from:"Philippe BENAS"

Re: [ccp4bb] sftools

2022-04-06 Thread Philippe BENAS

Dear Eleanor,
 I think it would be a good idea to use CAD from the CCP4i GUI: you can 
change/add cell parameters, crystal, wavelength, dataset and project names.

All the best,
Philippe

Philippe BENAS, Ph.D.

ARN UPR 9002 CNRS
IBMC Strasbourg
2, Allée Conrad Roentgen
F-67084 STRASBOURG cedex (Google Maps Code Plus: HQH7+VV 
Strasbourg)+33.3.8841.7109
E-mails: p.be...@ibmc-cnrs.unistra.fr, philippe_be...@yahoo.fr
URLs:  https://ibmc.cnrs.fr/,  https://ibmc.cnrs.fr/laboratoire/arn/

 

Le mardi 5 avril 2022 à 15:47:15 UTC+2, Eleanor Dodson 
<176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> a écrit :  
 
 

Does ANYONE know how to use this useful but ultra-frustrating program??
I have an mtz file which lacks WAVElength AND Dataset name.
I try to follow the sftools documentation, and get an output file which - lacks 
WAVElength AND Dataset name. 

G 

sftools <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
  



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[ccp4bb] Post-doctoral fellow (M/F) in molecular and structural biology (Cryo-EM)

2021-08-13 Thread Philippe BENAS


Posted on behalf of Dr. Franck Martin (CNRS IBMC, Strasbourg, France)

Please reply to f.mar...@ibmc-cnrs.unistra.fr

===
 




URGENT - Recovery Plan Project - Post-doctoral fellow(M/F) in molecular and 
structural biology (Cryo-EM)

 

Mission

You will be working asa post-doctoral researcher in a mixed public/private 
environment. The team'Evolution of translation initiation systems in 
eukaryotes' of the unit'Architecture and Reactivity of RNA' (UPR 9002 of the 
CNRS) of the Institute ofMolecular and Cellular Biology (IBMC) of Strasbourgin 
association with the company Novalix. NovAliX is a 180+ employees societybased 
in Illkirch (near Strasbourg).We offer to the pharmaceutical industry a 
complete range of services spanningbiophysics, biochemistry, structural 
biology, chemistry & drug discovery. Itis specified that this recruitment offer 
is part of the France RecoveryPlan on a research collaboration project with a 
company which will be submittedto the DRARI for validation. The project will 
consist in structurally andfunctionally characterizing macromolecular complexes 
allowing the initiation ofviral RNA of SARS-CoV-2. 

 

Activities

The approaches used will be based on the use ofcell-free translation extracts 
that will allow us to assemble and purifytranslation initiation complexes on 
our model messenger RNAs. The compositionof these complexes will be determined 
by mass spectrometry and their structureby advanced structural approaches.  
Thetechniques used will be: 

 

- Biochemical and molecular biology methods dedicatedto the study of proteins 
and nucleic acids and in particular RNA

- Cryo-EM sample preparation, optimizing samplevitrification conditions.

- Collect and analyse cryo-EM data. 3D reconstruction,structure determination 
and atomic model building.

- Preparation of in vitro cell-free translationextracts

 

The candidate will have to develop his/her projectindependently.  

 

Expectedqualifications and proficiencies

This includes the mastery of biochemical and molecularbiology approaches for 
the purification of ribonucleoprotein complexes. Strongexpertise in structural 
biology (Crystallography/Cryo-Electron Microscopy)especially on macromolecular 
complexes containing the ribosome will beconsidered as a plus. Ideally, the 
candidate should also be able to interpretelectron density maps to establish 
atomic models of ribonucleic complexescontaining the ribosome. The candidate 
must have defended his/her thesis in2019 or 2020. 

 

Environment

The candidate will join a biochemistry and molecularbiology team specialising 
in translation initiation in eukaryotes. Thestructural part of the project will 
be implemented within the company Novalix. TheNovalix cryo-EM platform is 
currently equipped with a Glacios microscopeoutfitted with a phase plate, 
Falcon 3 camera and microED setup. The candidatewill spend 20% of his/her time 
in the public laboratory for the preparation ofsamples and 80% of his/her time 
at Novalix for the structural aspect.

 

More on IBMC: https://ibmc.cnrs.fr/en/

More on Strasbourg:https://www.visitstrasbourg.fr/en/welcome-in-strasbourg/

More on Alsacearea: https://www.visit.alsace/en/

 

Work constrains and professional risks

The project will require the manipulation ofradioactivity and the synthesis of 
RNA. Therefore, the mastery of good laboratory practices will be considered 
aplus.

 

Application

Applications will only be made via the recruitmentwebsite but feel free ton 
contact Dr. Franck Martin for any further detailsincluding application rules.

Application website:

https://emploi.cnrs.fr/Offres/CDD/UPR9002-FRAMAR-006/Default.aspx?lang=EN

 

Salary

Gross salary will be between 2675and 3767 € per month according to working 
experience.

 

Contact information: f.mar...@ibmc-cnrs.unistra.fr


Philippe BENAS, Ph.D.

ARN UPR 9002 CNRS
IBMC Strasbourg
2, Allée Conrad Roentgen
F-67084 STRASBOURG cedex
+33.3.8841.7109
E-mails: p.be...@ibmc-cnrs.unistra.fr, philippe_be...@yahoo.fr
URLs:  https://ibmc.cnrs.fr/,  https://ibmc.cnrs.fr/laboratoire/arn/




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Re: [ccp4bb] (R)MS

2021-05-29 Thread Philippe BENAS

Dear CCP4bbers,

As Zbyszek and some others wrote, the explanation of B factors is linked to the 
mathematical expression of structure factors: the X-ray crystallographer 
primary data are projections of the reciprocal space. And it's probably better 
to keep this primary info in PDB files rather than RMS displacements on one 
hand and to try to make the story short on the other hand: 50 emails on the 
subject seem to be enough, don't they ?

All the best and have a nice weekend,
Philippe

Philippe BENAS, Ph.D.

ARN UPR 9002 CNRS
IBMC Strasbourg
2, Allée Conrad Roentgen
F-67084 STRASBOURG cedex
+33.3.8841.7109
E-mails: p.be...@ibmc-cnrs.unistra.fr, philippe_be...@yahoo.fr
URLs:  https://ibmc.cnrs.fr/,  https://ibmc.cnrs.fr/laboratoire/arn/

Le samedi 29 mai 2021 à 03:12:39 UTC+2, zbyszek  a 
écrit :  

 B-factors are definitely a measure of uncertainty in variance (square) 
units. The crystal lattice has multiple occurrence of the atoms that are 
equivalent by crystal symmetry. They will have the same fractional 
coordinates within the uncertainty of their position relative to the 
crystal lattice orientation definition. B-factors are the measure of 
this uncertainty (variance) in somewhat unusual units (Angstrom squared 
/ (8*pi*pi)). The fact that you can directly measure uncertainty by 
observing the width of the profile of the atomic distribution (shape of 
the uncertainty function) does not negate that this function represents 
uncertainty of atomic position relative to the crystal lattice.

As a comment: uncertainty of the centroid of the uncertainty 
distribution is a second order or recursive uncertainty. As this 
centroid is deposited as atomic coordinates in pdb files, its 
uncertainty is a separate subject from the uncertainty (variation) of 
the atom position in the crystal lattice. Unfortunately theories of 
uncertainty estimates of uncertainty estimates is more complex and for 
this reason crystallographers rarely deal productively with uncertainty 
of the x,y,z coordinates deposited.

A second comment: the B-factor really represents the sum of two 
uncertainties. One is the uncertainty of atom positions in the crystal 
lattice. The second is our experimental uncertainty about the knowledge 
of atom position. The first one has a physical interpretation. The 
second represents our data and analysis, e.g. phasing.

For these reasons, saying that the B-factor represents uncertainty 
estimates is very productive because it is all about uncertainty. 
Independent uncertainties are convolved with each other to produce a 
final uncertainty function. In terms of the width squared of that 
function, it represents the sum of the widths squared of the 
contributors. In fact this observation is behind the Central Limit 
Theorem.

Zbyszek

On 2021-05-28 19:05, James Holton wrote:
> I feel I should point out here that B-factors are NOT a measure of
> uncertainty.  They are a width.  This width itself may be uncertain,
> as may be the position of the center of the peak, but just because
> your peak is broad doesn't mean you don't know where the middle of it
> is.
> 
> As for why leave the mean variation squared?  I expect it is because
> it is supposed to be proportional to temperature. Hence the name
> "temperature factor".
> 
> -James Holton
> MAD Scientist
> 
> On 5/27/2021 11:09 AM, Gergely Katona wrote:
> 
>> Dear Jonathan,
>> 
>> In 1D sd may be intuitive, but in 3D it is not so much. The square
>> root of a symmetric covariance matrix is not universally defined and
>> it is not intuitive to me.
>> 
>> Best wishes,
>> 
>> Gergely
>> 
>> Gergely Katona, Professor, Chairman of the Chemistry Program Council
>> 
>> 
>> Department of Chemistry and Molecular Biology, University of
>> Gothenburg
>> 
>> Box 462, 40530 Göteborg, Sweden
>> 
>> Tel: +46-31-786-3959 / M: +46-70-912-3309 / Fax: +46-31-786-3910
>> 
>> Web: http://katonalab.eu, Email: gergely.kat...@gu.se
>> 
>> From: CCP4 bulletin board  On Behalf Of
>> Hughes, Jonathan
>> Sent: 27 May, 2021 18:53
>> To: CCP4BB@JISCMAIL.AC.UK
>> Subject: [ccp4bb] AW: [ccp4bb] (R)MS
>> 
>> hey!
>> 
>> thank y'all for the informative (and swift!) answers! but, if the B
>> factor (as defined) appears in a mathematical formulation, that
>> doesn't make it an "appropriate" parameter for mobility/uncertainty.
>> wouldn't √B be better, in the same way that, for humans, standard
>> deviation (RMSD) is a more appropriate parameter of variability than
>> variance? or am i missing something?
>> 
>> cheers
>> 
>> j
>> 
>> Von: Ian Tickle 
>> Gesendet: Donnerstag, 27. Mai 2021 18:32
>> An: Hughes, Jonathan 
>> Cc: CCP4BB@JISCMAIL.AC.UK
>&

Re: [ccp4bb] Using SFall for map conversion

2020-05-15 Thread Philippe BENAS

Dear Bernhard,

Is it an old map ?

Back to the old VAX times I had to dump CCP4 maps to ascii map files, then swap 
bytes from VAX-DOS to Unix before converting them again to a CCP4 map format (I 
think I was using mapman from USF) on a Unix workstation and be able to read 
them in Frodo-Strasbourg or O.

At least you could give it a shot and the ascii map file would help you 
figuring out the issue by a visual inspection of the header and sections.

All the best,
Philippe

Philippe BENAS, Ph.D.

ARN UPR 9002 CNRS
IBMC Strasbourg
2, Allée Konrad Röntgen
F-67084 STRASBOURG cedex
+33.3.8841.7109
E-mails: p.be...@ibmc-cnrs.unistra.fr, philippe_be...@yahoo.fr
URLs:   http://www-ibmc.u-strasbg.fr/ , http://www-ibmc.u-strasbg.fr/spip-arn/

 

Le jeudi 14 mai 2020 à 22:45:09 UTC+2, Bernhard Rupp 
 a écrit :  
 
 
Hi Fellows,

  

I am failing on conversion of a ccp4 map to mtz using Sfall

  

I provide as a scale reference a mtz with FP SIGFP and R free

  

All cell constants and SG 20 and map headers seem to agree.

  

But I receive following warning:

  

*** WARNING - your map spacegroup is different to the program default one ***

  

and later

  

>>>>>> CCP4 library signal library_file:Cannot open file (Warning)

    raised in tmpfile() failed, opening normal file instead. <<<<<<

    INPUT X USED AS  X

    INPUT Y USED AS  Z

    INPUT Z USED AS  Y

  

Which then leads to the imho - given above- justified complaint:

  

Check map header agrees with fixed requirements for SFcalc for this spacegroup.

Check Nxyz 180 200 120    180 200 120

  

Check map header agrees with fixed requirements for SFcalc for this  spacegroup.

Check Iuvw   3   2   1  3   1   2



SFALL:    Fatal disagreement between input info and map header

  

How do I fix this ? 

  

In principle all the information is there to do the job…

  

Many thx, BR

--

Bernhard Rupp

Crystallographiae Vindicis Militum Ordo

http://www.hofkristallamt.org/

b...@hofkristallamt.org

+1 925 209 7429

+43 676 571 0536

--

Many plausible ideas vanish 

at the presence of thought

--

  
 

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[ccp4bb] Re : [ccp4bb] Issues with stero in Wincoot

2019-07-03 Thread Philippe BENAS

Hi Ravikumar,

Yes, Indeed I have some feedbacks: Coot doesn't work under Win10. Switch back 
to Win7 under which it will work like a charm.

All the n'est,
Philippe

Philippe BENAS, Ph.D.

ARN UPR 9002 CNRS
IBMC Strasbourg
2, Allée Konrad Röntgen
F-67084 STRASBOURG cedex
+33.3.8841.7109

E-mails: p.be...@ibmc-cnrs.unistra.fr, philippe_be...@yahoo.fr
URLs:   http://www-ibmc.u-strasbg.fr/ , http://www-ibmc.u-strasbg.fr/spip-arn/





En date de : Mar 2.7.19, Reddiravikumar Kumar  a écrit :

 Objet: [ccp4bb] Issues with stero in Wincoot
 À: CCP4BB@JISCMAIL.AC.UK
 Date: Mardi 2 juillet 2019, 19h17
 
 Dear all,
               We are trying to install
 stereo in Wincoot in windows 10 pro, 64 bit computer. We
 have installed nvidia quadro K4000 graphics driver in our
 system. The stereo is working well with Pymol, but keep
 crashing on Wincoot. Can you anyone experienced the same
 issue and how can I fix this issue?
 Thanks,Ravikumar.  
 
 
 
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Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] High Rfree - ice ring

2019-04-09 Thread Philippe BENAS

Dear Sam,

As already pointed out by other CCP4bbers, I think trying to merge 
non-overlapping resolution shells cannot lead to good data. In addition it is 
very straight forward and fast to remove ice-rings during data processing with 
either XDS or imosflm, as also already pointed out. And your I_obs and 
Sig_I_obs will be much more accurate.

HTH,
Philippe

Philippe BENAS, Ph.D.

