Re: [ccp4bb] Add hydrogens

2021-09-29 Thread Tim Gruene
exe?SUBED1=CCP4BB=1 > > This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a > mailing list hosted by www.jiscmail.ac.uk, terms & conditions are > available at https://www.jiscmail.ac.uk/policyandsecurity/ -- -- Tim Gruene Head of the Centre for X-ray Structure

Re: [ccp4bb] criteria to set resolution limit

2021-09-12 Thread Tim Gruene
> To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 > > This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a > mailing list hosted by www.jiscmail.ac.uk, terms & conditions are > available at

Re: [ccp4bb] Some questions on tools for CCP4i2cloud: pdbset, pdbcur, coordconv, sftools

2021-08-30 Thread Tim Gruene
s issued to members of www.jiscmail.ac.uk/CCP4BB, a > mailing list hosted by www.jiscmail.ac.uk, terms & conditions are > available at https://www.jiscmail.ac.uk/policyandsecurity/ -- -- Tim Gruene Head of the Centre for X-ray Structure Analysis Faculty of Chemistry University of

Re: [ccp4bb] AI papers in experimental macromolecular structure determination

2021-08-03 Thread Tim Gruene
ics, Universität > Hamburg Luruper Chaussee 149 / Bldg. 610 (HARBOR) | 22761 Hamburg | > Germany Tel. +49 (0)40 42838 3651 > www.thorn-lab.de<http://www.thorn-lab.de> | www.insidecorona.net > > > ##

Re: [ccp4bb] using chooch

2021-07-20 Thread Tim Gruene
ssage was issued to members of www.jiscmail.ac.uk/CCP4BB, a > mailing list hosted by www.jiscmail.ac.uk, terms & conditions are > available at https://www.jiscmail.ac.uk/policyandsecurity/ -- -- Tim Gruene Head of the Centre for X-ray Structure Analysis Faculty of Chemistry Unive

Re: [ccp4bb] pictures in emails

2021-07-19 Thread Tim Gruene
subscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 > > This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a > mailing list hosted by www.jiscmail.ac.uk, terms & conditions are > available a

Re: [ccp4bb] Strange indexing problem

2021-07-05 Thread Tim Gruene
; This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a > mailing list hosted by www.jiscmail.ac.uk, terms & conditions are > available at https://www.jiscmail.ac.uk/policyandsecurity/ -- -- Tim Gruene Head of the Centre for X-ray Structur

Re: [ccp4bb] How to process two datasets 45 degrees apart?

2021-07-01 Thread Tim Gruene
www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 > > This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a > mailing list hosted by www.jiscmail.ac.uk, terms & conditions are > available at https://www.jiscmail.ac.uk/policyandsecurity/ -- -- Tim Gruene Head of

Re: [ccp4bb] Co crystalization with less soluble ligand.

2021-06-23 Thread Tim Gruene
t; > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 > > This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a >

Re: [ccp4bb] Should Rmerge be reported?

2021-06-10 Thread Tim Gruene
; Helmholtz-Zentrum Berlin für Materialien und Energie GmbH > > Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher > Forschungszentren e.V. > > Aufsichtsrat: Vorsitzender Dr. Volkmar Dietz, stv. Vorsitzende Dr. > Jutta Koch-Unterseher Geschäftsführung: Prof. Dr. Bernd

Re: [ccp4bb] Meaning of a pdb entry

2021-05-31 Thread Tim Gruene
ww.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 > > > > This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a > > mailing list hosted by www.jiscmail.ac.uk, terms & conditions are > > available at https://www.jiscmail.ac.uk/policyandsecurity/ >

Re: [ccp4bb] (R)MS

2021-05-27 Thread Tim Gruene
; To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 > > ############ > > To unsubscribe from the CCP4BB list, click the following link: > https:

Re: [ccp4bb] weight matrix selection

2021-04-08 Thread Tim Gruene
the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 > > This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a > mailing list hosted by www.jiscmail.ac.uk, terms & conditions are > available at https://www

