[ccp4bb] COOT download site

or has it moved? Thanks, Clemens -- Dr. Clemens Grimm Institut für Biochemie Biozentrum der Universität Würzburg Am Hubland D-97074 Würzburg Germany e-mail: clemens.gr...@biozentrum.uni-wuerzburg.de phone : +49 093

Re: [ccp4bb] COOT download site

h ccp4 On Thu, 4 Jun 2020 at 15:41, Clemens Grimm < clemens.gr...@biozentrum.uni-wuerzburg.de> wrote: Dear All, accessing the COOT download pages at http://www.ysbl.york.ac.uk/~emsley/software/binaries/nightlies/pre-release/ gives me an "The requested URL /~emsley/software/binaries/

Re: [ccp4bb] COOT download site

ote: Looks as if Clemens will be jumping straight into the future now with the new link. Were you on Coot 0.069? Jürgen On Jun 4, 2020, at 10:54 AM, Paul Emsley mailto:pems...@mrc-lmb.cam.ac.uk>> wrote: On 04/06/2020 15:41, Clemens Grimm wrote: Dear All, accessing the COOT downlo

[ccp4bb] Phenix: No reference model matches

-- Dr. Clemens Grimm Institut für Biochemie Biozentrum der Universität Würzburg Am Hubland D-97074 Würzburg Germany e-mail: clemens.gr...@biozentrum.uni-wuerzburg.de phone : +49 0931 31 84031

[ccp4bb] PhD Student Position

the names and contact details of two referees to: Dr. Clemens Grimm e-mail: clemens.gr...@biozentrum.uni-wuerzburg.de Institute für Biochemie Biozentrum der Universität Würzburg Am Hubland D-97074 Würzburg Germany -- Dr. Clemens Grimm

Re: [ccp4bb] units of the B factor

Zitat von marc.schi...@epfl.ch: Dale Tronrud wrote: While it is true that angles are defined by ratios which result in their values being independent of the units those lengths were measured, common sense says that a number is an insufficient description of an angle. If I tell you I measure

[ccp4bb] setting cell/spacegroup in imosflm

Dear all, I would like to set manually cell and SG in the iMosflm interface - is this possible? Thanks Clemens -- Dr. Clemens Grimm Institut für Biochemie Biozentrum der Universität Würzburg Am Hubland D-97074 Würzburg Germany e-mail

[ccp4bb] Postdoctoral Position at the University of Wuerzburg

opportunity employer with an affirmative action program for the disabled. -- Dr. Clemens Grimm Institut für Biochemie Biozentrum der Universität Würzburg Am Hubland D-97074 Würzburg Germany e-mail: clemens.gr...@biozentrum.uni-wuerzburg.de phone : +49

[ccp4bb] Processing of highly anisotropic data

-- Dr. Clemens Grimm Institut für Biochemie Biozentrum der Universität Würzburg Am Hubland D-97074 Würzburg Germany e-mail: clemens.gr...@biozentrum.uni-wuerzburg.de phone : +49 0931 888 84031 -

[ccp4bb] Vapor diffusion calculator

arle 1-240 2240 Campus Drive Evanston IL 60208 lab: 847.491.2438 cel: 773.608.9185 email: j-kell...@northwestern.edu *** ------ Dr. Clemens Grimm Institut für Biochemie Biozentrum der Universität Würzburg Am Hubland D

Re: [ccp4bb] Vapor diffusion calculator

Zitat von Imre Toeroe : Hi, this might be relevant here: http://scripts.iucr.org/cgi-bin/paper?S0907444995000436 Yes! thanks for the link. Imre Clemens Grimm wrote: regardless of what such a (kinetic) calculator will calculate at the end - we will have to feed it with data of the type

Re: [ccp4bb] automise ncont

Dr. Clemens Grimm Institut für Biochemie Biozentrum der Universität Würzburg Am Hubland D-97074 Würzburg Germany e-mail: clemens.gr...@biozentrum.uni-wuerzburg.de phone : +49 0931 888 84031 -

Re: [ccp4bb] Micro-g Crystal Growth and the literature

ld be reduced by 30-50%; AND if the end-product is the data, not the crystals . . . do you still think (profit) margins would be nominal? Is your assessment of "very low margins" based on assumed "very high costs?" Jack -- Dr. Clemens Grimm Institut für Biochemie Biozentrum der Universität Würzburg Am Hubland D-97074 Würzburg Germany e-mail: clemens.gr...@biozentrum.uni-wuerzburg.de phone : +49 0931 888 84031 -

Re: [ccp4bb] Micro-g Crystal Growth and the literature

rmaceutical industry (and other researchers, for that matter) could grow crystals in space, and extract critical data from the x-ray diffraction of these space-grown crystals (in space); AND if costs could be reduced by 30-50%; AND if the end-product is the data, not the crystals . . . do y

