Re: [ccp4bb] small crystals

Dear Jens, Careina this is not really an *advantage*, but rather a *convenience*. You can still use big crystals if you'd like to, but as they usually never survive more than one shot (few femtosec), you'd need a lot of these bigger crystals to collect a full data. And yes, I would also

Re: [ccp4bb] small crystals

Yes, Tim is right… for now… in few years, with the E-XFEL, we'll get to much less sample, and much more time available. But that's in few years. Leo On Dec 10, 2013, at 10:01 AM, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote: Dear Careina, you can also apply for beamtime at PETRA-III. You get

Re: [ccp4bb] small crystals

. Cheers, Leo On Dec 10, 2013, at 10:13 AM, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote: 'Will' is a fashionable word - but since even a Nobel prize was given based on promises never kept, who would be surprised... Best wishes from now, Tim On 12/10/2013 10:11 AM, CHAVAS Leonard wrote: Yes, Tim

[ccp4bb] Positions available - Photon Factory, Japan

letter(s) by email) Others : - KEK is an equal-opportunity employer and encourages applications from women. - This program will be evaluated in the third year. --- Chavas Leonard M.G., Ph.D. Assistant Professor Structural Biology Research Center

[ccp4bb] Disturbing feature with access rights

Dear all I came along a disturbing feature and I would appreciate to get your lights on this. After rebuilding our data server, plenty of access rights have been changed and various folders have been ‘secured’ by restricting access to few users and groups. The whole ccp4 suite has also been

Re: [ccp4bb] How to run CCP4 without source command

read the documentation? Probably somewhere it should be mentioned to have the 'source ' command in your bash file? I might have misunderstood your question though. Leo On 16 Nov 2014, at 07:30, 陈昂 angsc...@outlook.com wrote: Dear all: I have installed CCP4 suit on my computer. The OS IS

Re: [ccp4bb] Water molecules after refinement

Dear Jeorge are the water molecules without electron density properly coordinated? These could be ghosts... Additionally, did you solve the structure by molecular replacement? If so, in your search model, do you see these water molecules at the same / nearby location? Again, those could be

Re: [ccp4bb] Restraints after refinement

Dear Jeorge just as a curiosity: 1- do you see a continuous electron density for the ligand, before and after performing the refinement? 2- do you have only one copy of the molecule(s), and if not, do you see the same behaviour for all the ligands? 3- what are the B-factor values for the

Re: [ccp4bb] Question on Refmac5

Dear Dialing are you talking about the 'creating date' or the 'modified date'? Leo On Jan 6, 2015, at 2:55 AM, Dialing Pretty 03f1d08ed29c-dmarc-requ...@jiscmail.ac.uk wrote: Dear All, When I run Refmac, it would produce a refined PDB file and mtz file. My question is, if I

Re: [ccp4bb] Protein precipitating at higher concentration!!

Hi Ivan this will not be an answer to your question, but did you consider not concentrating 'too much' your sample? It happened few times to me that the protein was precipitating when concentrating for SEC because of the presence of other impurities. Trying the good old AS precipitation helped

Re: [ccp4bb] Spacegroups, screw axes and ordering

n against reporting P1 for > a crystal system consisting of higher symmetry? > > Cheers, > Quyen > >> On Jan 29, 2016, at 4:27 PM, CHAVAS Leonard >> <leonard.cha...@synchrotron-soleil.fr> wrote: >> >> Sorry if I don't buy it. Just personal fee

Re: [ccp4bb] Spacegroups, screw axes and ordering

-crystallographer would simply press a few buttons to generate a model > with auto build? > But I have a feeling those couple of buttons might not be so obvious to > people in other fields. > > Quyen > >> On Jan 29, 2016, at 3:16 PM, CHAVAS Leonard >> <leona

Re: [ccp4bb] Spacegroups, screw axes and ordering

Not sure I fully understand. Are we really talking about non-crystallographer scientists, often willing to understand how a biologically meaningful molecule / entity looks like? Are these non-crystallographers really interested in crystal packing issues? Is it so much difficult to press on a

Re: [ccp4bb] Implementation of the ESRF Data Policy

Dear all something I am not completely aware of: can the ESRF users decide on having their data destroyed from the ESRF servers? One way to go I would think could be proper would be to announce getting open access for all the data on the servers or wherever after 3 years (or few months for

Re: [ccp4bb] extra density between inter-chain cysteine

DTT perhaps? Cheers, leo > On 21 Mar 2016, at 14:04, Pedro Matias wrote: > > Does it make sense to consider 2 extra S-atoms bridging the 2 cysteines? What > would be the bond distances? What is the meaning of the red e.d. in the 2nd > figure? > > Às 12:44 de 21/03/2016,

