Re: [ccp4bb] refinement of 0.73A data in shelxl

That doesn't sound right re: PART numbers classically: PART 1 majority disordered atoms with FVAR/occupancy of e.g. "21." instead of usual "11." PART 2 minority disordered atoms with FVAR/occupancy of e.g. "-21." PART 0 The 21.000/-21.000 pairs makes the sum of occupancies add to 1

Re: [ccp4bb] refinement of 0.73A data in shelxl

Dear Matthias, some developers introduce new features of their refinement programs with the words " ... which has been there in SHELXL since the beginning of time". If you are only looking for two conformations, you are looking for the combination of free variable number N with part N and part

Re: [ccp4bb] refinement of 0.73A data in shelxl

I am not sure about in the PDB format or mmCIF format. However, other refinement programs have this ability too, e.g. the occupancy groups of refmac http://www.ysbl.york.ac.uk/refmac/data/refmac_keywords.html#Occupancy buster refine has a tool pdb2occ to help generate appropriate groupings in

Re: [ccp4bb] refinement of 0.73A data in shelxl

Hello, I think the secret of that type of coupled occupancy refinement lies in the SUMP command, but it's not one I have tangled with - others will know more.Jon CooperOn 6 Feb 2020 19:10, "Barone, Matthias" wrote: Sorry if the mail was not clear. I figured that out now yes. As I wrote in the

Re: [ccp4bb] refinement of 0.73A data in shelxl

Sorry if the mail was not clear. I figured that out now yes. As I wrote in the update, I found this stupid error I made and now everything looks good. Now that I got the feeling of how shelxl works, I miss one of it's features in the pdb format, namely the possibility to link occupancies of a do

[ccp4bb] Postdoc in Paris, France: Methods development for cryo-electron microscopy image analysis

Dear Colleagues: A postdoc position is available in my lab on methods development for studying continuous conformational changes of biomolecular complexes by cryo-electron microscopy (*https://doi.org/10.1002/pro.3772 * ; *https://doi.org/10.1016/j.sbi.2016.12.011

Re: [ccp4bb] refinement of 0.73A data in shelxl

Hello, hope I can help.OK, so here is the disp table... SFAC  C H CL N O   DISP $C     0.00510    0.00239     15.73708 DISP $H    -0.2    0.0      0.66954 DISP $CL    0.18845    0.21747   1035.16450 DISP $N     0.00954    0.00480     28.16118 DISP $O     0.01605    0.00875     47.79242If we

Re: [ccp4bb] Representation within tutors at workshops

Hi All, On Thu, Feb 6, 2020 at 3:12 PM Winter, Graeme (DLSLtd,RAL,LSCI) wrote: > So - sadly for the environment and funding agencies - I can see excellent > arguments for *both* expert users and developers to be attending the > workshops - which would also provide opportunities for early career

Re: [ccp4bb] Representation within tutors at workshops

Dear Selina, All, Apropos: For one, there are expert users for the software taught at these courses. Often, the software developers know these persons, and it would be great if they could nominate at least one or two persons who could teach in their place, having gender balance and (age) diver

Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] Representation within tutors at workshops

Greetings - an important recent article from Science, I thought would be good to include as background reading: “NIH’s new cluster hiring program aims to help schools attract diverse faculty” “The National Institutes of Health (NIH) is hoping universities will use a controversial—and largely un

Re: [ccp4bb] refinement of 0.73A data in shelxl

Dear Matias, I fear some of your earlier problems are due to this: The atom types for some of your ligand atoms, including the CL , are wrong in the PDB version REFMAC and PHENIX both get the formfactor from the atom type.. Of course this does not matter to SHELX once it reformats the coordinates

Re: [ccp4bb] Representation within tutors at workshops

Dear all, I couldn’t agree more to that what Rachelle wrote - thanks a lot! Being a rather junior member of the community myself, I would like to support two points in particular. For one, there are expert users for the software taught at these courses. Often, the software developers know thes

[ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] Macromolecular Crystallography workshop in South America 2020

Dear Bärbel, this is a good point. Last fall, I attended the bachelors ceremony for informatics students for my daughter. I was somewhat surprised to see that most German graduates were male, but that most Indian graduates were female. At the reception afterwards when talking to some people I d

Re: [ccp4bb] Macromolecular Crystallography workshop in South America 2020

Gosh Emmanual, your email is one amazing example of what the problem is, every single paragraph - thanks for putting that one out! My last email for this subject, I promise. Thanks a lot for the off-list feedbacks! Bärbel -- Bärbel Blaum, PhD Inthera Bioscience AG Einsiedlerstrass

Re: [ccp4bb] Macromolecular Crystallography workshop in South America 2020

And Eleanor Dodson, of course!!! E. From: "ΕΜΜΑΝΟΥΗΛ ΣΑΡΕΙΔΑΚΗΣ" To: "CCP4BB" Sent: Thursday, 6 February, 2020 12:15:07 Subject: Re: [ccp4bb] Macromolecular Crystallography workshop in South America 2020 Dear All, To strike a more positive note, crystallography (esp. macromolecular)

Re: [ccp4bb] Macromolecular Crystallography workshop in South America 2020

This all to me feels a bit like a slow-moving twitter storm (And yes I am a white, privileged male, I know…but I am Jewish, so I do have a little bit of insight into what prejudice looks like: growing up in the UK in the 1960s was to be exposed to casual anti-Semitism, amongst other kinds of rac

Re: [ccp4bb] Macromolecular Crystallography workshop in South America 2020

Dear All, To strike a more positive note, crystallography (esp. macromolecular) has always had a very high representation of women at top levels: Kathleen Lonsdale, Dorothy Crowfoot Hodgkin, Rosalind Franklin and Ada Yonath are the most famous names that immediately come to mind, but there ar

Re: [ccp4bb] Macromolecular Crystallography workshop in South America 2020

Dear all, yes, there are more male computational crystallographers than females – the question we can ask ourselves here is: Do we think there is some biological reason for this? Obviously there isn’t. So things are wrong as they stand. Are we, nevertheless, ok with this current state of aff

Re: [ccp4bb] Macromolecular Crystallography workshop in South America 2020

Dear all, As this discussion is receiving so much deserving attention, I should say that being an organiser of crystallography events in the past and in the future, we always strive to *intentionally* achieve a good gender balance of speakers. Sometimes we did even well, albeit often not well e

Re: [ccp4bb] Macromolecular Crystallography workshop in South America 2020

 Dear all, Glad to hear the awareness of sensitive ethical issues. From the observation of being in the crystallographic field for many years, the treatment and recognition for female minorities are probably much more profound than looking at the apparent numbers in tutoring the training cour

Re: [ccp4bb] Representation within tutors at workshops

Dear all, Representation is a topic that is near and dear to my heart, and several of the comments in this thread have resonated with me, both positively and otherwise, so it’s hard to stay on the sidelines. Here are a few of my thoughts. As Graeme and others have pointed out, I believe ­most o