http://www.igf.cnrs.fr/granier/?page_id=57=en).

The position will be opened, from January 1st 2017, to study the structural 
pharmacology of a viral G-protein coupled receptor (vGPCR) involved in 
tumorigenesis. The work will involve protein biochemistry, biophysics and x-ray 
crystallography. The aim is to understand the vGPCR signal transduction 
mechanisms at the molecular level to enable the rational design of 
vGPCR-targeted antiviral drugs.

Candidates should have a strong background in protein biochemistry with the 
ability to characterize protein expression and purification from a large 
variety of systems. Candidates should also have a solid knowledge of structural 
biology methods (crystallography, electron microscopy, NMR or any combination 
thereof), as well as an excellent publication record for his/her career stage.

For more informations and to apply please contact Dr Sébastien GRANIER and Dr 
Cédric Leyrat

sebastien.gran...@igf.cnrs.fr ; cedric.ley...@igf.cnrs.fr

Interested candidates should forward a Curriculum Vitae (CV in english), and 
two or three letters of reference or e-mail contacts.

Re: [ccp4bb] New version SHELXL 2016/6 and PDB2INS

2016-10-27 Thread Robert Esnouf 

Dear Phil,

The message indeed relates to picking up the system libc which is too old for 
the declared dependency in the make scripts. RedHat/CentOS/ScientficLinux are 
all based on 2.x kernels and upgrading on that path is unlikely to satisfy the 
dependency.

It seems there are three ways around this:

1) Get the version compiled with the lower libc requirement (which begs the 
question why have the newer one? It was probably just picking up the default)

2) Install a second libc that is newer and privately link it. I don't recommend 
this as it is long and involved

3) Look at the CERN devtoolset features. This mimics a newer system by 
statically linking in the required patches to allow you then to link against 
the older system library. This is the route we use with few problems.

There are many reasons to retain older versions of operating systems and 
kernels.

Regards,
Robert

--

Dr. Robert Esnouf,

University Research Lecturer,
Head of Research Computing Core,
NDM Research Computing Strategy Officer

Room 10/028, Wellcome Trust Centre for Human Genetics,
Old Road Campus, Roosevelt Drive, Oxford OX3 7BN, UK

Email: rob...@strubi.ox.ac.uk / rob...@well.ox.ac.uk
Tel:   (+44) - 1865 - 287783


 Original message 
>Date: Wed, 26 Oct 2016 17:46:15 +0200
>From: CCP4 bulletin board  (on behalf of George 
>Sheldrick )
>Subject: Re: [ccp4bb] New version SHELXL 2016/6 and PDB2INS  
>To: CCP4BB@JISCMAIL.AC.UK
>
>Dear Kay,
>
>Exactly. That is why we provided two Linux versions (called pdb2ins and 
>pdb2ins_oldlinux) on the SHELX server.
>So far two versions seem to be enough and for Macs and Windows only one 
>version seems to be required. If
>anyone finds this to be insufficient, please let Anna know giving 
>details of which OS or Linux distribution you
>are using.
>
>At the moment we are only providing 64-bit versions of pdb2ins and there 
>have been no complaints about that.
>This raises the question of whether I am wasting my time providing both 
>32- and 64-bit versions of all the SHELX
>programs?!
>
>Best wishes, George
>CC Anna
>
>On 10/26/2016 05:12 PM, Kay Diederichs wrote:
>> Hi Phil,
>>
>> the error message occurs because your glibc is too old for this binary. The 
>> glibc cannot easily be updated,  it is tied to the distribution, in your 
>> case RHEL6. A newer kernel does not change this, nor would an update to RHEL 
>> 6.8
>> This is why distributed Linux software should be built on dated 
>> distributions.
>>
>> Best,
>>
>> Kay
>>
>> On Wed, 26 Oct 2016 12:11:25 +0100, Phil Evans  
>> wrote:
>>
>>> Hi George
>>>
>>> I�m not sure that anyone here is using shelxl but I�ve just updated our 
>>> general 64-bit Linux versions anyway. shell starts OK, but with pdb2ins I 
>>> get a complaint. Do you understand this? (I should probably ask our local 
>>> guys)
>>>
>>> Our system is
>>> Scientific Linux release 6.7 (Carbon)
>>>
>>> ./pdb2ins
>>> ./pdb2ins: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by 
>>> /tmp/_MEIQO85tj/libz.so.1)
>>>
>>> best wishes
>>> Phil
>>>
>>>
 On 25 Oct 2016, at 20:31, George Sheldrick  
 wrote:

 SHELXL may be used to refine both small and macromolecular structures 
 against X-ray or neutron diffraction data, including non-merohedral twins. 
 A new version 2016/6 of SHELXL may now be downloaded from the SHELX 
 server. It has been well tested by about 20 volunteers to whom I am very 
 grateful. A new version of Anna Luebben's program PDB2INS is also 
 available there (for 64 bit systems only). PDB2INS makes the preparation 
 of the .ins and .hkl files to run macromolecular SHELXL refinements much 
 easier. For most structures deposited in the PDB since 2008 these two 
 files can be generated automatically and no changes are needed to run 
 SHELXL.

 George
 -- 
 Prof. George M. Sheldrick FRS
 Dept. Structural Chemistry,
 University of Goettingen,
 Tammannstr. 4,
 D37077 Goettingen, Germany
 Tel. +49-551-39-33021 or -33068
 Fax. +49-551-39-22582


>
>
>-- 
>Prof. George M. Sheldrick FRS
>Dept. Structural Chemistry,
>University of Goettingen,
>Tammannstr. 4,
>D37077 Goettingen, Germany
>Tel. +49-551-39-33021 or -33068
>Fax. +49-551-39-22582

[ccp4bb] Phoenix crystallisation robot

2016-10-27 Thread Inge Van Molle 
Dear all,

We are looking for someone to take over our Art Robins Phoenix crystallisation 
robot, including the base module with 96 syringe head, wash module, nano module 
and humidifier chamber.
The robot was purchased in 2008 and is in perfect condition.

Please contact me for more information.
Price to be discussed.

Kind regards,

Inge




Dr. Inge Van Molle
VIB Structural Biology Research Center
Structural Biology Brussels
Vrije Universiteit Brussel
Building E, Pleinlaan 2, 1050 Brussel, Belgium

Tel 003226291859
Mobile 0032486521278