ARN UPR 9002 CNRS
IBMC Strasbourg
15, rue René Descartes
F-67084 STRASBOURG cedex
+33.3.8841.7109

E-mails: p.be...@ibmc-cnrs.unistra.fr, philippe_be...@yahoo.fr
URLs:   http://www-ibmc.u-strasbg.fr/ , http://www-ibmc.u-strasbg.fr/spip-arn/





En date de : Mar 9.4.19, Sam Tang  a écrit :

 Objet: Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] High Rfree - ice ring
 À: CCP4BB@JISCMAIL.AC.UK
 Date: Mardi 9 avril 2019, 13h27
 
 Hello again.
 I
 agree the get-around strategy we took is not a good practice
 at all. 
 For our
 initial imosflm run we actually turned on 'exclude ice
 ring' button. The following was reported in the
 log:
 
 ICE RING SUMMARY:
  reso  ice_ring  mean_I
 mean_Sigma Estimated_I   Ratio Zscore Completeness
 Ave_Completeness 3.88   yes    39933.04   
 3690.30     1398.21   28.56  10.44        0.48 
     nan 3.67   yes    44809.76   
 4257.56      778.04   57.59  10.34        0.58 
     nan 3.43   yes     7270.25   
  885.61      532.75   13.65   7.61        0.54 
     nan 2.66   yes     2070.19   
  488.66      156.09   13.26   3.92        0.46 
     nan
 
 A total of >2200 reflections were
 already omited. 
 The
 range of poor R seems to correlate to the range 3.8-3.6A. I
 am thus also thinking there may be other issues (not visibly
 identified on images) other than ice rings.
 We actually first merged the two
 datasets (high and low resolutions) in pointless before
 presenting to aimless.
 We are trying over other different
 strategies to see if we can get a better tackle. Will report
 again soon.
 
 Sam
 
 On Tue, 9 Apr 2019
 at 18:47, Johan Turkenburg <2a539df422fe-dmarc-requ...@jiscmail.ac.uk>
 wrote:
 
 I agree with Harry that an ice ring should
 never require you to process the data in two separate runs,
 and hopefully this does not become a standard
 approach..
 How
 did you present those data to aimless so it could scale the
 two datasets that have no overlap at all?
 Johan
 On Tue, 9 Apr 2019
 at 10:07, Harry Powell <193323b1e616-dmarc-requ...@jiscmail.ac.uk>
 wrote:
 Hi Sam
 Did you use the ice-ring exclusion
 option in iMosflm (a button that has an image like a
 snowflake)? It should exclude data in _narrow_ resolution
 rings (substantially less than 0.2Å!) around the ice rings,
 and can be set for any combination of indexing, refinement
 and integration. There should not be any need to process the
 data twice, once for the low resolution data and once for
 the high.
 
 Harry
 --
 Dr Harry
 Powell
 
 
 
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 the following link:
 
 https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
 
 
 
 
 On 8 Apr 2019, at 19:50, Sam Tang
 wrote:
 Hello everyone
 Thanks a lot for your input and
 advices. To report on how we tackled the issue
 - 
 (1) We used
 imosflm to integrate the data.   (2) We
 eventually integrated the data in two resolution ranges, say
 45A-3.5A, and 3.3A-3A, and merge them by Aimless. I must add
 that indeed from the log file for our initial round the
 program had already identified some ice ring
 regions.
 Aimless
 statistics looked fine and we were able to get a MR solution
 which was refined to much better Rf/Rw.
 This is definitely not a smart
 solution because we effectively 'throw away' useful
 data between 3.5A-3.3A, but for the purpose of MR and
 refinement, it seems we have solved (or simply bypassed?)
 the problem.
 Suggestions on XDS/DIALS are
 appreciated. We are actually using this dataset as a test
 set for XDS/DIALS to deal with ice rings. Will further
 report if we've got anything interesting.
 Thanks again!
 Sam
 
 
 
 On Thu, 4 Apr 2019
 at 20:54, Clemens Vonrhein 
 wrote:
 Dear all,
 
 
 
 And if you want to process with XDS: autoPROC [1] will try
 to detect
 
 and exclude ice-rings automatically - if present [2].
 
 
 
 If you know that you have ice-rings you can force it [3] to
 exclude
 
 all known ice-rings ranges - but this might not be the best
 solution
 
 if you have "just" diffuse ice-rings (where the
 special treatment of
 
 background within DIALS might be better). Something to test
 and
 
 compare maybe?
 
 
 
 Cheers
 
 
 
 Clemens
 
 
 
 [1] https://www.globalphasing.com/autoproc/
 
     https://www.globalphasing.com/autoproc/wiki/index.cgi?IceRingHandling
 
 [2] 
https://www.globalphasing.com/autoproc/manual/autoPROC7.html#step1_spotnohkl
 
     https://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Ice_rings
 
 [3] 
https://www.globalphasing.com/autoproc/manual/appendix1.html#SetvarParameter_XdsExcludeIceRingsAutomatica

Re: [ccp4bb] Interesting pattern on a crystallization drop

2019-03-28 Thread Philippe BENAS

Hi Beatriz,
 
Very interesting indeed. Couldn't it be the ghost printing of some mechanical 
part used to make the mould of the crystallization tray ?
All the best,
Philippe

Philippe BENAS, Ph.D.

ARN UPR 9002 CNRS
IBMC Strasbourg
15, rue René Descartes
F-67084 STRASBOURG cedex
+33.3.8841.7109
E-mails: p.be...@ibmc-cnrs.unistra.fr, philippe_be...@yahoo.fr
URLs:   http://www-ibmc.u-strasbg.fr/ , http://www-ibmc.u-strasbg.fr/spip-arn/

 

Le mercredi 27 mars 2019 à 19:54:42 UTC+1, Beatriz Gomes Guimaraes 
 a écrit :  
 
  
Dear all,




I would like to share with you a surprising pattern I found when examining some 
crystallization plates (attached figures).




It is less obvious looking the photos, but apparently the "lines" are formed by 
precipitated protein and there are some "bubbles" with small drops inside.I 
wish they were microcrystals but I do not think this is the case.


I was suprised by the symmetry !




And it is not completely random because for the same condition the difference 
between the two drops are : protein alone ("hexagon") and protein + ligand 
("rhombus")



crystallization condition is:

0.01 M Cobalt(II) chloride hexahydrate

0.1 M Tris pH 8.5

20% w/v Polyvinylpyrrolidone K 15





Have you seen anything similar before?




Thank you for your comments!

Beatriz






--
Beatriz Guimarães
Laboratory of Structural Biology and Protein Engineering
Instituto Carlos Chagas - ICC / FIOCRUZ Paraná
Rua Prof. Algacyr Munhoz Mader, 3775   Bloco C
CIC 81350-010
Curitiba - PR, Brasil
Tel.:+55(41)3316-3225/2104-3438

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Re: [ccp4bb] 3D

2019-03-12 Thread Philippe BENAS

Dear all,

I do agree with Paul: VR is just perspective images that don't give you a 
stereoscopic view and is hence poorer.

This being said it is possible to build a structure in mono:  all you need is 
to have enough and the right projections in the plane...

I started 20 years ago using side by side stereo and as long as my eyes will be 
ok I could always get back at least to this option but it would be a real shame 
to loose hardware stereo...

All the best,
Philippe

Philippe BENAS, Ph.D.

ARN UPR 9002 CNRS
IBMC Strasbourg
15, rue René Descartes
F-67084 STRASBOURG cedex
+33.3.8841.7109

E-mails: p.be...@ibmc-cnrs.unistra.fr, philippe_be...@yahoo.fr
URLs:   http://www-ibmc.u-strasbg.fr/ , http://www-ibmc.u-strasbg.fr/spip-arn/

En date de : Lun 11.3.19, Paul Emsley  a écrit :

 Objet: Re: [ccp4bb] 3D
 À: CCP4BB@JISCMAIL.AC.UK
 Date: Lundi 11 mars 2019, 20h22

 On 11/03/19 15:55, Pedro Matias
 wrote:
 >
 > Reading the
 news piece, I would hardly consider the present-day VR
 > headsets to be "affordable" -
 except perhaps for the PSVR. With the
 >
 added downside that they are single-user.
 >
 > When can we expect a
 CootVR release ?
 >
 >

 VR is not
 really a substitute for stereo I feel (or vice versa).

 CootVR is available from
 github: it's in "beta" at the moment

 https://github.com/hamishtodd1/CVR

 The author of CootVR is Hamish
 Todd. There is a release planned for May
 (2019).

 Regards,

 Paul

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[ccp4bb] Re : [ccp4bb] Can anyone run refmac from the WINDOWS command prompt?

2019-02-13 Thread Philippe BENAS

Hi Kevin,

Since CCP4 v.7 there is an issue with the term Windows. I was used to run any 
CCP4 program from anywhere on my disks with v. 6.x but with v.7x you have to 
move every needed fiies to C:\CCP4\ccp4-7.0 (or something like this): Indeed 
where the shortcut of the CCP4 consol is located.

Some environment variables are not well set. Hum... I have to confess I wanted 
to do that during some spare time. The trouble is I never found spare time 
since the v.7.0 release...

HTH and all the best,
Philippe


Philippe BENAS, Ph.D.

ARN UPR 9002 CNRS
IBMC Strasbourg
15, rue René Descartes
F-67084 STRASBOURG cedex
+33.3.8841.7109

E-mails: p.be...@ibmc-cnrs.unistra.fr, philippe_be...@yahoo.fr
URLs:   http://www-ibmc.u-strasbg.fr/ , http://www-ibmc.u-strasbg.fr/spip-arn/





En date de : Mer 13.2.19, Kevin Cowtan 
<2ba34e97fcaf-dmarc-requ...@jiscmail.ac.uk> a écrit :

 Objet: [ccp4bb] Can anyone run refmac from the WINDOWS command prompt?
 À: CCP4BB@JISCMAIL.AC.UK
 Date: Mercredi 13 février 2019, 12h29
 
 Hi! Can anyone run refmac from the
 WINDOWS command prompt?
 I've been experimenting with
 various combinations of environment variables, but I always
 get an error. The one instance of this error on google is an
 unanswered CCP4BB question.
 Dictionary path has not
 been definedCheck the environment
 variable CLIBD_MONCurrent value of
 CLIBD_MON is
 C:\Apps\CCP4-7\7.0\lib\data\monomersIt should be set to wherever_dict/dic/===> 
Error: Wrong path for the dictionary
 files Refmac:  Wrong path for the dictionary
 files Refmac:  Wrong path for the
 dictionary files
 The directory
 C:\Apps\CCP4-7\7.0\lib\data\monomers
 contains the following:
  Directory of
 C:\Apps\CCP4-7\7.0\lib\data\monomers
 12/02/2019  15:42             
 .12/02/2019  15:42           
   ..12/02/2019  15:38         
     012/02/2019  15:39       
       112/02/2019  15:39     
         212/02/2019  15:39   
           312/02/2019  15:39 
             412/02/2019 
 15:39             
 512/02/2019  15:39           
   612/02/2019  15:39         
     712/02/2019  15:40       
       812/02/2019  15:40     
         912/02/2019  15:40   
           a12/02/2019  15:40 
             b12/02/2019 
 15:40             
 c28/11/2016  21:43             7,640
 COPYING12/02/2019  15:40       
       d28/11/2016  21:43           
  3,553 dnarna_basepairs.txt28/11/2016  21:43 
            3,553
 dnarna_basepairs_2.txt28/11/2016  21:43     
        5,248 dnarna_params.txt12/02/2019 
 15:40             
 e27/04/2018  10:59           105,193
 ener_lib.cif28/11/2016  23:06         
  105,136 ener_one_lib.cif12/02/2019  15:40   
           f12/02/2019  15:40 
             g12/02/2019 
 15:41             
 h12/02/2019  15:41           
   i12/02/2019  15:41         
     j12/02/2019  15:41       
       k12/02/2019  15:41     
         l12/02/2019  15:41   
           list12/02/2019 
 15:41             
 m28/11/2016  21:43         1,372,146
 mon_lib_ind.cif28/11/2016  21:43       
  6,490,087 mon_lib_ind2.cif28/11/2016  23:06 
              120
 mon_lib_one_ind.cif28/11/2016  23:06       
        396 mon_lib_one_ind2.cif12/02/2019 
 15:41             
 n31/08/2018  15:52            35,312
 new_entries.txt31/08/2018  15:52         
   23,685 not_replaced_entries.txt12/02/2019 
 15:41             
 o12/02/2019  15:41           
   p28/11/2016  21:43         2,490,954
 pdb_alt_names.txt28/11/2016  21:43         
    7,794 pdb_v2to3.py12/02/2019  15:41   
           q12/02/2019  15:41 
             r31/08/2018 
 15:52            29,731
 replaced_entries.txt31/08/2018  15:52       
        754 revert_list.txt12/02/2019 
 15:41             
 s12/02/2019  15:42           
   t28/11/2016  21:43               557
 template_link.pdb12/02/2019  15:42   
           u12/02/2019  15:42 
             v12/02/2019 
 15:42             
 w31/08/2018  15:52                24
 windows_reserved_words.txt12/02/2019  15:42   
           x12/02/2019  15:42 
             y12/02/2019 
 15:42              z-- 
 Professor Kevin
 CowtanYork Structural Biology
 Laboratory / Department of Chemistry
 University of York, Heslington, York, YO10 5DD,
 UK
 https://www.york.ac.uk/chemistry/staff/academic/a-c/kcowtan/
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Re: [ccp4bb] 3D Glasses (stereo)

2019-02-08 Thread Philippe BENAS

Hi,
All my Win7 workstations are dual boot Win7/Kubuntu-18.04. All work fine on 
both OS. In particular, Coot, PyMol, Discovery Studio etc work fine in stereo 
using Nvidia Vision 1 and 2 glasses and Asus VG278H monitors with built-in IR 
emitter.
I had a HP Z620 under Win10 for which PenGL stereo was working up to some makor 
update. But since then stereo no longer worked: as soon as Coot was shifting to 
hardware stereo it crashed. I think this was due to Windows restrictions in 
accessing the kernel. I sold this workstations but recently a friend was trying 
to have hardware stereo on a Win10 computer and we observed the same problem 
with Coot.
Nevertheless I read yesterday a paper annoucing that for the its next major 
update in April Win10 will allow to run all 32-bits programs without any 
restriction. So one can hope Coot will be again working in stereo under Win10.
HTH,Philippe
Philippe BENAS, Ph.D.