Re: [ccp4bb] cryptic error message trying to use LigPlot on an unknown ligand

2021-04-07 Thread Tim Gruene
returned by the PRODRG run. Always with the > same cryptic error message provided by the software (oops, app). > > Thanks, > > Fred. > -- -- Tim Gruene Head of the Centre for X-ray Structure Analysis Faculty of Chemistry University of Vienna Phone: +43-1-4277-70202

Re: [ccp4bb] Maniatis: Molecular Cloning

2021-03-26 Thread Tim Gruene
gt; > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 > > This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a > mailing list hosted by www.jiscmail.ac.uk, terms & conditions are

[ccp4bb] Maniatis: Molecular Cloning

2021-03-26 Thread Tim Gruene
Hello erveryone, does anyone know whether Maniatis/Fritsch/Sambrock "Molecular Cloning" are still being printed and sold? I could not find it by ISBN (0‐87969‐309‐6) at my favourite book store. Or is there anything comparable? Best regards, Tim -- -- Tim Gruene Head of the Centre

Re: [ccp4bb] Linux Distro for setting up workstations - Is CentOS still a good choice?

2021-02-20 Thread Tim Gruene
## > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 > > This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a > mailing list hosted by www.jiscmail.ac.uk, terms & conditions

Re: [ccp4bb] Contagious, Self-Distributing "Vaccines?"

2021-02-19 Thread Tim Gruene
economic growth is the > > real life saver. Does the prolonging of a reasonably measurable > > number well-lived lives in the West outweigh the extinguishing of a > > hard-to-assess number of much younger lives in the rest of the > > world? I'm glad I don't have to make tha

Re: [ccp4bb] Contagious, Self-Distributing "Vaccines?"

2021-02-19 Thread Tim Gruene
the following link: > >>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 > >>> > >> > >> -- > >> > >> To unsubscribe from the CCP4BB list, click the following link: > >> https://www.jisc

Re: [ccp4bb] Contagious, Self-Distributing "Vaccines?"

2021-02-17 Thread Tim Gruene
to manipulate A, B, C yet? > > Or maybe it's too scary for primetime...nightmare bio-warfare > apocalypse? > > Has this sort of thing been done, or does it have a name? > > Jacob -- -- Tim Gruene Head of the Centre for X-ray Structure Analysis Faculty of Chemistr

Re: [ccp4bb] RCrane in Coot 0.8.9.2 for Mac

2021-02-09 Thread Tim Gruene
sage was issued to members of www.jiscmail.ac.uk/CCP4BB, a > mailing list hosted by www.jiscmail.ac.uk, terms & conditions are > available at https://www.jiscmail.ac.uk/policyandsecurity/ -- -- Tim Gruene Head of the Centre

Re: [ccp4bb] Reprocessing images collected on an Eiger2 detector using Xia2Dials on CCP4i2's GUI

2021-01-04 Thread Tim Gruene
; attachments are free from viruses and we cannot accept liability > > for any damage which you may sustain as a result of software > > viruses which may be transmitted in or with the message. > > Diamond Light

Re: [ccp4bb] version for old AMD processors

2020-12-10 Thread Tim Gruene
was issued to members of www.jiscmail.ac.uk/CCP4BB, a > mailing list hosted by www.jiscmail.ac.uk, terms & conditions are > available at https://www.jiscmail.ac.uk/policyandsecurity/ -- -- Tim Gruene Head of the Centre for X-ray

Re: [ccp4bb] wsl2 Ubuntu 20.04

2020-12-07 Thread Tim Gruene
4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 > > This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a > mailing list hosted by www.jiscmail.ac.uk, terms & conditions are > available at https://www.jiscmail.ac.uk/p

[ccp4bb] Workshop on electron crystallography Dec 17th 2020

2020-12-04 Thread Tim Gruene
to the registration at the workshop URL https://www.uni-ulm.de/en/einrichtungen/hrem/christmas-elec-crystall/christmas-elec-crystall/ The workshop program will soon be available. Best regards, TG on behalf of Tatiana Gorelik, Mauro Gemmi, Lukas Palatinus, and Stephanie Kodjikian -- -- Tim Gruene