Re: [ccp4bb] extra density between inter-chain cysteine

, leo > On 21 Mar 2016, at 15:09, Manjula Ramu <manjula@gmail.com> wrote: > > I had no reducing agent in my protein buffer as wel as in crystal condition. > I have only sodium citrate in the condition. > > On Mar 21, 2016 6:54 PM, "CHAVAS Leonard" >

Re: [ccp4bb] Another puzzle: 5gnn: SOLVED

Could we write to them as a community? As the 'CCP4 Peer Reviewing Organisation for Structural Biology'? Great job indeed! Cheers, leo - Leonard Chavas - Synchrotron SOLEIL Proxima-I L'Orme des Merisiers Saint-Aubin - BP 48 91192 Gif-sur-Yvette Cedex France - Phone: +33 169 359 746 Mobile:

Re: [ccp4bb] Fine Phi Slicing

Just to comment on what Graeme just introduced. We (and I know we are not the first ones and not the only ones) are pushing our user community towards this procedure as a standard: lowering the transmission (less juicy, yet...) and getting few data with various chi. It does help greatly in

Re: [ccp4bb] Fine Phi Slicing

Attenuation... cut the beam with primary slits! We do not use attenuators, only for getting very very low when performing energy scans. Else, cutting the flux at the source is somehow much more reliable. Not mentioning scattering coming from the attenuators as well... Cheers, leo - Leonard

Re: [ccp4bb] Fine Phi Slicing

- > On 14 Jul 2017, at 14:07, CHAVAS Leonard > <leonard.cha...@synchrotron-soleil.fr> wrote: > > Just to comment on what Graeme just introduced. We (and I know we are not the > first ones and not the only ones) are pushing our user community towards this > procedure

Re: [ccp4bb] Protein or DNA crystals

Dear Kumar you said 'shot from other conditions': we do not know then if you shot these crystals or not. Else: - DNA should give you an X pattern, most of the time. - protein should give you at least low resolution pattern, or faint rings if it is powder pattern like - salt should give you

Re: [ccp4bb] Contouring 2Fo-Fc map, large blobs in Fo-Fc

Do you have continuous chains all the way through? Any possibility of domain swapping? leo - Leonard Chavas - Synchrotron SOLEIL Proxima-I L'Orme des Merisiers Saint-Aubin - BP 48 91192 Gif-sur-Yvette Cedex France - Phone: +33 169 359 746 Mobile: +33 644 321 614 E-mail:

Re: [ccp4bb] new ContaMiner features

Dear all, to join Pierre's comments on what 'strange' things happen at the beamlines... yet not too strange for (too) many people: huge screening of salt crystals, complete data collection of dramatically low resolution data, full power coupled with 360Deg data collection etc. etc. etc. We do

Re: [ccp4bb] new ContaMiner features

Dear Gerard I should certainly be the one to blame, as I was the one spotting this behaviour to Stefan. Telling this, it could indeed be a problem with the data set, yet submitting the original mtz to ContaMiner provided with the strangely hoped and expected ContaMiner negative result. I made

Re: [ccp4bb] Should we still keep copies of all raw data?

Hi Frank on the same lines: do we keep our crystals after frying them? Or do molecular biologists keep their agarose gels? Hummm... evolution and technologies do progress. Yet, I would support keeping images, just as you may (but really will most likely never) want to re-process those with

[ccp4bb] Post-doctoral position at the Synchrotron SOLEIL (France)

Dear all please consider the following post-doctoral position available at the Synchrotron SOLEIL in France. Would you or colleagues be interested, I would greatly appreciate if you could forward this message to them. Cheers, leo Postdoctoral position in life sciences (24 months) Synchrotron

[ccp4bb] Thoughtful remark...

Dear all I had one interesting comment today at the beamline, that I would like to share with you for your advice on how to answer this... Is it better to have no diffraction from a crystal you shoot, or to have no crystal in the loop? Hum, difficult one... Cheers, leo - Leonard Chavas -

Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] Better Beamline suggestion!

Dear Chandra SLS and ourselves (SOLEIL) are dealing rather often with large unit cells and fancy crystal orientations. No great secret, and things have already been mentioned: combining three-axis goniometry, large area Pixel detector, low background, small wedges and/or helical scans,

Re: [ccp4bb] How many microfocus beamlines are in the world?

I tend to like considering below 10microns as a micro-focus, below the micron as a sub-micron beamline. I don't know if any nano-focus, sort to say. XFELs are dealing with 100 nm, without the wings, which is really sub-micron to me. Regards, Leo - Leonard Chavas - Synchrotron SOLEIL PROXIMA-1

Re: [ccp4bb] dewar horror stories

Users had issues, back at SOLEIL in France, with FedEx, DHL, UPS, French post... at many levels. I guess it just depends on luck, or bad luck in the present case. The worst case encountered so far though was Dewars lost in transit for a couple of weeks. Not to mention countries where import