ARN UPR 9002 CNRS
IBMC Strasbourg
15, rue René Descartes
F-67084 STRASBOURG cedex
+33.3.8841.7109
E-mails: p.be...@ibmc-cnrs.unistra.fr, philippe_be...@yahoo.fr
URLs:   http://www-ibmc.u-strasbg.fr/ , http://www-ibmc.u-strasbg.fr/spip-arn/

 

Le vendredi 8 février 2019 à 12:57:23 UTC+1, Sanaz Asadollahpour 
 a écrit :  
 
 Hi guys,
We have previously used stereo glasses from crystal eyes on a Dell
precision 690 Pc (with 4 processors) on the windows XP. Then we changed
to NIVIDIA 3D vision system which also worked fine for some time. But
now we have several problems working with 3D Vision using windows7.
what experience do you have with viewing stereo e.g. in COOT. We would
like to maintain the stereo system with windows microsoft( no Linux)
for modeling protein structures into electron density. 

information and suggestions on this issue are appreciated.
Best regards,
Sanaz Asadollahpour and Klaus Piontek from Organic Chemistry university
Freiburg in Germany 



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Re: [ccp4bb] 3D stereo and (pymol) Win 10/laptops

2019-02-01 Thread Philippe BENAS

Hi Jan, Pedro, CCP4ers and Cooters,

Sure Pedro, you're right: real 3D, I mean stereo due to differences in the path 
length of the pictures respectively in the left and right eye, haven't made it 
in Europe except in the UK. I think in the States as well Nvidia didn't get the 
expected success. As a result Nvidia stereo glasses are no longer made for 
about 4 years or so, even if you can still find old new ones in some 
specialized stores or second hand goggles on eBay. So the only solution might 
be to find an old Asus GX51 or GX53... And on the contrary to my previous email 
there are not running Intel core CPUs of the 2nd or 3rd generation but the 
first !

Holographic solutions seem to have been abandoned as well. The sickness some 
might suffer from while using stereo glasses does not happen with such products 
and real 3D could have been made more popular by this way. Unfortunately the 
price of holographic solutions made them unaffordable...

As for VR, it is not more than looking at your models using a perspective 
drawing, a long-time available option in many programs. VR just adds a 
perception of depth and the caveat is that your model is no longer orthographic 
but distorted to create the perspective view and hence might eventually lead to 
bad interpretations... For designing a car it might be interesting knowing that 
2D projections will be used for actually building the car. For building a 
crystallographic model it would be probably wiser to use several orthogonal 
views as many of us are doing (a lot of students indeed) or stick to stereo, 
either as side-by-side views or using stereo glasses.

Best,
Philippe

Philippe BENAS, Ph.D.

ARN UPR 9002 CNRS
IBMC Strasbourg
15, rue René Descartes
F-67084 STRASBOURG cedex
+33.3.8841.7109
E-mails: p.be...@ibmc-cnrs.unistra.fr, philippe_be...@yahoo.fr
URLs:   http://www-ibmc.u-strasbg.fr/ , http://www-ibmc.u-strasbg.fr/spip-arn/

   Le vendredi 1 février 2019 à 15:20:01 UTC+1, Pedro Matias 
 a écrit :  
 
  
Hi all,
 
Thanks Philippe, for the comprehensive discussion of the problem.
 
I may also add that about 2 years ago I inquired our local DELL reseller about 
laptops with Quadro cards (for running WinCoot in 3D stereo) because they had 
listed in the US site models that supposedly would work. Sadly, those models 
had been discontinued and replaced by a new series that no longer had a 120Hz 
display. I was unable to test whether stereo would still work with an external 
monitor but that would defeat the mobility purpose anyway.
 
Also, it seems that with the new VR trend, NVIDIA is letting 3D vision fade 
away - am I wrong?
 
 
Best, 
 
 
Pedro
 
 Às 13:20 de 01/02/2019, Philippe BENAS escreveu:
  
  Hi Georg,
 
 My first answer would be it's a bad idea for several reasons:
  
 1. PRICE/PERF
 Laptops are always much more expensive than worstations for a given 
performance and often you cannot reach the performances of a desktop or tower 
computer with a laptop.   
 2. QUADRO + 120 Hz DISPLAY
 Then if you want to use hardware stereo you will not only need a Quadro GPU as 
Pedro mentioned but also a screen with a vertical frequency of 120 Hz or higher 
and an external IR emitter. If you install Win7 it might work. If you install 
Win10 it won't with the current version of Coot (PyMol, Discovery Studio will). 
If you want to run linux as OS then you will need in addition a stereo VESA 
3-pin connector (between the graphic and the IR emitter) which I think doesn't 
exists for laptop graphic cards.  
  Using an external monitor won't make it either unless your laptop has a DVI-D 
output (very few I think were manufactured and are no longer) or a Display Port 
1.3 or 1.4 and your monitor also has a DVI-D or a DP 1.3 or 1.4 input.
  Using a Thunderbolt 3 (TB3) output will not help either because I don't think 
you will any monitor with a Thunderbolt input running at a vertical frequency 
of 120 Hz. Then even 3D Club (http://www.club-3d.com) does not make a 
Thunderbolt to DVI-D active adaptor with a refresh rate higher than 60 Hz, i.e. 
you cannot use an external monitor with a DVI-D input.
 
  So it not easy to have Quadro based hardware stereo on a laptop (I tried at 
some point to use the OpenGL drivers for GeForce that were available for 
developers and supposed to allow OpenGL 3D but without success).
 You might find old Asus or Acer laptops (intel core of the 2nd or 3rd 
generation) with screens running at 120 Hz and  built-in IR emitter but they 
are using GeForce graphic cards. At this point you might try to replace the 
GeForce by a mobile Quadro (if it can fit into the PCIe slot).
  
 Alternatively to double requirement of a Quadro and a 120 Hz monitor, you 
could make use of the WiFi mini PCIe port of any laptop and use an external 
Quadro GPU that you will have to  supply with electrical power (see 
https://www.youtube.com/watch?v=6CwuDbXsQck (FR) or 
https://www.youtube.com/watch?v=Dq0ZE8wmv-Q (EN) ) or use some commercial eGPU 
solution

Re: [ccp4bb] 3D stereo and (pymol) Win 10

2019-02-01 Thread Philippe BENAS

Hi Georg,

My first answer would be it's a bad idea for several reasons:

1. PRICE/PERF
Laptops are always much more expensive than worstations for a given performance
and often you cannot reach the performances of a desktop or tower computer with
a laptop.
2. QUADRO + 120 Hz DISPLAY
Then if you want to use hardware stereo you will not only need a Quadro GPU as
Pedro mentioned but also a screen with a vertical frequency of 120 Hz or higher
and an external IR emitter. If you install Win7 it might work. If you install
Win10 it won't with the current version of Coot (PyMol, Discovery Studio will).
If you want to run linux as OS then you will need in addition a stereo VESA
3-pin connector (between the graphic and the IR emitter) which I think doesn't
exists for laptop graphic cards.
Using an external monitor won't make it either unless your laptop has a DVI-D
output (very few I think were manufactured and are no longer) or a Display Port
1.3 or 1.4 and your monitor also has a DVI-D or a DP 1.3 or 1.4 input.
Using a Thunderbolt 3 (TB3) output will not help either because I don't think
you will any monitor with a Thunderbolt input running at a vertical frequency
of 120 Hz. Then even 3D Club (http://www.club-3d.com) does not make a
Thunderbolt to DVI-D active adaptor with a refresh rate higher than 60 Hz, i.e.
you cannot use an external monitor with a DVI-D input.

So it not easy to have Quadro based hardware stereo on a laptop (I tried at
some point to use the OpenGL drivers for GeForce that were available for
developers and supposed to allow OpenGL 3D but without success).
You might find old Asus or Acer laptops (intel core of the 2nd or 3rd
generation) with screens running at 120 Hz and built-in IR emitter but they are
using GeForce graphic cards. At this point you might try to replace the GeForce
by a mobile Quadro (if it can fit into the PCIe slot).

Alternatively to double requirement of a Quadro and a 120 Hz monitor, you could
make use of the WiFi mini PCIe port of any laptop and use an external Quadro
GPU that you will have to supply with electrical power (see
https://www.youtube.com/watch?v=6CwuDbXsQck (FR) or
https://www.youtube.com/watch?v=Dq0ZE8wmv-Q (EN) ) or use some commercial eGPU
solution (often using the TB3 port; e.g.
https://www.pcworld.com/article/2984716/laptop-computers/how-to-transform-your-laptop-into-a-gaming-powerhouse-with-an-external-graphics-card.html
) but with their restrictions (laptop compatibility list and I'm not sure it
will work under linux).I haven't tested these solutions as the benefit in
portability of a laptop ins then lost.

And overall I think you're better of buying any cheap second hand workstation,
Quadro graphic card and a 27" monitor @ 120 Hz.

Best regards,
Philippe
Philippe BENAS, Ph.D.

ARN UPR 9002 CNRS
IBMC Strasbourg
15, rue René Descartes
F-67084 STRASBOURG cedex
+33.3.8841.7109
E-mails: p.be...@ibmc-cnrs.unistra.fr, philippe_be...@yahoo.fr
URLs: http://www-ibmc.u-strasbg.fr/ , http://www-ibmc.u-strasbg.fr/spip-arn/

Le vendredi 1 février 2019 à 10:11:48 UTC+1, Pedro Matias
a écrit :

Hi,

You need a laptop with a NVIDIA Quadro card that supports quadbuffered 3D
stereo under Linux. I found this page

https://www.nvidia.com/en-us/design-visualization/quadro-for-mobile-workstations/
that may help find a laptop with the needed specs.
For example, you can find info about a DELL laptop with a QUADRO P4200 at

https://www.dell.com/en-us/work/shop/dell-laptops-and-notebooks/precision-7730-mobile-workstation/spd/precision-17-7730-laptop?view=configurations

but you need to make sure the display supports 120/144 Hz refresh rate.

Best regards,

Pedro

Às 22:52 de 31/01/2019, Georg Mlynek escreveu:

Dear all, I am considering to buy a new laptop and would like to install the
latest ubuntu version and have 3D glasses. Following the discussions in the
lasts years, this issue seems to be not trivial. Which setup of laptop and 3D
glasses will work plug and play?

And what about VR. When is coot and pymol VR ready?

Best regards, Georg.

On 31.01.19 10:54, Philippe BENAS wrote:

Dear all,
I had an HP Z620 that was dual boot Kubuntu 14.03 and Win 10. Coot was
working in stereo mode without any problem for a year or so. But after one of
their major updates Coot crashed as soon as the built-in IR emitter of my Asus
VG278H turned on, as described Pedro and Jan.
My personal guess is that the new Win 10 kernels no longer accept some direct
exchanges from programs to hardware parts, probably for safety issues. So I
came to the same conclusion as Pedro: stick to Win 7 if you want to run Coot
under Windows or use a linux distribution or dual boot workstation.
Nevertheless PyMol was just working fine in stereo mode under Win 10. At
least until last september when I sold my Z620 for a Z820 (Kubuntu 18.04/Win7).
May be PyMol developers at Schrödinger could give their tips and t

Re: [ccp4bb] 3D stereo and (pymol) Win 10

2019-01-31 Thread Philippe BENAS

Dear all,
I had an HP Z620 that was dual boot Kubuntu 14.03 and Win 10. Coot was working
in stereo mode without any problem for a year or so. But after one of their
major updates Coot crashed as soon as the built-in IR emitter of my Asus VG278H
turned on, as described Pedro and Jan.
My personal guess is that the new Win 10 kernels no longer accept some direct
exchanges from programs to hardware parts, probably for safety issues. So I
came to the same conclusion as Pedro: stick to Win 7 if you want to run Coot
under Windows or use a linux distribution or dual boot workstation.
Nevertheless PyMol was just working fine in stereo mode under Win 10. At least
until last september when I sold my Z620 for a Z820 (Kubuntu 18.04/Win7). May
be PyMol developers at Schrödinger could give their tips and tricks to Bernard
Lohkamp to whom I send my warmest aknowledgments for porting Coot under Windows.

Best regards,
Philippe

Philippe BENAS, Ph.D.

Le jeudi 31 janvier 2019 à 10:18:42 UTC+1, Pedro Matias
a écrit :

Hi all,

The problem with COOT stereo and Windows 10 is that the COOT binary is not
compatible with the newer OpenGL drivers or somesuch in Windows 10. So, COOT
runs fine in Windows 10 but crashes if you enter hardware stereo mode. However,
PyMOL works fine in stereo in Windows 10.

According to Bernhard Lohkamp, the Windows COOT developer, this problem has not
yet been fixed because he has no access to a Windows 10 PC.

Therefore, stick to Windows 7 if you want to run COOT stereo on a cheap Quadro
card.

Best regards,

Pedro

Às 04:38 de 31/01/2019, Jim Fairman escreveu:

I had a Windows 7 machine that would run Quad buffered stereo back around
2009, haven't had a chance to try with Windows 10.
On Wed, Jan 30, 2019, 02:03 Jan Stransky wrote:

Dear all,

I started looking into the never ending story of stereo in crystallography...
As with our standardized linux setup we probably are not willing to move to
X.org-world, if was wondering, if anybody was succesful to make stereo working
in Windows 10. I did read some NVIDIA forum, and it seems that 3d vision is
not very supported by NVIDIA, even for gamers... Was anybody able to mke it
work with Geforce cards, to save few bucks?

Best regards,

Jan

Dne 03.01.2018 v 10:42 Wim Burmeister napsal(a):

I answer a bit late, but I repost a message on 3D graphics from Mai 2017 :

Hello,

we just wanted to share our experience in finding a configuration which allows
to use 3D graphics under linux using Nvidia GeForce 3D glasses.

We had quite a hard time to find a configurations which works correctly.

We finally used Debian linux with a xfce desktop. Other recent desktops use a
tiling which is not compatible with 3D graphics.

The hardware consists of

- a DELL Precision T5810 desktop computer with an Nvidia Quadro M4000 (8
Gbyte memory, 4 DP) graphics card
- Nvidia GeForce 3D Vision 2 (NVIDIA GEF 3D VISION 2 GLASSES KIT) active
stereo glasses
- a stereo connector PNY Quadro 4000 3D for the synchronization of graphics
card and glasses
- an ASUS 24" LED 3D - VG248QE display
- a DisplayPort-DisplayPort cable

The Nvidia linux drivers from version 367.57 can handle the current version of
the Nvidia glasses.