Re: [ccp4bb] Stabilizing Mitegen reusable bases/mounts

2020-11-15 Thread Tim Gruene
gi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 > > This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a > mailing list hosted by www.jiscmail.ac.uk, terms & conditions are > available at https://www.jiscmail.ac.uk/policyandsecurity/ -- -- Tim

Re: [ccp4bb] Rietveld refinement of polycrystalline electron diffraction data

2020-11-12 Thread Tim Gruene
application, I would be happy to hear! > > > > If any additional clarification is need, I'll fill it in! > > > > Best, > > Kamil > > > > > > > > To unsubscr

Re: [ccp4bb] R free rising

2020-11-04 Thread Tim Gruene
Nika > > > > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 > > This message was issued to members of

Re: [ccp4bb] [xds] how to specify measuring angle

2020-10-08 Thread Tim Gruene
age was issued to members of www.jiscmail.ac.uk/CCP4BB, a > mailing list hosted by www.jiscmail.ac.uk, terms & conditions are > available at https://www.jiscmail.ac.uk/policyandsecurity/ -- -- Tim Gruene Head of the Centre

Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] AW: Going back to Coot 0.8

2020-09-09 Thread Tim Gruene
t; https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 > > This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a > mailing list hosted by www.jiscmail.ac.uk, terms & conditions are >

Re: [ccp4bb] AW: Going back to Coot 0.8

2020-09-09 Thread Tim Gruene
ail.ac.uk/policyandsecurity/ > > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 > > This message was issued to members o

Re: [ccp4bb] Omega angles with molprobity

2020-09-04 Thread Tim Gruene
probity tool provides that info. Any idea? > > Many thanks! > > Best wishes > > Joana Pereira > -- -- Tim Gruene Head of the Centre for X-ray Structure Analysis Faculty of Chemistry University of Vienna Phon

Re: [ccp4bb] diffdump in CCP4 7.1

2020-08-21 Thread Tim Gruene
alent script in CCP4 7.1? > > > > Thanks, > > Jan > -- -- Tim Gruene Head of the Centre for X-ray Structure Analysis Faculty of Chemistry University of Vienna Phone: +43-1-4277-70202 GPG Key ID = A46BEE1A

Re: [ccp4bb] Problems with refinement of nucleic acid structure

2020-07-30 Thread Tim Gruene
too high for this small > object and very high resolution, in my opinion. > > Best regards, > > Rafal > > > > To unsubscribe from th

Re: [ccp4bb] [EXTERNAL] chirality with electron diffraction

2020-07-20 Thread Tim Gruene
in theory > can be done, but only difficult in practice? > > Best, > Herman > > > > -Ursprüngliche Nachricht- > Von: Tim Gruene > Gesendet: Montag, 20. Juli 2020 11:03 > An: CCP4 bulletin board ; Schreuder, Herman > /DE Betreff: [EXTERNAL] chirality wit

[ccp4bb] chirality with electron diffraction

2020-07-20 Thread Tim Gruene
the liberty to adjust the subject. -- -- Tim Gruene Head of the Centre for X-ray Structure Analysis Faculty of Chemistry University of Vienna Phone: +43-1-4277-70202 GPG Key ID = A46BEE1A To unsubscribe from the CCP4BB list

Re: [ccp4bb] Quote source inquiry

2020-07-17 Thread Tim Gruene
fferent cell parameters) then refine cell again. Please also > > note that if you are refining cell parameters then the resolution > > of the data will also change (if you are refining all six > > parameters then changes will be anisotropic) > > > > > > In gene

Re: [ccp4bb] Quote source inquiry

2020-07-16 Thread Tim Gruene
; > radius and "a" the thickness of a pizza. Then the volume > > >of that pizza is equal to pi*z*z*a ! > > > ** > > > > > > ##

Re: [ccp4bb] Accessing full list of programs in CCP4I2

2020-07-07 Thread Tim Gruene
WA-JISC.exe?SUBED1=CCP4BB=1 > > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 > > #

Re: [ccp4bb] Lost extension bar in Coot

2020-06-11 Thread Tim Gruene
was issued to members of www.jiscmail.ac.uk/CCP4BB, a > mailing list hosted by www.jiscmail.ac.uk, terms & conditions are > available at https://www.jiscmail.ac.uk/policyandsecurity/ -- -- Tim Gruene Head of the Centre for X-ray Structure Analysis Faculty of Chemistry Univers

