Re: [ccp4bb] problem transferring ccp4i2 projects from one computer to another

Dear Stuart Thank you for your reply Yes, you are right. The reports are not displayed for any project (not just the imported ones). What should I look at to solve the problem ? Stefano - Mail original - > De: "Stuart McNicholas" > À: "Stefano Trapani" &

Re: [ccp4bb] superpose crystal objects in CCP4MG or other software

the possibility of easily performing steps 1-4 (i.e. changing the origin and orientation of a crystal with respect to the orthogonal reference frame) would be a valuable tool in CCP4MG (or any other graphics crystallographic software). Best regards. Stefano Trapani Le 2021-06-03 01:49, Jon

Re: [ccp4bb] superpose crystal objects in CCP4MG or other software

Hi Boaz Thank you. That works in Chimera (first superpose, then symmetry expand) but not in CCP4MG (independently of the order of the operations). It would be nice to have an equivalent option implemented in CCP4MG. Best regards Stefano Trapani Le 2021-06-02 16:20, Boaz Shaanan a

Re: [ccp4bb] superpose crystal objects in CCP4MG or other software

ansform coordinates -> > Enter transformation > ii) Save the molecule: Molecule Icon -> File save/restore -> Save to file. > iii) Load in the saved molecule > iv) For the new file: Molecule Icon -> Create crystal object. > > (Maybe ii) and iii) are not necessary.) &

Re: [ccp4bb] {Disarmed} AW: [ccp4bb] superpose crystal objects in CCP4MG or other software

bulletin board IM AUFTRAG VON Stefano > Trapani > GESENDET: Mittwoch, 2. Juni 2021 14:31 > AN: CCP4BB@JISCMAIL.AC.UK > BETREFF: [ccp4bb] superpose crystal objects in CCP4MG or other software > > Dear all > > I would like to visually compare (using some molecular graphics sof

[ccp4bb] superpose crystal objects in CCP4MG or other software

stent with the new origin/orientation ? * If yes: can the transformation be defined by a least-squares superposition between molecules from the two crystal objects ? Best regards -- Stefano Trapani Maître de Conférences http://www.cbs.cnrs.fr/index.php/fr/personnel?PERS=Stefano

[ccp4bb] matrix decomposition problem

wondering if : * further solutions may exist * there is a criterion to establish the existence /number of these solutions * there is a practical way of calculating them -- Stefano Trapani Maître de Conférences http://www.cbs.cnrs.fr/index.php/fr/personnel?PERS=Stefano

Re: [ccp4bb] OT: Terminal Command-P

Le 2019-04-01 08:53, Paul Emsley a écrit : > Dear All, Sometime I use a Mac. A niggling issue I have is that, in a > Terminal, Command-P doesn't act like Alt-P in (say) a gnome-terminal try ESC-p (not simultaneously) --- Stefano Trapani Maître de Conférences http://www.

Re: [ccp4bb] collective term for hydrogen bonds and salt bridges

27;s what I was referring to when I mentioned "enthalpic > interactions". > > And I think you're saying the same thing - which is cool. > > On 19/09/2018 15:06, Stefano Trapani wrote: >> Hi Frank > > I mean that, in my opinion, the term "entha

Re: [ccp4bb] collective term for hydrogen bonds and salt bridges

> measure it. Which is what that abstract also goes on about. > > On 19/09/2018 10:54, Stefano Trapani wrote: > > Le 2018-09-19 11:59, Frank von Delft a écrit : > > I believe medicinal chemists do indeed talk about "enthalpic interactions". > Frank >

Re: [ccp4bb] collective term for hydrogen bonds and salt bridges

ducation 1998 _75_ (1), 116 DOI: 10.1021/ed075p116 https://pubs.acs.org/doi/abs/10.1021/ed075p116 [6] Stefano > On 19/09/2018 10:40, Stefano Trapani wrote: > > Le 2018-09-18 19:31, Daniel M. Himmel, Ph. D. a écrit : > > (where hydrophobic interactions result from v

Re: [ccp4bb] collective term for hydrogen bonds and salt bridges

] Being mainly of an entropic nature, hydrophobic "contacts" are not the direct result of real microscopic "forces" that act between apolar groups. The terms "forces" and "interactions" in widely used expressions like "hydrophobic forces" and "

Re: [ccp4bb] definition of "apo" and alternatives?

See also the IUPAC reccomandations : https://goldbook.iupac.org/html/A/A00417.html https://goldbook.iupac.org/html/H/H02836.html --- Stefano Trapani Maître de Conférences http://www.cbs.cnrs.fr/index.php/fr/personnel?PERS=Stefano%20Trapani - Centre de

[ccp4bb] Some TLS issues in REFMAC5

/refine.2d.pdb:ATOM 3 CB ALA A 1 19.748 -5.555 8.682 1.00 11.10 C ./refine.2d.pdb:ATOM 4 C ALA A 1 18.905 -4.806 6.397 1.00 10.36 C ./refine.2d.pdb:ATOM 5 O ALA A 1 17.698 -4.380 6.390 1.00 11.19 O -- Stefano Trapani Maître de Conférences http://www.cbs.cnrs.fr/index.php/fr/personnel?PERS=Stefano%20T

Re: [ccp4bb] MR phasing using Negative Stain EM reconstruction

Dear Pascal have a look at : https://doi.org/10.1107/S0907444910002763 Acta Cryst. (2010). D66, 514-521 Macromolecular crystal data phased by negative-stained electron-microscopy reconstructions S. Trapani, G. Schoehn, J. Navaza and C. Abergel Best, --- Stefano Trapani Maître de

Re: [ccp4bb] AMoRe fails to use model coordinates

You could try the stand-alone version of AMoRe from Jorge Navaza's web site. http://mem.ibs.fr/JORGE/index.html Stefano TRAPANI Maître de Conférences Centre de Biochimie Structurale (CBS) CNRS UMR 5048; UM1; UM2; INSERM UMR 554 29 rue de Navacelles 34090 MONTPELLIER Cedex - France Tel

[ccp4bb] theta

(the angle between the incident or diffracted ray and the reflecting crystal planes). However, I hear sometimes calling theta the scattering angle. Is this just a misuse of the term ? Stefano TRAPANI Centre de Biochimie Structurale (CBS) CNRS UMR 5048; UM1; UM2; INSERM UMR 554 29 rue de Navacell

[ccp4bb] Alternative origin list in CCP4 documentation

--- Stefano TRAPANI Centre de Biochimie Structurale (CBS) CNRS UMR 5048; UM 1; UM 2; INSERM UMR 554 29 rue de Navacelles 34090 MONTPELLIER Cedex, France Tel : +33 (0)4 67 41 77 29 Fax : +33 (0)4 67 41 79 13

[ccp4bb] small-protein EM models for crystal structure solution

you -- -- Stefano Trapani, PhD Laboratoire de Microscopie Électronique Structurale Institut de Biologie Structurale (IBS) J.P. Ebel UMR 5075, CNRS 41, rue Jules Horowitz F-38027 GRENOBLE Cedex 1 phones: (from France: replace ++33 with 0) ++33 4 3878.9262 FAX: ++3