For an obscure reason a direct DP-DP connection between graphics card and
display is absolutely required in order to obtain fully working stereo. If a
DP-DVI dual link adapter is used, the stereo does not work on the top and the
bottom part of the screen. This is true for a native DELL active adaptor or
generic models. The exact reason remains unresolved, but the solution is to use
a direct DP-DP connection. This limits the available choice of displays which
require 120 Hz for 1080*1980 screen resolution and a DP input. We have been
choosing a “Nvidia 3D ready” model.

There has been a considerate about of exchange about this problem on

https://devtalk.nvidia.com/default/topic/992892/linux/partially-working-stereoscopic-effect-with-3d-vision-under-debian-linux/

The setup comes with a price tag of about 1600 € free of taxes.

coot, pymol and chimera work straight without problems in hardware stereo mode.
The experience is absolutely great.

Best

Wim
--

Wim Burmeister
Professeur
Institut de Biologie Structurale (IBS) CIBB
71 avenue des Martyrs
CS 20192
38044 Grenoble Cedex 9, FRANCE
E-mail: wim.burmeis...@ibs.fr
Tel: +33 (0) 457 42 87 41 Fax: +33 (0) 476 20 94 00
website

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Re: [ccp4bb] OT: Nvidia 3D vision 2 glasses with Ubuntu workstation

2019-01-09 Thread Philippe BENAS

Hi Dirk,
Thanks a lot for your post. It will be indeed really helpful in our lab.
Best regards,Philippe Philippe BENAS, Ph.D.

ARN UPR 9002 CNRS
IBMC Strasbourg
15, rue René Descartes
F-67084 STRASBOURG cedex
+33.3.8841.7109
E-mails: p.be...@ibmc-cnrs.unistra.fr, philippe_be...@yahoo.fr
URLs:   http://www-ibmc.u-strasbg.fr/ , http://www-ibmc.u-strasbg.fr/spip-arn/



  De : Dirk Kostrewa 
 À : CCP4BB@JISCMAIL.AC.UK 
 Envoyé le : Mardi 8 janvier 2019 10h01
 Objet : Re: [ccp4bb] OT: Nvidia 3D vision 2 glasses with Ubuntu workstation
   
Dear colleagues,

since approximately end of last year, there is indeed a 3D stereo 
problem under CentOS/Scientific Linux 7.6. I found the odd reason for 
this by a small warning message in the Xorg-log file and some 
trial-and-error and just want to share this with you, in case, you come 
across the same problem:

My xorg.conf contains the usual switch-off of the composite extension, 
since this is incompatible with 3D stereo:

Section "Extensions"
     Option "Composite" "Disable"
EndSection

However, in recent Xorg-log files, there is a warning that the extension 
"Composite" is not recognized, but the extension "COMPOSITE" is loaded. 
This doesn't lead to 3D stereo problems on the KDE desktop, but disables 
3D stereo on the MATE and probably the XFCE desktop. The solution is 
both odd and easy - you have to modify the composite option in your 
xorg.conf as follows:

Section "Extensions"
     Option "COMPOSITE" "Disable"
EndSection

I have no idea, since when Xorg is case-sensitive, or whether this has 
anything to do with the Nvidia driver (I use the one from ELRepo). 
Anyway, this solution appears to work.

Best wishes,

Dirk.

On 20.12.18 22:28, Kay Diederichs wrote:
> Unfortunately, monitors with built-in emitter are no longer being 
> manufactured. The NVIDIA website has not been updated for years. So that path 
> leads nowhere.
>
> Stereo has worked well for us (for existing monitors with built-in emitter, 
> and with Quadro cards /USB emitter) until and including CentOS 7.5. Recently, 
> this stopped after updating to CentOS 7.6 - coot finds the stereo-capable 
> hardware and reports the switch to stereo, but the monitor does not flip the 
> pictures. We are investigating. We are using the Nvidia drivers through the 
> EPEL repository.
>
> best,
>
> Kay
>
>
> On Thu, 20 Dec 2018 16:11:56 -0500, David Schuller  
> wrote:
>
>> I can see two possible paths here:
>>
>> 1) Make the card work with an emitter
>>
>> or 2) Switch to a monitor with a built-in emitter
>>
>> Datasheet on the graphics card:
>> <https://www.nvidia.com/content/dam/en-zz/Solutions/design-visualization/productspage/quadro/quadro-desktop/quadro-pascal-p4000-data-sheet-us-nvidia-704358-r2-web.pdf>
>>
>> "3D Stereo support with Stereo Connector1
>> ...
>> 1 VGA/DVI/HDMI/stereo support via adapter/connector/bracket"
>>
>> The task then is to identify the correct bracket to work with this card,
>> and find a source for purchase.
>> Something like this:
>>
>> https://www.bhphotovideo.com/c/product/652465-REG/PNY_Technologies_900_50762__000_Stereo_Bracket_for_Quadro.html
>> "PNY Technoligies Stereo Bracket for Quadro FX 3800"
>>> Is this part also compatible with the Quadro P4000? I do not know.
>> http://www8.hp.com/h20195/v2/GetPDF.aspx/c04658472.pdf
>> "NVidia 3D Stereo Bracket...
>> Supports NVIDIA Quadro® K4000, K5000, K6000, K4200, K5200,
>> M4000, M5000, M6000, P4000, P5000, P6000 graphics cards"
>>
>>> Seems promising.
>> -
>> Here is a web page listing compatible monitors. You can filter for those
>> with "built-in emitter"
>>
>> https://www.nvidia.com/object/3d-vision-displays.html
>>
>>
>>
>>
>>
>> On 12/20/18 3:45 PM, Adarsh Kumar wrote:
>>> Hello everyone
>>>
>>> We have just purchased a Dell workstation for crystallography data 
>>> analysis. We were trying to use Nvidia 3D vision 2 glasses with it, but 
>>> failed to do so. Please help me out with this one. Some relevant 
>>> information is as follows:
>>> OS: Ubuntu 16.04 LTS
>>> Graphics : Quadro P4000 (unfortunately doesn't have a 3-pin DIN socket)
>>> Monitor: Asus VG248QE
>>>
>>> Thanks and regards
>>> Adarsh Kumar
>>> Suo Lab
>>> Florida State University College of Medicine
>>>
>>> 
>>>
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Re: [ccp4bb] OT: Nvidia 3D vision 2 glasses with Ubuntu workstation

2018-12-21 Thread Philippe BENAS

Dear Fritz and others,

Would you know if stereo will also work with the latest LTS Kubuntu (18.04) and 
with an external stereo IR emitter ?
I had and still have workstations working fine under Kubuntu 16.04 LTS and 
built-in IR emitters but I have to install a station with an external USB IR 
emitter running Kubuntu 18.04.

Many thanks in advance,
Philippe
 Philippe BENAS, Ph.D.

ARN UPR 9002 CNRS
IBMC Strasbourg
15, rue René Descartes
F-67084 STRASBOURG cedex
+33.3.8841.7109
E-mails: p.be...@ibmc-cnrs.unistra.fr, philippe_be...@yahoo.fr
URLs:   http://www-ibmc.u-strasbg.fr/ , http://www-ibmc.u-strasbg.fr/spip-arn/



  De : Guenter Fritz 
 À : CCP4BB@JISCMAIL.AC.UK 
 Envoyé le : Jeudi 20 décembre 2018 23h34
 Objet : Re: [ccp4bb] OT: Nvidia 3D vision 2 glasses with Ubuntu workstation
   
Dear Adarsh,

just an add-on to the instructions of the others. Since GNOME is not 
anymore compatible with stereo, we use successfully Xubuntu (18.04) with 
NVIDIA drivers.
Best , Guenter
> Hello everyone
>
> We have just purchased a Dell workstation for crystallography data analysis. 
> We were trying to use Nvidia 3D vision 2 glasses with it, but failed to do 
> so. Please help me out with this one. Some relevant information is as follows:
> OS: Ubuntu 16.04 LTS
> Graphics : Quadro P4000 (unfortunately doesn't have a 3-pin DIN socket)
> Monitor: Asus VG248QE
>
> Thanks and regards
> Adarsh Kumar
> Suo Lab
> Florida State University College of Medicine
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
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Re: [ccp4bb] Strange Diffraction pattern! Protein/DNA complex or DNA alone crystal?

2018-03-13 Thread Philippe BENAS

Dear Joseph,
I fully agree with Daniel Himmel's answer but you might be able to "index" your 
reflections and get a approximate cell parameters.
I did that in the past with crystals that diffracted very poorly up to 15 
angst. I used HKL200 at that time, cheated with the distance (HKL2000 won't 
accept indexing with too low resolution spots) and selected individual spots 
manually.It was enough for making Matthews analysis for each putative space 
group.The complex formation between the protein and the RNA was confirmed by a 
stoechiometric amount of each macromolecule resulting from OD spectra 
deconvolution taken on dissolved crystals, using a spectrum for the protein 
alone and a spectrum for the RNA alone as references.
Best regards,
Philippe Philippe BENAS, Ph.D.

Laboratoire de Cristallographie et RMN Biologiques, UMR 8015 CNRS
Faculté de Pharmacie, Université Paris Descartes
Case 48
Av, de l'Observatoire
F-75270 PARIS cedex 06
+33.1.5373.1599
E-mails: philippe.be...@parisdescartes.fr, philippe_be...@yahoo.fr
URLs: http://lcrbw.pharmacie.univ-paris5.fr/ , 
http://lcrbw.pharmacie.univ-paris5.fr/spip.php?article18



  De : Joseph Ho <sbddintai...@gmail.com>
 À : CCP4BB@JISCMAIL.AC.UK 
 Envoyé le : Lundi 12 mars 2018 12h54
 Objet : [ccp4bb] Strange Diffraction pattern! Protein/DNA complex or DNA alone 
crystal?
   
Dear all:


I would like to seek your wisdom on our latest diffraction pattern. We
have been working on protein/DNA complex. The protein and DNA have
similar MW. By binding assay, we know the minimal length of DNA. (The
Kd is 0.1-1 microMolar and we can see the complex formation in size
exclusion chromatography up to 200mM NaCl but also some unbound form)
After trying different length of DNA, we recently obtained many
crystal hits (the percipient is either PEG400 or MPD). The final ratio
(prior to protein crystallization) between protein and DNA is 1:1.6
considering some loss of protein during concentration. The crystal is
birefringent. Since high conc. of PEG400 (MPD), the crystals were
directly frozen in liquid N2. However, crystals only diffract to 8-10
angstrom (anisotropic) and also  weird striking line are present
(please see attachment). Do you think if it is  DNA alone crystal or
protein/DNA complex crystal?
How should I improve the diffraction quality?



PS. We have done some tests. For example, set up the same conditions
with DNA alone. I also tried to dissolve crystals in Bradford assay
solution and I believe I saw some blueish color. But none of these
tests are conclusive.

Thanks for your suggestion.

Joseph

Re: [ccp4bb] Off-topic question

2018-03-05 Thread Philippe BENAS

Hi Jobi,
Phenol/CHCl3 extraction, iPrOH precipitation and then nucleic acid sequencing.

Best regards,Philippe Philippe BENAS, Ph.D.

Laboratoire de Cristallographie et RMN Biologiques, UMR 8015 CNRS
Faculté de Pharmacie, Université Paris Descartes
Case 48
Av, de l'Observatoire
F-75270 PARIS cedex 06
+33.1.5373.1599
E-mails: philippe.be...@parisdescartes.fr, philippe_be...@yahoo.fr
URLs: http://lcrbw.pharmacie.univ-paris5.fr/ , 
http://lcrbw.pharmacie.univ-paris5.fr/spip.php?article18



  De : Jobichen Chacko <jobich...@gmail.com>
 À : CCP4BB@JISCMAIL.AC.UK 
 Envoyé le : Mardi 6 mars 2018 5h11
 Objet : [ccp4bb] Off-topic question
   
Dear All,
We are trying to identify/sequence a DNA/RNA fragment (around 100bp) which was 
co-purified along with our protein.
The expression was done in E.coli.
Any suggestions on how to do this.
Thank you.
Jobi

Re: [ccp4bb] phenix refinement about cis-proline

2018-03-02 Thread Philippe BENAS

Dear Niegel,
May be Shijun had to cancel his registration to the PhenixBB as I had to do 
since 2015 due to "too many bounces" whatever the email address I used, 
professional, yahoo or gmail ?... Has this been fixed at some point ?

All the best,Philippe
 Philippe BENAS, Ph.D.

Laboratoire de Cristallographie et RMN Biologiques, UMR 8015 CNRS
Faculté de Pharmacie, Université Paris Descartes
Case 48
Av, de l'Observatoire
F-75270 PARIS cedex 06
+33.1.5373.1599
E-mails: philippe.be...@parisdescartes.fr, philippe_be...@yahoo.fr
URLs: http://lcrbw.pharmacie.univ-paris5.fr/ , 
http://lcrbw.pharmacie.univ-paris5.fr/spip.php?article18



  De : Nigel Moriarty <nwmoria...@lbl.gov>
 À : CCP4BB@JISCMAIL.AC.UK 
 Envoyé le : Vendredi 2 mars 2018 8h25
 Objet : Re: [ccp4bb] phenix refinement about cis-proline
  


Shijun
You can ask all the questions you like about Phenix on PhenixBB. However, to 
answer your question, you can set all peptides to trans using
apply_all_trans=True
or more specific control using
apply_cis_trans_specification {    cis_trans_mod = cis *trans    
residue_selection = None  }
to any number of peptides.
Cheers
Nigel
---Nigel W. Moriarty
Building 33R0349, Molecular Biophysics and Integrated BioimagingLawrence 
Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709     Email : nwmoria...@lbl.gov
Fax   : 510-486-5909       Web  : CCI.LBL.gov
On Thu, Mar 1, 2018 at 10:58 PM, 张士军 <21620150150...@stu.xmu.edu.cn> wrote:

Dear all    I am refining a structure which has cis-Pro and trans-Pro, the 
tans-Pro is gone when I set the "threshold degrees for cis-peptide " from 
default 45 to 65, but still has cis-Pro. While no significant change when I set 
it to 15. My question is how to set in phenix refinement to clear the Pro 
residues in cis- or trans- conformations.Best Regards shijun

Re: [ccp4bb] Unknown electron density

2017-10-27 Thread Philippe BENAS

And another question: is the protein known to work with a cofactor that you 
could have kept all along the purification ?
Best regards,Philippe Philippe BENAS, Ph.D.
Dog in the manger
"Un importun survient qui trouble l'intimité, qui arrête l'expansion, qui glace 
le plaisir, - probablement comme un étranger tombant au milieu d'enfants en 
train de danser une ronde", Alfred Delvau, Dictionnaire de la langue verte 
(1866).