Re: [ccp4bb] Question about small molecule crystallography

2020-06-02 Thread Tim Gruene
rançois Hoh > > Centre de Biochimie Structurale, > UMR 5048 CNRS, UMR 1054 INSERM > 29, rue de navacelles > 34090 Montpellier Cedex, France. > Phone: +33 467 417 706 > Fax: +33 467 417 913 > > > -- -- Tim Gruene Head of

Re: [ccp4bb] Strange Pseudosymmetry Effects

2020-05-28 Thread Tim Gruene
> > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 > > This message was

Re: [ccp4bb] What refinement programs are fully Open Source?

2020-05-07 Thread Tim Gruene
03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2Fwebadmin%3FSUBED1%3DCCP4BB%26A%3D1data=02%7C01%7Cpr159%40leicester.ac.uk%7Cf8cc2fb23bb84707d7a708d7f2a96338%7Caebecd6a31d44b0195ce8274afe853d9%7C0%7C0%7C637244681

Re: [ccp4bb] disinfecting keyboards

2020-05-06 Thread Tim Gruene
hat suffered from having > >> the writing removed with that or 100% ethanol. Both work and as > >> long as they are 100% (no water), the keyboard and mouse have no > >> issues. > >> > >> > >> Diana > >> > >> > >> *

[ccp4bb] disinfecting keyboards

2020-04-29 Thread Tim Gruene
. But maybe there are other ways that won't require gloves? Best regards, Tim -- -- Tim Gruene Head of the Centre for X-ray Structure Analysis Faculty of Chemistry University of Vienna Phone: +43-1-4277-70202 GPG Key ID = A46BEE1A

Re: [ccp4bb] superimposition of 3D structures with the DNA part only

2020-04-24 Thread Tim Gruene
superpose (two protein:dsDNA > complexes). Not using the protein part, but superposition through the > dsDNA. > > I'm not quite certain what is the "best" way of doing this. > > Your suggestions will be appreciated, thanks. > > Fred. Vellieux > -- -- T

Re: [ccp4bb] New phasing approach

2020-04-01 Thread Tim Gruene
6 571 0536 > > -- > > Many plausible ideas vanish > > at the presence of thought > > -- > > > > > ########

Re: [ccp4bb] COVID-19 protease inhibitors - 2nd call for designs - Thurs midnight

2020-04-01 Thread Tim Gruene
/cgi-bin/webadmin?SUBED1=CCP4BB=1> > #### > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 -- -- Tim Gruene Head of the Centre for

Re: [ccp4bb] [g...@globalphasing.com: [ccp4bb] An error in the IUCr Online Dictionary of Crystallography] (fwd)

2020-03-11 Thread Tim Gruene
stromathematical curiosity: let "z" be the > radius and "a" the thickness of a pizza. Then the volume > of that pizza is equal to pi*z*z*a ! > ** > > ############ > > To unsubscribe from the CCP4BB list, click the following link: > https

[ccp4bb] arpnavigator: change contour plane orientation

2020-03-07 Thread Tim Gruene
Dear all, the arpnavigator can display the contour levels of a map ("map style plane"). Does anyone know how to change the orientation of the plane, i.e. the normal of the cutting plane? Best regards, Tim -- -- Tim Gruene Head of the Centre for X-ray Structure Analysis Faculty of

Re: [ccp4bb] Overrefinement considerations and Refmac5.

2020-03-07 Thread Tim Gruene
0.1948 > 0.2880 > > 0.0076 > > 1.6308 > > 0.1176 > > > > *Refinement Parameters* > [image: image.png] > > So like nothing looks satisfying I decided to ask my questions here... > > What do you recommend to fix my problem, which is a too large difference > between R and Rfree? > > Thank you for answ

Re: [ccp4bb] Hydrogens in PDB File

2020-03-01 Thread Tim Gruene
r refinement, > >> then it’s only fair that they be present in the deposited structure so > >> that downstream users know what went into generating the reported > >> statistics) to the practical (if the paper’s conclusions don’t rely on > >> any arguments based

Re: [ccp4bb] MX data processing with GPUs??

