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)

.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

Re: [ccp4bb] (R)MS

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

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 +33.3.8841.7109 E-mails

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 +33.3.8841.7109 E

Re: [ccp4bb] 3D

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

[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

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

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

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-i

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?

ng 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

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 cedex

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, - probablement

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", Alfred Delvau, Dicti

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'intimité

Re: [ccp4bb] Unknown electron density

l 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'

[ccp4bb] My apologies to the PDB-REDO team

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

Re: [ccp4bb] Incorrect Structure in the PDB

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 langu

Re: [ccp4bb] Incorrect Structure in the PDB

? 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 ve

Re: [ccp4bb] Incorrect Structure in the PDB

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 la

[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 :

[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

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

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

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 manager Laboratoire de Cristallographie et

Re: [ccp4bb] RMSD of dimers

) ? 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

Re: [ccp4bb] Validity of Ion Sites in PDB

. [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