Laboratoire de Cristallographie et RMN Biologiques, UMR 8015 CNRS
Faculté de Pharmacie, Université Paris Descartes
Case 48
Av, de l'Observatoire
F-75270 PARIS cedex 06
+33.1.5373.1599
E-mails: philippe.be...@parisdescartes.fr, philippe_be...@yahoo.fr
URLs: http://lcrbw.pharmacie.univ-paris5.fr/ , 
http://lcrbw.pharmacie.univ-paris5.fr/spip.php?article18



  De : Vijaykumar Pillalamarri <vijaypkuma...@gmail.com>
 À : Philippe BENAS <philippe_be...@yahoo.fr> 
Cc : "CCP4BB@JISCMAIL.AC.UK" <CCP4BB@jiscmail.ac.uk>
 Envoyé le : Vendredi 27 octobre 2017 14h08
 Objet : Re: [ccp4bb] Unknown electron density
   
Dear Philippe,
Here is the images showing anomalous map at Co contoured at 5.
Thanks,Vijaykumar
On 27 October 2017 at 14:05, Philippe BENAS <philippe_be...@yahoo.fr> wrote:

Hello Vijaykumar,
Well, 27 e- * 0.4 = 10.8 e- which is very close to 8 (O).In addition I don't 
recognize the expected Co2+ coordination in your structure. I think evidence 
from an anomalous signal would be wellcome. Evidence from another crystal is 
not a proof for this crystal structure. It could be just a little stronger if 
the two crystals come from the same drop.
You can get anomalous info even if the crystal was not collected at the 
wavelength that maximises f". For instance, the crystal for which I provided 
the two snapshots was collected at 0.95 Angst. Not only the anomalous signal is 
well defined for the Co2+ but also for disulfide bridges. Lamdba around 1 
Angst. is a common value for native data collection on synchrotrons so that I'm 
pretty sure you can get such signal from your data.
And a good trick is to always process your data assuming the Friedel Law is not 
respected so that you can get quick access to the anomalous signal in case you 
need it.
HTH,Philippe Philippe BENAS, Ph.D.
Dog in the manger
"Un importun survient qui trouble l'intimité, qui arrête l'expansion, qui glace 
le plaisir, - probablement comme un étranger tombant au milieu d'enfants en 
train de danser une ronde", Alfred Delvau, Dictionnaire de la langue verte 
(1866).

Laboratoire de Cristallographie et RMN Biologiques, UMR 8015 CNRS
Faculté de Pharmacie, Université Paris Descartes
Case 48
Av, de l'Observatoire
F-75270 PARIS cedex 06
+33.1.5373.1599
E-mails: philippe.benas@parisdescartes. fr, philippe_be...@yahoo.fr
URLs: http://lcrbw.pharmacie.univ- paris5.fr/ , http://lcrbw.pharmacie.univ- 
paris5.fr/spip.php?article18



  De : Vijaykumar Pillalamarri <vijaypkuma...@gmail.com>
 À : CCP4BB@JISCMAIL.AC.UK 
 Envoyé le : Vendredi 27 octobre 2017 8h59
 Objet : Re: [ccp4bb] Unknown electron density
   
Dear Dr. Philippe,
There is no symmetry axis nearby the density. I did not computed anomalous map 
for this structure. In this structure, the occupancy of Co is only 0.4 (May be 
because I have added less Co).  We have proved the presence of Co in one of our 
another crystal structure of same protein.
Thanks,Vijaykumar
On 26 October 2017 at 23:11, Philippe BENAS <0d88e888355a-dmarc- 
requ...@jiscmail.ac.uk> wrote:

Dear all and Vijaykumar,
I am personally much more concerned about the Co density which does not seem as 
strong as expected for an atom with Z = 27, aren't you ?

Also I was wondering if there is no symmetry axis around your unkown density. 
Symmetry axes are often a garbage place for all the unexplained density 
everywhere else in the a.u.
Would you have by any chance computed an anomalous map ? It could help for both 
your unknown density and the Co.
Attached is a snapshot of 1.58 Angst. resolution structure showing a 2mFo-DFc 
map in blue and contoured at 2 sigma level as well as an anomalous map 
contoured at 8 sigma (snap1.png). snap2.png shows the 2mFo-DFc at 4 sigma.

Best regards,Philippe Philippe BENAS, Ph.D.
Dog in the manger
"Un importun survient qui trouble l'intimité, qui arrête l'expansion, qui glace 
le plaisir, - probablement comme un étranger tombant au milieu d'enfants en 
train de danser une ronde", Alfred Delvau, Dictionnaire de la langue verte 
(1866).

Laboratoire de Cristallographie et RMN Biologiques, UMR 8015 CNRS
Faculté de Pharmacie, Université Paris Descartes
Case 48
Av, de l'Observatoire
F-75270 PARIS cedex 06
+33.1.5373.1599
E-mails: philippe.benas@parisdescartes. fr, philippe_be...@yahoo.fr
URLs: http://lcrbw.pharmacie.univ- paris5.fr/ , http://lcrbw.pharmacie.univ- 
paris5.fr/spip.php?article18



  De : Nick Pearce <n.m.pea...@uu.nl>
 À : CCP4BB@JISCMAIL.AC.UK 
 Envoyé le

Re: [ccp4bb] Unknown electron density

2017-10-27 Thread Philippe BENAS

And did you try SA omit maps ?
Best,
P.
 Philippe BENAS, Ph.D.
Dog in the manger
"Un importun survient qui trouble l'intimité, qui arrête l'expansion, qui glace 
le plaisir, - probablement comme un étranger tombant au milieu d'enfants en 
train de danser une ronde", Alfred Delvau, Dictionnaire de la langue verte 
(1866).

Laboratoire de Cristallographie et RMN Biologiques, UMR 8015 CNRS
Faculté de Pharmacie, Université Paris Descartes
Case 48
Av, de l'Observatoire
F-75270 PARIS cedex 06
+33.1.5373.1599
E-mails: philippe.be...@parisdescartes.fr, philippe_be...@yahoo.fr
URLs: http://lcrbw.pharmacie.univ-paris5.fr/ , 
http://lcrbw.pharmacie.univ-paris5.fr/spip.php?article18



  De : Vijaykumar Pillalamarri <vijaypkuma...@gmail.com>
 À : Philippe BENAS <philippe_be...@yahoo.fr> 
Cc : "CCP4BB@JISCMAIL.AC.UK" <CCP4BB@jiscmail.ac.uk>
 Envoyé le : Vendredi 27 octobre 2017 14h08
 Objet : Re: [ccp4bb] Unknown electron density
   
Dear Philippe,
Here is the images showing anomalous map at Co contoured at 5.
Thanks,Vijaykumar
On 27 October 2017 at 14:05, Philippe BENAS <philippe_be...@yahoo.fr> wrote:

Hello Vijaykumar,
Well, 27 e- * 0.4 = 10.8 e- which is very close to 8 (O).In addition I don't 
recognize the expected Co2+ coordination in your structure. I think evidence 
from an anomalous signal would be wellcome. Evidence from another crystal is 
not a proof for this crystal structure. It could be just a little stronger if 
the two crystals come from the same drop.
You can get anomalous info even if the crystal was not collected at the 
wavelength that maximises f". For instance, the crystal for which I provided 
the two snapshots was collected at 0.95 Angst. Not only the anomalous signal is 
well defined for the Co2+ but also for disulfide bridges. Lamdba around 1 
Angst. is a common value for native data collection on synchrotrons so that I'm 
pretty sure you can get such signal from your data.
And a good trick is to always process your data assuming the Friedel Law is not 
respected so that you can get quick access to the anomalous signal in case you 
need it.
HTH,Philippe Philippe BENAS, Ph.D.
Dog in the manger
"Un importun survient qui trouble l'intimité, qui arrête l'expansion, qui glace 
le plaisir, - probablement comme un étranger tombant au milieu d'enfants en 
train de danser une ronde", Alfred Delvau, Dictionnaire de la langue verte 
(1866).

Laboratoire de Cristallographie et RMN Biologiques, UMR 8015 CNRS
Faculté de Pharmacie, Université Paris Descartes
Case 48
Av, de l'Observatoire
F-75270 PARIS cedex 06
+33.1.5373.1599
E-mails: philippe.benas@parisdescartes. fr, philippe_be...@yahoo.fr
URLs: http://lcrbw.pharmacie.univ- paris5.fr/ , http://lcrbw.pharmacie.univ- 
paris5.fr/spip.php?article18



  De : Vijaykumar Pillalamarri <vijaypkuma...@gmail.com>
 À : CCP4BB@JISCMAIL.AC.UK 
 Envoyé le : Vendredi 27 octobre 2017 8h59
 Objet : Re: [ccp4bb] Unknown electron density
   
Dear Dr. Philippe,
There is no symmetry axis nearby the density. I did not computed anomalous map 
for this structure. In this structure, the occupancy of Co is only 0.4 (May be 
because I have added less Co).  We have proved the presence of Co in one of our 
another crystal structure of same protein.
Thanks,Vijaykumar
On 26 October 2017 at 23:11, Philippe BENAS <0d88e888355a-dmarc- 
requ...@jiscmail.ac.uk> wrote:

Dear all and Vijaykumar,
I am personally much more concerned about the Co density which does not seem as 
strong as expected for an atom with Z = 27, aren't you ?

Also I was wondering if there is no symmetry axis around your unkown density. 
Symmetry axes are often a garbage place for all the unexplained density 
everywhere else in the a.u.
Would you have by any chance computed an anomalous map ? It could help for both 
your unknown density and the Co.
Attached is a snapshot of 1.58 Angst. resolution structure showing a 2mFo-DFc 
map in blue and contoured at 2 sigma level as well as an anomalous map 
contoured at 8 sigma (snap1.png). snap2.png shows the 2mFo-DFc at 4 sigma.

Best regards,Philippe Philippe BENAS, Ph.D.
Dog in the manger
"Un importun survient qui trouble l'intimité, qui arrête l'expansion, qui glace 
le plaisir, - probablement comme un étranger tombant au milieu d'enfants en 
train de danser une ronde", Alfred Delvau, Dictionnaire de la langue verte 
(1866).

Laboratoire de Cristallographie et RMN Biologiques, UMR 8015 CNRS
Faculté de Pharmacie, Université Paris Descartes
Case 48
Av, de l'Observatoire
F-75270 PARIS cedex 06
+33.1.5373.1599
E-mails: philippe.benas@parisdescartes. fr, philippe_be...@yahoo.fr
URLs: http://lcrbw.pharmacie.univ- paris5.fr/ , http://lcrbw.pharmacie.univ- 
paris5.fr/spip.php?article18



  De : Nick Pearce <n.m.pea...@uu.nl>
 À : CCP4BB@JISCMAIL.AC.UK 
 Envoyé le : Jeudi 26 octobre 2017 18h19
 Objet : Re: [ccp4bb] Unknown electron density
  
I agree that the difference density

Re: [ccp4bb] Unknown electron density

2017-10-27 Thread Philippe BENAS

Dear Vijaykumar,
That looks great. So now what is the distance between the Co2+ and the unknown 
density blob ? Would it be compatible with a coordination bond of the Co2+ or 
not ?

Best regards,Philippe
 Philippe BENAS, Ph.D.
Dog in the manger
"Un importun survient qui trouble l'intimité, qui arrête l'expansion, qui glace 
le plaisir, - probablement comme un étranger tombant au milieu d'enfants en 
train de danser une ronde", Alfred Delvau, Dictionnaire de la langue verte 
(1866).

Laboratoire de Cristallographie et RMN Biologiques, UMR 8015 CNRS
Faculté de Pharmacie, Université Paris Descartes
Case 48
Av, de l'Observatoire
F-75270 PARIS cedex 06
+33.1.5373.1599
E-mails: philippe.be...@parisdescartes.fr, philippe_be...@yahoo.fr
URLs: http://lcrbw.pharmacie.univ-paris5.fr/ , 
http://lcrbw.pharmacie.univ-paris5.fr/spip.php?article18



  De : Vijaykumar Pillalamarri <vijaypkuma...@gmail.com>
 À : Philippe BENAS <philippe_be...@yahoo.fr> 
Cc : "CCP4BB@JISCMAIL.AC.UK" <CCP4BB@jiscmail.ac.uk>
 Envoyé le : Vendredi 27 octobre 2017 14h08
 Objet : Re: [ccp4bb] Unknown electron density
   
Dear Philippe,
Here is the images showing anomalous map at Co contoured at 5.
Thanks,Vijaykumar
On 27 October 2017 at 14:05, Philippe BENAS <philippe_be...@yahoo.fr> wrote:

Hello Vijaykumar,
Well, 27 e- * 0.4 = 10.8 e- which is very close to 8 (O).In addition I don't 
recognize the expected Co2+ coordination in your structure. I think evidence 
from an anomalous signal would be wellcome. Evidence from another crystal is 
not a proof for this crystal structure. It could be just a little stronger if 
the two crystals come from the same drop.
You can get anomalous info even if the crystal was not collected at the 
wavelength that maximises f". For instance, the crystal for which I provided 
the two snapshots was collected at 0.95 Angst. Not only the anomalous signal is 
well defined for the Co2+ but also for disulfide bridges. Lamdba around 1 
Angst. is a common value for native data collection on synchrotrons so that I'm 
pretty sure you can get such signal from your data.
And a good trick is to always process your data assuming the Friedel Law is not 
respected so that you can get quick access to the anomalous signal in case you 
need it.
HTH,Philippe Philippe BENAS, Ph.D.
Dog in the manger
"Un importun survient qui trouble l'intimité, qui arrête l'expansion, qui glace 
le plaisir, - probablement comme un étranger tombant au milieu d'enfants en 
train de danser une ronde", Alfred Delvau, Dictionnaire de la langue verte 
(1866).