2020-02-18 Thread Tim Gruene
carefully and consider possible > querying to the sender before copying, disclosing or distributing it. If > you have received this email by mistake, please notify the sender and > delete it immediately. > > #### > &

Re: [ccp4bb] [3dem] [ccpem] Which resolution?

2020-02-12 Thread Tim Gruene
d references > therein (https://www.biorxiv.org/content/10.1101/224402v1) and check my > #WhyOWhy tweets (@marin_van_heel). See also: van Heel - Unveiling ribosomal > structures: the final phases - Current opinion in structural biology 10 > (2000) 259-264. > > Cheers, > Marin >

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

2020-02-07 Thread Tim Gruene
ifferent non-zero PART number are excluded; this is suitable for a > solvent molecule disordered on a special position of higher symmetry > than the molecule can take". > > I use PART 1/PART 2/PART 0 all the time in "small molecule world" but > I've used PART -1 precisely o

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

2020-02-06 Thread Tim Gruene
factor is derived from the > number next to the name." Once I adjusted the numbers in the second column > of my inhibitors to match the DISP list numbering, Rfree dropped to 16.96% > and the map looks notably better (see attached snap shot). > > > Again, thank you very much for

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

2020-02-05 Thread Tim Gruene
ribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 > > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 > > > > > To

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

2020-02-04 Thread Tim Gruene
ss it correctly? > > > > > > Thank you very much for your help! > > Best, matthias > > > > > > > > > > > > > Dr. Matthias Barone > > AG Kuehne, Rational Drug Design > > > Leibniz-Forschungsinstitut für Molekulare Pharmakologie (F

Re: [ccp4bb] Protein concentration for the initial crystallisation trials

2020-01-08 Thread Tim Gruene
ther than the > classic PCT from Hampton? Armando > > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 -- -- Tim Gruene Head of the

Re: [ccp4bb] 8/ 2263 spots indexed XDS

2019-11-29 Thread Tim Gruene
scribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 -- -- Tim Gruene Head of the Centre for X-ray Structure Analysis Faculty of Chemistry University of Vienna Phone: +43-1-4277-70202 GPG Key ID = A46BEE1A ##

Re: [ccp4bb] Shelx and debian 10

2019-10-08 Thread Tim Gruene
iously). > > Note that -rpath is not the same as -L: -L is used at link-time to find > the libraries needed to check that all the symbols are resolvable. > -rpath is used to locate shared libraries at run-time: its argument > doesn't even have to exist at link-time. If you go down this

Re: [ccp4bb] Shelx and debian 10

2019-10-07 Thread Tim Gruene
tria > > > > +43 (676) 571-0536 > > > > bernhard.r...@i-med.ac.at > > > > -- > > -- > > > > k.k. Hofkristallamt > > > > San Diego, CA 92084 > > > > 001 (925) 209-7429 > >

Re: [ccp4bb] Rfree from another mtz file

2019-09-16 Thread Tim Gruene
## > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 -- -- Tim Gruene Head of the Centre for X-ray Structure Analysis Faculty of Chemistry University of Vienna

Re: [ccp4bb] AW: [bruker-axs] cbf to sfrm

2019-08-29 Thread Tim Gruene
atform. > > > > I did not debug this new feature very thoroughly, but it worked for me so > far. > > Any bug reports are welcome to this address > tim.gru...@univie.ac.at<mailto:tim.gru...@univie.ac.at> > > > > I hope this is helpful for one or two users.

