Re: [ccp4bb] sftools

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

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

ntact 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

Re: [ccp4bb] (R)MS

ather 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

Re: [ccp4bb] Using SFall for map conversion

-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

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

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 +33.3.8841.710

Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] High Rfree - ice ring

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

Re: [ccp4bb] Interesting pattern on a crystallization drop

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 +33.3.8841.7

Re: [ccp4bb] 3D

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

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

. 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

Re: [ccp4bb] 3D Glasses (stereo)

,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

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

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-mail

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

x27;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, phil

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

under Windows. 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

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

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

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

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

Re: [ccp4bb] Strange Diffraction pattern! Protein/DNA complex or DNA alone crystal?

le 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, Univer

Re: [ccp4bb] Off-topic question

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

Re: [ccp4bb] phenix refinement about cis-proline

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. Labo

Re: [ccp4bb] Unknown electron density

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, - pro

Re: [ccp4bb] Unknown electron density

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", Alfre

Re: [ccp4bb] Unknown electron density

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'int

Re: [ccp4bb] Unknown electron density

edel 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

[ccp4bb] My apologies to the PDB-REDO team

arena 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

Re: [ccp4bb] Incorrect Structure in the PDB

ng). 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, Dict

Re: [ccp4bb] Incorrect Structure in the PDB

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, Dic

Re: [ccp4bb] Incorrect Structure in the PDB

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, Dictio

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

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.f

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

- 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 cristallo

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

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

Re: [ccp4bb] RMSD of dimers

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 man

Re: [ccp4bb] RMSD of dimers

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-pari

Re: [ccp4bb] Validity of Ion Sites in PDB

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 comput

Re: [ccp4bb] AW: [ccp4bb] help with strange density map

  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