Laboratoire de Cristallographie et RMN Biologiques, UMR 8015 CNRS
Faculté de Pharmacie, Université Paris Descartes
Case 48
Av, de l'Observatoire
F-75270 PARIS cedex 06
+33.1.5373.1599
E-mails: philippe.benas@parisdescartes. fr, philippe_be...@yahoo.fr
URLs: http://lcrbw.pharmacie.univ- paris5.fr/ , http://lcrbw.pharmacie.univ- 
paris5.fr/spip.php?article18



  De : Vijaykumar Pillalamarri <vijaypkuma...@gmail.com>
 À : CCP4BB@JISCMAIL.AC.UK 
 Envoyé le : Vendredi 27 octobre 2017 8h59
 Objet : Re: [ccp4bb] Unknown electron density
   
Dear Dr. Philippe,
There is no symmetry axis nearby the density. I did not computed anomalous map 
for this structure. In this structure, the occupancy of Co is only 0.4 (May be 
because I have added less Co).  We have proved the presence of Co in one of our 
another crystal structure of same protein.
Thanks,Vijaykumar
On 26 October 2017 at 23:11, Philippe BENAS <0d88e888355a-dmarc- 
requ...@jiscmail.ac.uk> wrote:

Dear all and Vijaykumar,
I am personally much more concerned about the Co density which does not seem as 
strong as expected for an atom with Z = 27, aren't you ?

Also I was wondering if there is no symmetry axis around your unkown density. 
Symmetry axes are often a garbage place for all the unexplained density 
everywhere else in the a.u.
Would you have by any chance computed an anomalous map ? It could help for both 
your unknown density and the Co.
Attached is a snapshot of 1.58 Angst. resolution structure showing a 2mFo-DFc 
map in blue and contoured at 2 sigma level as well as an anomalous map 
contoured at 8 sigma (snap1.png). snap2.png shows the 2mFo-DFc at 4 sigma.

Best regards,Philippe Philippe BENAS, Ph.D.
Dog in the manger
"Un importun survient qui trouble l'intimité, qui arrête l'expansion, qui glace 
le plaisir, - probablement comme un étranger tombant au milieu d'enfants en 
train de danser une ronde", Alfred Delvau, Dictionnaire de la langue verte 
(1866).

Laboratoire de Cristallographie et RMN Biologiques, UMR 8015 CNRS
Faculté de Pharmacie, Université Paris Descartes
Case 48
Av, de l'Observatoire
F-75270 PARIS cedex 06
+33.1.5373.1599
E-mails: philippe.benas@parisdescartes. fr, philippe_be...@yahoo.fr
URLs: http://lcrbw.pharmacie.univ- paris5.fr/ , http://lcrbw.pharmacie.univ- 
paris5.fr/spip.php?article18



  De : Nick Pearce <n.m.pea..

Re: [ccp4bb] Unknown electron density

2017-10-27 Thread Philippe BENAS

Hello Vijaykumar,
Well, 27 e- * 0.4 = 10.8 e- which is very close to 8 (O).In addition I don't 
recognize the expected Co2+ coordination in your structure. I think evidence 
from an anomalous signal would be wellcome. Evidence from another crystal is 
not a proof for this crystal structure. It could be just a little stronger if 
the two crystals come from the same drop.
You can get anomalous info even if the crystal was not collected at the 
wavelength that maximises f". For instance, the crystal for which I provided 
the two snapshots was collected at 0.95 Angst. Not only the anomalous signal is 
well defined for the Co2+ but also for disulfide bridges. Lamdba around 1 
Angst. is a common value for native data collection on synchrotrons so that I'm 
pretty sure you can get such signal from your data.
And a good trick is to always process your data assuming the Friedel Law is not 
respected so that you can get quick access to the anomalous signal in case you 
need it.
HTH,Philippe Philippe BENAS, Ph.D.
Dog in the manger
"Un importun survient qui trouble l'intimité, qui arrête l'expansion, qui glace 
le plaisir, - probablement comme un étranger tombant au milieu d'enfants en 
train de danser une ronde", Alfred Delvau, Dictionnaire de la langue verte 
(1866).

Laboratoire de Cristallographie et RMN Biologiques, UMR 8015 CNRS
Faculté de Pharmacie, Université Paris Descartes
Case 48
Av, de l'Observatoire
F-75270 PARIS cedex 06
+33.1.5373.1599
E-mails: philippe.be...@parisdescartes.fr, philippe_be...@yahoo.fr
URLs: http://lcrbw.pharmacie.univ-paris5.fr/ , 
http://lcrbw.pharmacie.univ-paris5.fr/spip.php?article18



  De : Vijaykumar Pillalamarri <vijaypkuma...@gmail.com>
 À : CCP4BB@JISCMAIL.AC.UK 
 Envoyé le : Vendredi 27 octobre 2017 8h59
 Objet : Re: [ccp4bb] Unknown electron density
   
Dear Dr. Philippe,
There is no symmetry axis nearby the density. I did not computed anomalous map 
for this structure. In this structure, the occupancy of Co is only 0.4 (May be 
because I have added less Co).  We have proved the presence of Co in one of our 
another crystal structure of same protein.
Thanks,Vijaykumar
On 26 October 2017 at 23:11, Philippe BENAS 
<0d88e888355a-dmarc-requ...@jiscmail.ac.uk> wrote:

Dear all and Vijaykumar,
I am personally much more concerned about the Co density which does not seem as 
strong as expected for an atom with Z = 27, aren't you ?

Also I was wondering if there is no symmetry axis around your unkown density. 
Symmetry axes are often a garbage place for all the unexplained density 
everywhere else in the a.u.
Would you have by any chance computed an anomalous map ? It could help for both 
your unknown density and the Co.
Attached is a snapshot of 1.58 Angst. resolution structure showing a 2mFo-DFc 
map in blue and contoured at 2 sigma level as well as an anomalous map 
contoured at 8 sigma (snap1.png). snap2.png shows the 2mFo-DFc at 4 sigma.

Best regards,Philippe Philippe BENAS, Ph.D.
Dog in the manger
"Un importun survient qui trouble l'intimité, qui arrête l'expansion, qui glace 
le plaisir, - probablement comme un étranger tombant au milieu d'enfants en 
train de danser une ronde", Alfred Delvau, Dictionnaire de la langue verte 
(1866).

Laboratoire de Cristallographie et RMN Biologiques, UMR 8015 CNRS
Faculté de Pharmacie, Université Paris Descartes
Case 48
Av, de l'Observatoire
F-75270 PARIS cedex 06
+33.1.5373.1599
E-mails: philippe.benas@parisdescartes. fr, philippe_be...@yahoo.fr
URLs: http://lcrbw.pharmacie.univ- paris5.fr/ , http://lcrbw.pharmacie.univ- 
paris5.fr/spip.php?article18



  De : Nick Pearce <n.m.pea...@uu.nl>
 À : CCP4BB@JISCMAIL.AC.UK 
 Envoyé le : Jeudi 26 octobre 2017 18h19
 Objet : Re: [ccp4bb] Unknown electron density
  
I agree that the difference density isn’t “noise". However, just because it’s 
not noise doesn’t mean that it is modellable (with an atomic model) — the 
crystallographic density is an average over billions of molecules, and if its 
not obvious at 1.6Å what is bound, then it’s probably a superposition of states 
(or a highly disordered molecule with large B-factors, which in this case 
amounts to pretty much the same thing). When it’s a superposition of states in 
solvent regions, there are too many free parameters to build a reliable model: 
you don’t know how many alternate conformations to model, or how many species 
of molecules there are. It could be 1 conformer of PEG with 1 superposed 
conformer of water or 2 of PEG + 1 of water or 1 of PEG + 1 of something else + 
1 of water… or literally anything…
So unless you have some prior information as to what is bound, I would play it 
safe and model nothing — the conservative approach.

Thanks,Nick
—
Nick (Nicholas) PearcePost-doctoral ResearcherLab of Piet GrosCrystal & 
Structural Chemistry GroupUniversiteit Utrecht

On 26 Oct 2017, at 18:00, Vijaykumar Pillalamarri <vijaypkuma...@gmail.com> 
wr

[ccp4bb] My apologies to the PDB-REDO team

2017-06-27 Thread Philippe BENAS

Dear all,
I realized I didn't properly aknowledge the team who made PDB REDO. So let me 
please correct my mistake by citing here the PDB REDO references (as found on 
the PDB REDO website) and providing a list of interesting papers to all :
   
   - Joosten RP, Long F, Murshudov GN, Perrakis A. The PDB_REDO server for 
macromolecular structure model optimization. IUCrJ. 2014; 1:213-220. Reprint.
   - Joosten RP, Joosten K, Murshudov GN, Perrakis A. PDB_REDO: constructive 
validation, more than just looking for errors. Acta Cryst. 2012; D68:484-496. 
Reprint.
   - Joosten RP, Joosten K, Cohen SX, Vriend G, Perrakis A. Automatic 
rebuilding and optimization of crystallographic structures in the Protein Data 
Bank. Bioinformatics 2011; 27:3392-3398. Reprint.
   - Joosten RP, Vriend G. PDB improvement starts with data deposition. Science 
2007; 317:195-196. Reprint.
   - Joosten RP, Womack T, Vriend G, Bricogne G. Re-refinement from deposited 
X-ray data can deliver improved models for most PDB entries. Acta Cryst. 2009; 
D65:176-185. Reprint.
   - Joosten RP, Salzemann J, Bloch V, Stockinger H, Berglund A-C, Blanchet C, 
Bongcam-Rudloff E, Combet C, Da Costa AL, Deleage G, Diarena M, Fabbretti R, 
Fettahi G, Flegel V, Gisel A, Kasam V, Kervinen T, Korpelainen E, Mattila K, 
Pagni M,Reichstadt M, Breton V, Tickle IJ, Vriend G. PDB_REDO: automated 
re-refinement of X-ray structure models in the PDB. J. Appl. Cryst. 2009; 
42:376-384. Reprint.

 
Best,
Philippe
 Philippe BENAS, Ph.D.
Dog in the manger
"Un importun survient qui trouble l'intimité, qui arrête l'expansion, qui glace 
le plaisir, - probablement comme un étranger tombant au milieu d'enfants en 
train de danser une ronde", Alfred Delvau, Dictionnaire de la langue verte 
(1866).

Laboratoire de Cristallographie et RMN Biologiques, UMR 8015 CNRS
Faculté de Pharmacie, Université Paris Descartes
Case 48
Av, de l'Observatoire
F-75270 PARIS cedex 06
+33.1.5373.1599
E-mails: philippe.be...@parisdescartes.fr, philippe_be...@yahoo.fr
URLs: http://lcrbw.pharmacie.univ-paris5.fr/ , 
http://lcrbw.pharmacie.univ-paris5.fr/spip.php?article18

Re: [ccp4bb] Incorrect Structure in the PDB

2017-06-27 Thread Philippe BENAS

I think the PDB (and Gerard DVD) got the answer with their quite new validation 
report provided for each entry.On the other hand PDBredo (Tassos & Co) is an 
excellent tool to compare a currently deposited structure and its reprocessed 
version (although it doesn't tell about the phasing).
Best,Philippe Philippe BENAS, Ph.D.
Dog in the manger
"Un importun survient qui trouble l'intimité, qui arrête l'expansion, qui glace 
le plaisir, - probablement comme un étranger tombant au milieu d'enfants en 
train de danser une ronde", Alfred Delvau, Dictionnaire de la langue verte 
(1866).

Laboratoire de Cristallographie et RMN Biologiques, UMR 8015 CNRS
Faculté de Pharmacie, Université Paris Descartes
Case 48
Av, de l'Observatoire
F-75270 PARIS cedex 06
+33.1.5373.1599
E-mails: philippe.be...@parisdescartes.fr, philippe_be...@yahoo.fr
URLs: http://lcrbw.pharmacie.univ-paris5.fr/ , 
http://lcrbw.pharmacie.univ-paris5.fr/spip.php?article18



  De : "Goldman, Adrian" <adrian.gold...@helsinki.fi>
 À : CCP4BB@JISCMAIL.AC.UK 
 Envoyé le : Mardi 27 juin 2017 10h59
 Objet : Re: [ccp4bb] Incorrect Structure in the PDB
   
I agree: I don’t think this is fraud, and was never even suggesting it.  If it 
were fraud, _I_ at least would back-transform my structure so that there 
weren’t horrible red and green blobs all over the place…!  I think it’s just 
sloppy - and the question remains, as posed by the original poster: what and 
how to do about the many examples?
Adrian


On 27 Jun 2017, at 11:55, Bernhard Rupp <hofkristall...@gmail.com> wrote:
I beg to differ. You are not pulling a murthy simply by depositing a poor or 
even wrong structure. Although the borderline beteeen sloppy work (and 
selfdeception) and reckless misleading of others can be floating, real cases of 
fraud and fabrication are almost exceptionally rare.
Best, br
On Jun 27, 2017 10:44, "Philippe BENAS" 
<0d88e888355a-dmarc-requ...@jiscmail.ac.uk> wrote:

Dear Adrian,
OK, I understand. You might be perfectly right. Moreover as I wrote it is 
difficult to tell something from a single mono view picture.And as you are 
pointing out their Ramachadran plots doe not look good at all. So they are poor 
crystallographers. But the question that remains is to know if their structure 
is really wron, I mean if the backbone is incorrect or not. For sure they might 
end up with a poor reputation as crystallographers if they publish so badly 
refined structures. But they might end up asKrishnaMurthy if the backbone of 
their published structures are wrong !

All the best,Philippe Philippe BENAS, Ph.D.
Dog in the manger
"Un importun survient qui trouble l'intimité, qui arrête l'expansion, qui glace 
le plaisir, - probablement comme un étranger tombant au milieu d'enfants en 
train de danser une ronde", Alfred Delvau,Dictionnaire de la langue verte 
(1866).

Laboratoire de Cristallographie et RMN Biologiques, UMR 8015 CNRS
Faculté de Pharmacie, Université Paris Descartes
Case 48
Av, de l'Observatoire
F-75270 PARIS cedex 06
+33.1.5373.1599
E-mails:philippe.benas@parisdescartes. fr, philippe_be...@yahoo.fr
URLs: http://lcrbw.pharmacie.univ- paris5.fr/ , http://lcrbw.pharmacie.univ- 
paris5.fr/spip.php?article18



De : "Goldman, Adrian" <adrian.gold...@helsinki.fi>
À : Philippe BENAS <philippe_be...@yahoo.fr>
Envoyé le : Mardi 27 juin 2017 10h30
Objet : Re: [ccp4bb] Incorrect Structure in the PDB

Philippe
All I did was take their deposited mtz and coordinates.  The peak in question 
in green is about 7 sigma.  This structure (at 2 Å) has 3% 
ramanachandran-forbidden; one of their lower-resolution structures is 22%!  And 
no, given that the action of a fourier transform hasn’t changed, this is not 
the best structure that could have been built at that time (2002…).
Adrian

On 27 Jun 2017, at 11:22, Philippe BENAS <philippe_be...@yahoo.fr> wrote:
Dear Adrian, dear all, It does not look very clear to me that the side chain 
for this tyrosine is at a wrong place for instance (indeed Chi2 torsion angle 
could have multiple values = highly rotating aromatic ring). But it seems 
rather that the main chain is not correctly traced, which is probably worse. In 
addition it is difficult to tell something from just a mono view... This being 
said data collected by one group or another vary. For instance, resolution and 
hence R/free R can (generally) be improved. This does not imply that the 
structure coming from the lower resolution structure in wrong: it is just 
probably the best model that could have been built with the available data at 
that time.And on the contrary to other techniques we, crystallographers, have 
the chance of the Fourier transform which permits to have statistical 
indicators, such as R and free R, which give an indication about the accuracy 
of the reported structure. Similarly when solving the structure by experimental 
phasing we have also such indicator

Re: [ccp4bb] Incorrect Structure in the PDB

2017-06-27 Thread Philippe BENAS

Dear Bernhard,
I totally agree with you and it was absolutely the meaning of my first email 
while thinking the used F were coming from Adrian's data. And by the way of the 
second as well. This being said what about groups that publish always poor 
structures ? Ins't it in some way dishonest ?