Re: [ccp4bb] [6HR5] collected on an Eiger so Rmerge not relevant

2019-08-01 Thread Tim Gruene
ay be confidential or protected from disclosure and is > only for review and use by the intended recipient. Access by anyone else is > unauthorized. Any unauthorized reader is hereby notified that any review, > use, dissemination, disclosure or copying of this information, or any act > or omiss

[ccp4bb] cbf to sfrm

2019-07-28 Thread Tim Gruene
, of SAINT, and of the SFRM header format. Kind regards, Tim cc Bruker mailing list, CCP4BB, phenixBB -- -- Tim Gruene Head of the Centre for X-ray Structure Analysis Faculty of Chemistry University of Vienna Phone: +43-1-4277-70202 GPG Key ID

Re: [ccp4bb] Resonant Scattering Directionality

2019-07-26 Thread Tim Gruene
; > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 -- -- Tim Gruene Head of the Centre for X-ray Structure Analysis Faculty of Chemistry University of Vienna Phone: +43-1-4277-70202 GPG Key ID = A46BEE1A ###

Re: [ccp4bb] RES: [ccp4bb] Se-SAD phasing

2019-07-19 Thread Tim Gruene
. > > > > Disclaimer: This email and its attachments may contain confidential > > and/or privileged information. Observe its content carefully and > > consider possible querying to the sender before copying, disclosing or > > distributing it. If you have received th

Re: [ccp4bb] Does ncs bias R-free? And if so, can it be avoided by special selection of the free set?

2019-06-05 Thread Tim Gruene
_lattice_symmetry = False > > collecting the same statistics > >(also scripted in multirefine.csh) > > > >Finally, use ref2chr.eff to refine (as previously mentined) a monomer > >in I422 (2chr.pdb) 10 times with 10% free, 50 macrocycles (also scripted >

[ccp4bb] PhD position in electron crystallography

2019-05-09 Thread Tim Gruene
send a letter of motivation, their CV, and contact details of at least one reference to me. Best regards, Tim Gruene -- -- Tim Gruene Head of the Centre for X-ray Structure Analysis Faculty of Chemistry University of Vienna Phone: +43-1-4277-70202 GPG Key ID = A46BEE1A

Re: [ccp4bb] Coot and symmetry-related waters.

2019-05-01 Thread Tim Gruene
Any clues much appreciated. > Jon.C. > > > > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 -- -- Tim Gruene Head of the Centre for X-ray Structure Analysis Faculty of Chemistry Universi

Re: [ccp4bb] High Rfree in last Shell

2019-04-16 Thread Tim Gruene
# > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 -- -- Tim Gruene Head of the Centre for X-ray Structure Analysis Faculty of Chemistry University of Vienna Phone: +43-

Re: [ccp4bb] visualising anis B factors

2019-01-23 Thread Tim Gruene
from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 > > > > To unsubscribe

Re: [ccp4bb] visualising anis B factors

2019-01-23 Thread Tim Gruene
gt; > Eleanor Dodson > > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 -- -- Tim Gruene des. Head of the Centre for X-ray Structure Analysis Faculty of Che

Re: [ccp4bb] hybrid photon counter in the home lab

2019-01-16 Thread Tim Gruene
Thank you in advance. > Wolfram Tempel > > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 -- -- Tim Gruene GPG Key ID = A46BEE1A To unsubscr

Re: [ccp4bb] Live stream of CCP4 Study Weekend?

2019-01-09 Thread Tim Gruene
###### > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 -- -- Paul Scherrer Institut Tim Gruene - persoenlich - OSUA/204 Forschungsstrasse 111 CH-5232 Villigen PSI pho

[ccp4bb] Science Mag - breakthrough 2018

2018-12-02 Thread Tim Gruene
Dear all, crystallography provides on of the candidates for the 'breakthrough of the year 2018' at Science Magazin ("Rapid chemical structures"). You can make your pick at http://www.sciencemag.org/news/2018/11/choose-your-2018-breakthrough-year Best, Tim -- -- Paul Scherrer In

Re: [ccp4bb] Long term storage for raw images/ crystallographic data sets

2018-11-29 Thread Tim Gruene
BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 -- -- Paul Scherrer Institut Tim Gruene - persoenlich - OSUA/204 Forschungsstrasse 111 CH-5232 Villigen PSI phone: +41 (0)56 310 5297 GPG Key ID = A46BEE1A

Re: [ccp4bb] transform NMR ensemble with pdbset

2018-11-08 Thread Tim Gruene
link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 > -- -- Paul Scherrer Institut Tim Gruene - persoenlich - OSUA/204 Forschungsstrasse 111 CH-5232 Villigen PSI phone: +41 (0)56 310 5297 GPG Key ID = A46BEE1A #

Re: [ccp4bb] Issue with high Rfree (0.25) for a high-resolution dataset (1.05 Ang)

2018-10-11 Thread Tim Gruene
r distance so I couldn’t > collect at a higher resolution :( > > Thanks again, > Guto > > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 >

Re: [ccp4bb] preparing ellipsoidally truncated data for PDB deposition

2018-09-27 Thread Tim Gruene
> > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 -- -- Paul Scherrer Institut Tim Gruene - persoenlich - OSUA/204 Forschungsstrasse 111 CH-5232 Villigen PSI phone: +41 (0)56 310 5297 GPG Key ID = A46BEE1A #

Re: [ccp4bb] Building libccp4 static.

2018-09-24 Thread Tim Gruene
here's a syntax error there somewhere.  I can't see it but > then I'm not a Bourne shell expert. > > Any ideas? > > Thanks! > > -- Ian > > > ---- > > To unsubscribe from the CCP4BB list, click the foll

Re: [ccp4bb] crystals that dont diffract :( :(

2018-08-14 Thread Tim Gruene
that help? > Careina > > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 > -- -- Paul Scherrer Institut Tim Gruene - persoenlich - OSUA/204 CH-5232 Villigen PSI phone:

Re: [ccp4bb] screw axes /system. absenses and phaser/MR solutions

2018-08-09 Thread Tim Gruene
> Thanks for comments, > > Tommi > > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 > -- -- Paul Scherrer Institut Tim Gruene - persoenlich - OSUA/204 CH-5232 V

Re: [ccp4bb] cell discrepancies and stuck refinement using different XDS-versions

2018-08-06 Thread Tim Gruene
e smaller cell is also found by Xia2/dials via the CCP4i2 interface.) > > Thus I am wondering, what are the differences between the two > XDS-versions? (I remember vaguely that there was a tread about different > XDS-versions, but couldn't find it..) > > Cheers Sabine -- -- Pa

Re: [ccp4bb] data processing with split/bad crystals

2018-07-16 Thread Tim Gruene
Institute of Biotechnology > University of Helsinki > Viikinkaari 1 (P.O. Box 65) > 00014 Helsinki, Finland > > > > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jis

Re: [ccp4bb] According correct space group assignment...

2018-04-20 Thread Tim Gruene
ted to almost 1 A, so it should be enough for > trials with direct methods/ab initio solution. What I should do first to > find correct SG and/or cell parameters? > > Best regards, > > Rafal -- -- Paul Scherrer Institut Tim Gruene - persoenlich - OSUA/204 CH-5232 Villigen PSI phone: +4

Re: [ccp4bb] Observation:Parameter ratio

2018-02-17 Thread Tim Gruene
and experiment ? Is there > any thumbrule for this ratio, and how it is dependent on the resolution of > the data. Please shed some light on these aspects. > Thank you > With kind regards > Prem -- -- Paul Scherrer Institut Tim Gruene - persoenlich - OFLC/104 CH-5232 Villigen PSI phone:

Re: [ccp4bb] coordinate transformation

2017-12-14 Thread Tim Gruene
es > OK > Drag the View to the Origin # it's marked with an "O" > Middle-mouse click on an Symmetry-related Atom # that's close to the origin > Extensions -> Modelling -> Symm Shift Reference Chain Here -- -- Paul Scherrer Institut Tim Gruene - persoenlich - OFLC/104 CH-5232 Villigen PSI phone: +41 (0)56 310 5297 GPG Key ID = A46BEE1A signature.asc Description: This is a digitally signed message part.