Best,Philippe Philippe BENAS, Ph.D.
Dog in the manger
"Un importun survient qui trouble l'intimité, qui arrête l'expansion, qui glace 
le plaisir, - probablement comme un étranger tombant au milieu d'enfants en 
train de danser une ronde", Alfred Delvau, Dictionnaire de la langue verte 
(1866).

Laboratoire de Cristallographie et RMN Biologiques, UMR 8015 CNRS
Faculté de Pharmacie, Université Paris Descartes
Case 48
Av, de l'Observatoire
F-75270 PARIS cedex 06
+33.1.5373.1599
E-mails: philippe.be...@parisdescartes.fr, philippe_be...@yahoo.fr
URLs: http://lcrbw.pharmacie.univ-paris5.fr/ , 
http://lcrbw.pharmacie.univ-paris5.fr/spip.php?article18



  De : Bernhard Rupp <hofkristall...@gmail.com>
 À : Philippe BENAS <philippe_be...@yahoo.fr> 
Cc : "CCP4BB@JISCMAIL.AC.UK" <CCP4BB@jiscmail.ac.uk>
 Envoyé le : Mardi 27 juin 2017 10h55
 Objet : Re: [ccp4bb] Incorrect Structure in the PDB
   
I beg to differ. You are not pulling a murthy simply by depositing a poor or 
even wrong structure. Although the borderline beteeen sloppy work (and 
selfdeception) and reckless misleading of others can be floating, real cases of 
fraud and fabrication are almost exceptionally rare.
Best, br
On Jun 27, 2017 10:44, "Philippe BENAS" 
<0d88e888355a-dmarc-requ...@jiscmail.ac.uk> wrote:

Dear Adrian,
OK, I understand. You might be perfectly right. Moreover as I wrote it is 
difficult to tell something from a single mono view picture.And as you are 
pointing out their Ramachadran plots doe not look good at all. So they are poor 
crystallographers. But the question that remains is to know if their structure 
is really wron, I mean if the backbone is incorrect or not. For sure they might 
end up with a poor reputation as crystallographers if they publish so badly 
refined structures. But they might end up as Krishna Murthy if the backbone of 
their published structures are wrong !

All the best,Philippe Philippe BENAS, Ph.D.
Dog in the manger
"Un importun survient qui trouble l'intimité, qui arrête l'expansion, qui glace 
le plaisir, - probablement comme un étranger tombant au milieu d'enfants en 
train de danser une ronde", Alfred Delvau, Dictionnaire de la langue verte 
(1866).

Laboratoire de Cristallographie et RMN Biologiques, UMR 8015 CNRS
Faculté de Pharmacie, Université Paris Descartes
Case 48
Av, de l'Observatoire
F-75270 PARIS cedex 06
+33.1.5373.1599
E-mails: philippe.benas@parisdescartes. fr, philippe_be...@yahoo.fr
URLs: http://lcrbw.pharmacie.univ- paris5.fr/ , http://lcrbw.pharmacie.univ- 
paris5.fr/spip.php?article18



  De : "Goldman, Adrian" <adrian.gold...@helsinki.fi>
 À : Philippe BENAS <philippe_be...@yahoo.fr> 
 Envoyé le : Mardi 27 juin 2017 10h30
 Objet : Re: [ccp4bb] Incorrect Structure in the PDB
   
Philippe
All I did was take their deposited mtz and coordinates.  The peak in question 
in green is about 7 sigma.  This structure (at 2 Å) has 3% 
ramanachandran-forbidden; one of their lower-resolution structures is 22%!  And 
no, given that the action of a fourier transform hasn’t changed, this is not 
the best structure that could have been built at that time (2002…).
Adrian

On 27 Jun 2017, at 11:22, Philippe BENAS <philippe_be...@yahoo.fr> wrote:
Dear Adrian, dear all, It does not look very clear to me that the side chain 
for this tyrosine is at a wrong place for instance (indeed Chi2 torsion angle 
could have multiple values = highly rotating aromatic ring). But it seems 
rather that the main chain is not correctly traced, which is probably worse. In 
addition it is difficult to tell something from just a mono view... This being 
said data collected by one group or another vary. For instance, resolution and 
hence R/free R can (generally) be improved. This does not imply that the 
structure coming from the lower resolution structure in wrong: it is just 
probably the best model that could have been built with the available data at 
that time.And on the contrary to other techniques we, crystallographers, have 
the chance of the Fourier transform which permits to have statistical 
indicators, such as R and free R, which give an indication about the accuracy 
of the reported structure. Similarly when solving the structure by experimental 
phasing we have also such indicators (e.g. the figure of merit, Rcullis, 
...).All these statistical factors (including those related to the collected 
I(hkl) themselves) allow to give more or less confidence to a deposited model. 
Now there are cases where people report a modelled part in their structure and 
this sounds fair to me as long as it is correctly stat

Re: [ccp4bb] Incorrect Structure in the PDB

2017-06-27 Thread Philippe BENAS

Dear Adrian,
OK, I understand. You might be perfectly right. Moreover as I wrote it is 
difficult to tell something from a single mono view picture.And as you are 
pointing out their Ramachadran plots doe not look good at all. So they are poor 
crystallographers. But the question that remains is to know if their structure 
is really wron, I mean if the backbone is incorrect or not. For sure they might 
end up with a poor reputation as crystallographers if they publish so badly 
refined structures. But they might end up as Krishna Murthy if the backbone of 
their published structures are wrong !

All the best,Philippe Philippe BENAS, Ph.D.
Dog in the manger
"Un importun survient qui trouble l'intimité, qui arrête l'expansion, qui glace 
le plaisir, - probablement comme un étranger tombant au milieu d'enfants en 
train de danser une ronde", Alfred Delvau, Dictionnaire de la langue verte 
(1866).

Laboratoire de Cristallographie et RMN Biologiques, UMR 8015 CNRS
Faculté de Pharmacie, Université Paris Descartes
Case 48
Av, de l'Observatoire
F-75270 PARIS cedex 06
+33.1.5373.1599
E-mails: philippe.be...@parisdescartes.fr, philippe_be...@yahoo.fr
URLs: http://lcrbw.pharmacie.univ-paris5.fr/ , 
http://lcrbw.pharmacie.univ-paris5.fr/spip.php?article18



  De : "Goldman, Adrian" <adrian.gold...@helsinki.fi>
 À : Philippe BENAS <philippe_be...@yahoo.fr> 
 Envoyé le : Mardi 27 juin 2017 10h30
 Objet : Re: [ccp4bb] Incorrect Structure in the PDB
   
Philippe
All I did was take their deposited mtz and coordinates.  The peak in question 
in green is about 7 sigma.  This structure (at 2 Å) has 3% 
ramanachandran-forbidden; one of their lower-resolution structures is 22%!  And 
no, given that the action of a fourier transform hasn’t changed, this is not 
the best structure that could have been built at that time (2002…).
Adrian

On 27 Jun 2017, at 11:22, Philippe BENAS <philippe_be...@yahoo.fr> wrote:
Dear Adrian, dear all, It does not look very clear to me that the side chain 
for this tyrosine is at a wrong place for instance (indeed Chi2 torsion angle 
could have multiple values = highly rotating aromatic ring). But it seems 
rather that the main chain is not correctly traced, which is probably worse. In 
addition it is difficult to tell something from just a mono view... This being 
said data collected by one group or another vary. For instance, resolution and 
hence R/free R can (generally) be improved. This does not imply that the 
structure coming from the lower resolution structure in wrong: it is just 
probably the best model that could have been built with the available data at 
that time.And on the contrary to other techniques we, crystallographers, have 
the chance of the Fourier transform which permits to have statistical 
indicators, such as R and free R, which give an indication about the accuracy 
of the reported structure. Similarly when solving the structure by experimental 
phasing we have also such indicators (e.g. the figure of merit, Rcullis, 
...).All these statistical factors (including those related to the collected 
I(hkl) themselves) allow to give more or less confidence to a deposited model. 
Now there are cases where people report a modelled part in their structure and 
this sounds fair to me as long as it is correctly stated in the publication and 
the PDB file. Another scenario would be a poorly resolved, I mean with 
erroneous phases, and this is probably the most tricky case (too long to debate 
in this email)
And finally the last case corresponds to real scientific frauds such as the C. 
Murthy's case and that in principle end with multiple retractions, PDB 
withdrawals and a broken scientific career (even if take 15 years to get the 
crook). And such structures must be reported to the PDB for sure ! Best 
regards,Philippe Philippe BENAS, Ph.D.
Dog in the manger
"Un importun survient qui trouble l'intimité, qui arrête l'expansion, qui glace 
le plaisir, - probablement comme un étranger tombant au milieu d'enfants en 
train de danser une ronde",Alfred Delvau,Dictionnaire de la langue verte (1866).

Laboratoire de Cristallographie et RMN Biologiques, UMR 8015 CNRS
Faculté de Pharmacie, Université Paris Descartes
Case 48
Av, de l'Observatoire
F-75270 PARIS cedex 06
+33.1.5373.1599
E-mails:philippe.be...@parisdescartes.fr, philippe_be...@yahoo.fr
URLs: http://lcrbw.pharmacie.univ-paris5.fr/ 
,http://lcrbw.pharmacie.univ-paris5.fr/spip.php?article18



De : "Goldman, Adrian" <adrian.gold...@helsinki.fi>
À : CCP4BB@JISCMAIL.AC.UK 
Envoyé le : Mardi 27 juin 2017 9h36
Objet : Re: [ccp4bb] Incorrect Structure in the PDB

There are plenty of such structures in the PDB.  We have one that we are 
rerefining at the moment - and indeed there is a whole slew of structures from 
the same author, all done sloppily.  Here’s an example of a 2 Å (!) structure.  
The Tyr clearly goes into the green blob above it, and the loop conformation

[ccp4bb] Tr : Sad nrews Pr. CPPENS passed away (quoting [AFC] Décès du prof P. COPPENS)

2017-06-25 Thread Philippe BENAS

Dear all,
In English is probably better...
The French Crystallographic Association was told about a sad news: Pr. COPPENS 
passed away.
More info ar: http://www.buffalo.edu/news/releases/2017/06/031.html

Warmest regards to our US colleagues.

- Mail transféré -

 De : "presid...@afc.asso.fr" 
 À : a...@impmc.upmc.fr 
 Envoyé le : Dimanche 25 juin 2017 13h19
 Objet : [AFC] Décès du prof P. COPPENS
   
Chers collègues,

C'est avec tristesse que nous apprenons le décès du Professeur Philip 
Coppens, l'un des géants de la cristallographie des cinquante dernières 
années.

L'AFC publiera dans les jours qui viennent une nécrologie rédigée par 
Claude Lecomte.
En attendant vous trouverez des informations sur ce grand scientifique à 
partir du site de l'Université de Buffalo:

http://www.buffalo.edu/news/releases/2017/06/031.html

Très cordialement,

Philippe Guionneau
Président de l'AFC

[ccp4bb] Tr : [AFC] Décès du prof P. COPPENS

2017-06-25 Thread Philippe BENAS

- Mail transféré -


 De : "presid...@afc.asso.fr" 
 À : a...@impmc.upmc.fr 
 Envoyé le : Dimanche 25 juin 2017 13h19
 Objet : [AFC] Décès du prof P. COPPENS
   
Chers collègues,

C'est avec tristesse que nous apprenons le décès du Professeur Philip 
Coppens, l'un des géants de la cristallographie des cinquante dernières 
années.

L'AFC publiera dans les jours qui viennent une nécrologie rédigée par 
Claude Lecomte.
En attendant vous trouverez des informations sur ce grand scientifique à 
partir du site de l'Université de Buffalo:

http://www.buffalo.edu/news/releases/2017/06/031.html

Très cordialement,

Philippe Guionneau
Président de l'AFC

Re: [ccp4bb] just out of totally idle curiosity ...

2016-11-09 Thread Philippe BENAS

Men,
We are are the end of a civilization. Just look at History. All signs are there.
As roman or greek empires it seems it is now our turn. Will we last another 
century or two ? May be yes. But we are inevitably towards the end.
In older civilizations common sense was maintained in large part by scientists 
who were also  the philosophers, thinkers and and some how politicians. 
Nowadays our voice is just lost into the wild...

Cheers to all and may we try our best, at our scale or on a larger one, to 
avoid a dark future...

Philippe
 Philippe BENAS, Ph.D.
X-ray diffraction and computing facilities manager

Laboratoire de Cristallographie et RMN Biologiques, UMR 8015 CNRS
Faculté de Pharmacie, Université Paris Descartes
Case 48
Av, de l'Observatoire
F-75270 PARIS cedex 06
+33.1.5373.1599
E-mails: philippe.be...@parisdescartes.fr, philippe_be...@yahoo.fr
URLs: http://lcrbw.pharmacie.univ-paris5.fr/ , 
http://lcrbw.pharmacie.univ-paris5.fr/spip.php?article18



  De : David Briggs <drdavidcbri...@gmail.com>
 À : CCP4BB@JISCMAIL.AC.UK 
 Envoyé le : Mercredi 9 novembre 2016 8h46
 Objet : Re: [ccp4bb] just out of totally idle curiosity ...
   
In the UK we have an authoritarian nationalist government seemingly hell bent 
on the destruction of our economy, so maybe give it a few years.Maybe try 
Germany? Actually - wait until after their election in 2017? Ditto for France.
On Wed, Nov 9, 2016, 06:33 Ricardo Padua <rpa...@brandeis.edu> wrote:

Science in Brazil will struggle with the "new" government as well, so I 
wouldn't count on that.

On Wed, Nov 9, 2016 at 12:56 AM, kaiser <kai...@caltech.edu> wrote:

 Yeah, given Europe and Canada are obvious, I think Brazil and Japan are 
actually viable alternatives if the first choices are getting too crowded. They 
do have synchrotrons and "internets".


Sent from my T-Mobile 4G LTE Device

 Original message 
From: "William G. Scott" <wgsc...@ucsc.edu> 
Date: 11/8/16 21:37 (GMT-08:00) 
To: CCP4BB@JISCMAIL.AC.UK 
Subject: [ccp4bb] just out of totally idle curiosity ... 

What’s the job situation in Europe looking like for refugee scientists these 
days?



William G. Scott
Director, Program in Biochemistry and Molecular Biology
Professor, Department of Chemistry and Biochemistry
and The Center for the Molecular Biology of RNA
University of California at Santa Cruz
Santa Cruz, California 95064
USA

http://scottlab.ucsc.edu




-- 
Ricardo Padua
Postdoctoral fellow HHMI
Kern Lab
Brandeis University
Waltham, MA


-- 

|   |
| 
|  |   | David Briggs PhDabout.me/david_briggs |

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|  |

Re: [ccp4bb] RMSD of dimers

2015-02-26 Thread Philippe BENAS

Oops, sorry: lsqman gives you the rmsd between pairs not moleman.
Additional comment: PDBSET should also give you the rmsd between B1 abd B2 
using the coordinates generated by lsqman.
Phil Philippe BENAS, Ph.D.
X-ray diffraction and computing facilities manager

Laboratoire de Cristallographie et RMN Biologiques, UMR 8015 CNRS
E-mails: philippe.be...@parisdescartes.fr, philippe_be...@yahoo.fr
URLs: http://lcrbw.pharmacie.univ-paris5.fr/ , 
http://lcrbw.pharmacie.univ-paris5.fr/spip.php?article18


  De : Philippe BENAS philippe_be...@yahoo.fr
 À : CCP4BB@JISCMAIL.AC.UK 
 Envoyé le : Jeudi 26 février 2015 15h00
 Objet : Re: [ccp4bb] RMSD of dimers
   
Dear CCP4bbers,
If I remember correctly you can do this in LSQMAN (EXPLICIT superimposition 
command if I remember well): the superimposition is made between residues of 
chain A2 onto those of chain A1, then you apply the rotation/translation to all 
the A2B2 dimer and moleman gives you the rmsd between the two pairs of dimers. 
Alternatively, I think LSQMAN allows you to calculate the rmsd between B1 and 
B2 after having applied the transformation to the all dimer.Have a look on 
GJK-DVD pages at http://xray.bmc.uu.se/usf/ .

And finally isn't Coot doing this as well (using command lines) ? I think I did 
this once...

HTS,Philippe Philippe BENAS, Ph.D.
X-ray diffraction and computing facilities manager

Laboratoire de Cristallographie et RMN Biologiques, UMR 8015 CNRS
E-mails: philippe.be...@parisdescartes.fr, philippe_be...@yahoo.fr
URLs: http://lcrbw.pharmacie.univ-paris5.fr/ , 
http://lcrbw.pharmacie.univ-paris5.fr/spip.php?article18


  De : Eugene Krissinel eugene.krissi...@stfc.ac.uk
 À : CCP4BB@JISCMAIL.AC.UK 
 Envoyé le : Jeudi 26 février 2015 14h17
 Objet : Re: [ccp4bb] RMSD of dimers
   


 No, the question seems to be slightly different. While one can use either 
CCP4's SSM or GESAMT to superpose 2 dimers, these algorithms would balance RMSD 
between both chains and produce something optimal for both chains. What is 
required, however, is optimal superposition on one pair of chains (one from 
each dimer) but measuring RMSD on the other pair of chains from same dimers. 
Nothing impossible in principle but no corresponding option in general-purpose 
aligners (this requires something like masks/selections for residues to 
superimpose and residues to measure the RMSD on). If this were a common and 
frequent problem, we could have it implemented in SSM/GESAMT.
 
 Eugene
 
 

On 26/02/2015 12:47, Eleanor Dodson wrote:
  
 
 Doesnt pisa give you some of this information? It lists all likely homodimers 
and I think gives RMSD too
  Eleanor
  
 On 24 February 2015 at 22:00, Thomas Holder thomas.hol...@schrodinger.com 
wrote:
 
Hi Dan,
 
 gaps/insertions should be no problem for PyMOL's rms_cur command, as long as 
chain identifiers match (and all other atomic identifiers!).
 
 See http://pymolwiki.org/index.php/Fit for a description of the matchmaker 
argument.
 
 Cheers,
   Thomas
  
 On 24 Feb 2015, at 16:30, D Bonsor dbon...@ihv.umaryland.edu wrote:
 
  I have a family of homodimers (denoted A1B1, A2B2, A3B3...) which I have 
  superimposed using Chain A. Several programs will produce the RMSD of Chain 
  A2, A3, A4... to Chain A1. However, I would like to know the RMSDs of Chain 
  B2, B3, B4... to Chain B1 when I have superimposed the structures relative 
  to Chain A. I have tried using Pymol though there are gaps/insertions so 
  rms/rms_cur will not work. Does anyone else have any other suggestions?
 
  Thanks in advance,
 
  Dan
 
   --
 Thomas Holder
 PyMOL Principal Developer
 Schrödinger, Inc.

Re: [ccp4bb] RMSD of dimers

2015-02-26 Thread Philippe BENAS

Dear CCP4bbers,
If I remember correctly you can do this in LSQMAN (EXPLICIT superimposition 
command if I remember well): the superimposition is made between residues of 
chain A2 onto those of chain A1, then you apply the rotation/translation to all 
the A2B2 dimer and moleman gives you the rmsd between the two pairs of dimers. 
Alternatively, I think LSQMAN allows you to calculate the rmsd between B1 and 
B2 after having applied the transformation to the all dimer.Have a look on 
GJK-DVD pages at http://xray.bmc.uu.se/usf/ .

And finally isn't Coot doing this as well (using command lines) ? I think I did 
this once...

HTS,Philippe Philippe BENAS, Ph.D.
X-ray diffraction and computing facilities manager

Laboratoire de Cristallographie et RMN Biologiques, UMR 8015 CNRS
E-mails: philippe.be...@parisdescartes.fr, philippe_be...@yahoo.fr
URLs: http://lcrbw.pharmacie.univ-paris5.fr/ , 
http://lcrbw.pharmacie.univ-paris5.fr/spip.php?article18


  De : Eugene Krissinel eugene.krissi...@stfc.ac.uk
 À : CCP4BB@JISCMAIL.AC.UK 
 Envoyé le : Jeudi 26 février 2015 14h17
 Objet : Re: [ccp4bb] RMSD of dimers
   
 No, the question seems to be slightly different. While one can use either 
CCP4's SSM or GESAMT to superpose 2 dimers, these algorithms would balance RMSD 
between both chains and produce something optimal for both chains. What is 
required, however, is optimal superposition on one pair of chains (one from 
each dimer) but measuring RMSD on the other pair of chains from same dimers. 
Nothing impossible in principle but no corresponding option in general-purpose 
aligners (this requires something like masks/selections for residues to 
superimpose and residues to measure the RMSD on). If this were a common and 
frequent problem, we could have it implemented in SSM/GESAMT.
 
 Eugene
 
 

On 26/02/2015 12:47, Eleanor Dodson wrote:
  
 
 Doesnt pisa give you some of this information? It lists all likely homodimers 
and I think gives RMSD too
  Eleanor
  
 On 24 February 2015 at 22:00, Thomas Holder thomas.hol...@schrodinger.com 
wrote:
 
Hi Dan,
 
 gaps/insertions should be no problem for PyMOL's rms_cur command, as long as 
chain identifiers match (and all other atomic identifiers!).
 
 See http://pymolwiki.org/index.php/Fit for a description of the matchmaker 
argument.
 
 Cheers,
   Thomas
  
 On 24 Feb 2015, at 16:30, D Bonsor dbon...@ihv.umaryland.edu wrote:
 
  I have a family of homodimers (denoted A1B1, A2B2, A3B3...) which I have 
  superimposed using Chain A. Several programs will produce the RMSD of Chain 
  A2, A3, A4... to Chain A1. However, I would like to know the RMSDs of Chain 
  B2, B3, B4... to Chain B1 when I have superimposed the structures relative 
  to Chain A. I have tried using Pymol though there are gaps/insertions so 
  rms/rms_cur will not work. Does anyone else have any other suggestions?
 
  Thanks in advance,
 
  Dan
 
   --
 Thomas Holder
 PyMOL Principal Developer
 Schrödinger, Inc.

Re: [ccp4bb] Validity of Ion Sites in PDB

2014-03-07 Thread Philippe BENAS

Dear all and dear Jacob

Please have also a look at another paper from Manfred where they show that 
both difference electron-density maps and anomalous difference 
electron-density maps suggest that in crystals grown from a sodium sulfate 
solution PPE binds Na+ in its metal-binding site. [Porcine  pancreatic  
elastase] :
Weiss,
M. S., Panjikar, S., Nowak, E.  Tucker, P. A. (2002). Acta crystallographica. 
Section D, Biological crystallography 58,
1407-1412


All the best,
Philippe
 


Philippe BENAS, Ph.D.
X-ray diffraction and computing facilities manager

Laboratoire de Cristallographie et RMN Biologiques, UMR 8015 CNRS

E-mails: philippe.be...@parisdescartes.fr, philippe_be...@yahoo.fr
URLs: http://lcrbw.pharmacie.univ-paris5.fr/ , 
http://lcrbw.pharmacie.univ-paris5.fr/spip.php?article18








 De : Manfred S. Weiss manfred.we...@helmholtz-berlin.de
À : CCP4BB@JISCMAIL.AC.UK 
Envoyé le : Vendredi 7 mars 2014 13h02
Objet : Re: [ccp4bb] Validity of Ion Sites in PDB
 

There is another paper out there, which describes the use of long
wavelengths
to define anomalously scattering substructures. This method certainly
helps to
distinguish water molecules from something else, such as chloride for
instance.

http://journals.iucr.org/d/issues/2007/03/00/dz5094/index.html

Cheers, Manfred


On 07.03.2014 11:12, Murray, James W wrote:
 Dear all,

 It is well known that  you can look at anomalous difference maps to see 
 heavier atoms - although I think not enough people do it. One technique that 
 I think is powerful, but under-used is to calculate element-specific maps by 
 taking the difference of anomalous difference data from just above and below 
 the absorption edge. This paper introduces the technique and explains it well 
 http://journals.iucr.org/d/issues/2005/05/00/he5321/index.html. I suspect if 
 this method were more used, many mis-labeled metals in proteins would come to 
 light.

 James

 --
 Dr. James W. Murray
 Lecturer in Biotechnology
 Dept. Life Sciences
 Imperial College, London
 Tel: +44 (0)20 759 48895
 
 From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Tim Gruene 
 [t...@shelx.uni-ac.gwdg.de]
 Sent: Friday, March 07, 2014 9:44 AM
 To: CCP4BB@JISCMAIL.AC.UK
 Subject: Re: [ccp4bb] Validity of Ion Sites in PDB

 -BEGIN PGP SIGNED MESSAGE-
 Hash: SHA1

 Dear Jacob,

 the 'check-my-metal' server at http://csgid.org/csgid/metal_sites/
 lists a couple of references which might be of interest.

 As usual in crytallography one must understand the science in order to
 understand the reliability of the models from the PDB. They are not
 the truth but only models to explain the data from a diffraction
 experiment.

 Best,
 Tim



 On 03/06/2014 08:45 PM, Keller, Jacob wrote:
 Dear Crystallographers,

 I was curious whether there has been a rigorous evaluation of ion
 binding sites in the structures in the pdb, by PDB-REDO or
 otherwise. I imagine that there is a considerably broad spectrum of
 habits and rigor in assigning solute blobs to ion X or water, and
 in fact it would be difficult in many cases to determine which ion
 a given blob really is, but there should be at least some fraction
 of ions/waters which can be shown from the x-ray data and known
 geometry to be X and not Y. This could be by small anomalous
 signals (Cl and H2O for example), geometric considerations, or
 something else. Maybe this does not even matter in most cases, but
 it might be important in others...

 All the best,

 Jacob Keller


 *** Jacob Pearson Keller,
 PhD Looger Lab/HHMI Janelia Farms Research Campus 19700 Helix Dr,
 Ashburn, VA 20147 email: kell...@janelia.hhmi.org
 ***

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

 GPG Key ID = A46BEE1A

 -BEGIN PGP SIGNATURE-
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 Comment: Using GnuPG with Icedove - http://www.enigmail.net/

 iD8DBQFTGZUEUxlJ7aRr7hoRAtC+AKDr6cJzgWgUAWPO6AYmDHMlFs6gbwCg8+E/
 Yj2NVdKiYBq9O28v9eCQWDA=
 =YkXc
 -END PGP SIGNATURE-

--
Dr. Manfred. S. Weiss
Helmholtz-Zentrum Berlin für Materialien und Energie
Macromolecular Crystallography (HZB-MX)
Albert-Einstein-Str. 15
D-12489 Berlin
GERMANY
Fon:   +49-30-806213149
Fax:   +49-30-806214975
Web:  http://www.helmholtz-berlin.de/bessy-mx
Email: mswe...@helmholtz-berlin.de




Helmholtz-Zentrum Berlin für Materialien und Energie GmbH

Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V.

Aufsichtsrat: Vorsitzender Prof. Dr. Dr. h.c. mult. Joachim Treusch, stv. 
Vorsitzende Dr. Beatrix Vierkorn-Rudolph
Geschäftsführung: Prof. Dr. Anke Rita Kaysser-Pyzalla, Thomas Frederking

Sitz Berlin, AG Charlottenburg, 89 HRB 5583

Postadresse:
Hahn-Meitner-Platz 1
D

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[ccp4bb] Tr : Sad nrews Pr. CPPENS passed away (quoting [AFC] Décès du prof P. COPPENS)

[ccp4bb] Tr : [AFC] Décès du prof P. COPPENS

Re: [ccp4bb] just out of totally idle curiosity ...

Re: [ccp4bb] RMSD of dimers

Re: [ccp4bb] RMSD of dimers

Re: [ccp4bb] Validity of Ion Sites in PDB

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