Re: [ccp4bb] mmCIF and CIF

2017-11-14 Thread Tim Gruene
s, > > does anybody know how to transform an mmCIF file of the Protein Data > Bank into a CIF file (the slightly different format used in small > molecule crystallography)? > > Thanks, > > Oliviero -- -- Paul Scherrer Institut Tim Gruene - persoenlich - OFLC/104 CH-5232 Vi

Re: [ccp4bb] software to map surface residues

2017-11-04 Thread Tim Gruene
xtract the 3D coordinates of > the surface residues of a given protein/PDB file? Thanks so much~~ > > Kai > > Buck Institute -- -- Paul Scherrer Institut Tim Gruene - persoenlich - OFLC/104 CH-5232 Villigen PSI phone: +41 (0)56 310 5297 GPG Key ID = A46BEE1A signature.asc Desc

Re: [ccp4bb] mtz2hkl for shelx

2017-10-27 Thread Tim Gruene
; 1499 Reflections with FreeR_flag = 0 marked as test set (-1) > > > I tried FREERFLAG suggestion but to no avail. How do I fix this? > > Thank you, > Abhishek -- -- Paul Scherrer Institut Dr. Tim Gruene - persoenlich - Principal Investigator Biology and Chemistry OFLC/104 CH-5232 Villigen PSI Phone: +41 (0)56 310 5297 GPG Key ID = A46BEE1A signature.asc Description: This is a digitally signed message part.

Re: [ccp4bb] ccp4 website not secure

2017-10-11 Thread Tim Gruene
wrote: > >> If anyone from CCP4 website has noticed that... > >> Your connection is not secure > >> > >> > >> The owner of www.ccp4.ac.uk has configured their web site improperly. > >> To protect your information from being stolen, Firefox ha

Re: [ccp4bb] include corners in mosflm

2017-09-27 Thread Tim Gruene
issing reflections in map calculation may > make maps more biased. A reasonable solution to this would be to use 2 > different resolution limits in refinement and map calculation - not hard to > script for that yet I don't know if any refinement software provides such > option natively. Ed. -

Re: [ccp4bb] PAK=0 problem

2017-09-22 Thread Tim Gruene
; -James Holton > MAD Scientist > > On 9/15/2017 4:32 AM, rohit kumar wrote: > > why R/Rfree not going down from 21/25? -- -- Paul Scherrer Institut Tim Gruene - persoenlich - OFLC/104 CH-5232 Villigen PSI phone: +41 (0)56 310 5297 GPG Key ID = A46BEE1A

Re: [ccp4bb] CHAINSAW ERROR

2017-09-03 Thread Tim Gruene
ile : *CLUSTAL O(1.2.4) multiple sequence > >> alignment* > >> > >> I also typed CLUSTAL W instead of CLUSTAL O but ccp4 gave me the same > >> error message. > >> > >> Any suggestion will be appreciated. > >> > >> Kindly, > >> > >> Vicky -- -- Paul Scherrer Institut Tim Gruene - persoenlich - OFLC/104 CH-5232 Villigen PSI phone: +41 (0)56 310 5297 GPG Key ID = A46BEE1A signature.asc Description: This is a digitally signed message part.

Re: [ccp4bb] "reset" a structure before re-refinement

2017-08-20 Thread Tim Gruene
there a protocol out there to gently perturb atomic > > positions so that re-running refinement can essentially > > put them back without bias from the original > > refinement? In particular, if trying to perfor

Re: [ccp4bb] "reset" a structure before re-refinement

2017-08-18 Thread Tim Gruene
and > > Diederichs paired refinement protocol, I do not want to run the lower > > resolution refinements with the "memory" of the weak high resolution data > > present... and only have the refined structure to work from... > > > > Am using refmac5, but any pdb randomizer

[ccp4bb] Reminder: PSI / CCP4 Workshop "3D Electron Crystallography for Macromolecular Compounds"

2017-08-15 Thread Tim Gruene
ico.psi.ch/conferenceDisplay.py?confId=5525 We extended the number of participants by 10 places. Please register before 1st September 2017. On behalf of the organisers, Tim Gruene -- -- Paul Scherrer Institut Dr. Tim Gruene - persoenlich - Principal Investigator Biology and Chemistry OFLC/1

Re: [ccp4bb] SHELXE: peptide occupancy refined to negative value

2017-07-11 Thread Tim Gruene
t these? (I > could do MR, but there must be a more elegant way...) Better yet, what > might cause the "negative occupancy" error and how do I avoid it? > > Thanks and all best. > > > Andreas -- -- Paul Scherrer Institut Dr. Tim Gruene - persoenlich - Principal Inv

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