Re: [ccp4bb] Lindemann glass

Hilgenberg (Malsfeld, Germany) currently offer their remaining stock. Clemens Zitat von James Holton : Does anyone know the formula or supplier of what was once called "Lindemann glass"? It is a silicon-free high-boron glass that has no elements in it heavier than oxygen. Used to be used

[ccp4bb] Ultra-low water B-facors after TLS refinement

-- Dr. Clemens Grimm Institut für Biochemie Biozentrum der Universität Würzburg Am Hubland D-97074 Würzburg Germany e-mail: clemens.gr...@biozentrum.uni-wuerzburg.de phone : +49 0931 888 84031 -

[ccp4bb] PhD Position in Wuerzburg / Germany

, academic certificates and the name and contact detail of one referee to Dr. Clemens Grimm e-mail: [EMAIL PROTECTED] Institut fuer Biochemie Biozentrum der Universitaet Wuerzburg Am Hubland D-97074 Wuerzburg

[ccp4bb] Ferritin crystallisation

Dear all, scanning the literature, it seems that horse spleen Ferritin has so far been crystallised only in presence of Cadmium ions. Is this correct? Does anybody know of conditions lacking Cd? Clemens

Re: [ccp4bb] problem of crystallization

Hi Jennifer, clear drops can still be brought to supersaturation by: -transfer to wells with lower vapour pressure: exchange or add LiCl or other concentrated salt solutions in the reservoir -temperature gradient: place trays on ice/cold surface while hanging drops are at higher temperature, th

Re: [ccp4bb] pH-ing Jeffamine ED-2001

this is also my experience. However, above pH 8, the buffering effect of the Jeffamines' amino groups starts to be significant and (rough) pre-adjusting of the pH might be necessary. Clemens Quoting Yogesh Gupta PhD <[EMAIL PROTECTED]>: Hi Amit, Changing the pH of Jeffamine is not so easy . I

[ccp4bb] dry shipper on airplaine

Dear all, I wonder if it would be still/again possible to check in a dry shipper for a flight inside Europe. What is your experience? Cheers, Clemens

Re: [ccp4bb] Arp/warp space group P 21 2 21

seems to be a 'non-standard' setting. Refmac also has problems with this spacegroup, reindexing to P21 21 2 fixed the problem for me. Clemens Quoting PhilEvans <[EMAIL PROTECTED]>: Is there a reason why Arp/warp doesn't like space group P 21 2 21? Phil

Re: [ccp4bb] Arp/warp space group P 21 2 21

yes, actually my experience with P 21 2 21 dates back to midyear 2007. Retesting with the current refmac version runs fine. Clemens Quoting Ian Tickle <[EMAIL PROTECTED]>: Victor 'P 21 2 21' *is* the conventional indexing if a <= b <= c, i.e. it's the setting agreed for deposition of cryst

Re: [ccp4bb] Reducer and crystallization

Hi Sam, The effect of reducing agents like beta-ME, DTT or TCEP is exactly as you say, the prevention of disulphide formation or cleavage of existing disulphide bridges and therefore prevention of aggregation if inter-molecular disulphide bridges can be formed. A balancing of reducing power, or b

[ccp4bb] re-indexing, re-orienting and TLS-tensors

Dear all, after re-indexing a dataset I had to re-orient my coordinates accordingly. The model contains some 24 TLS-tensors. Now my question is how to apply the rotation matrix also to the TLS-tensors. What is the mathematical operation and is there a program that can do the job for me? Thanks, C

Re: [ccp4bb] re-indexing, re-orienting and TLS-tensors

like that? Clemens Quoting Eleanor Dodson <[EMAIL PROTECTED]>: I would run the TLS again! Eleanor Clemens Grimm wrote: Dear all, after re-indexing a dataset I had to re-orient my coordinates accordingly. The model contains some 24 TLS-tensors. Now my question is how to apply the rota

Re: [ccp4bb] how to promote folding for an unfolded protein

Hi Jenny, there are probably as many 'folding enhancers' as there are crystallization additives. Arginine might only be the most popular, followed by things like proline and other amino acids. The mode of action of those can partly be explained by their mild chaotropic properties. For a difficult

[ccp4bb] PhD Position in Structural Biology

of interest, curriculum vitae, academic certificates and the names and contact details of two referees to: Dr. Clemens Grimm Institute for Biochemistry Biocentre of the University Am Hubland D-97074 Wuerzburg Germany e-mail: [EMAIL PROTECTED]

[ccp4bb] The mystery of the S-tensor WAS: re-indexing, re-orienting and TLS-tensors

OG to COR or vice versa), which is unlikely if all you are doing is re-indexing. Having p=0 (and P=O) of course considerably simplifies the equations, i.e.: T' = RTR~ and the same transformation is applied separately to L and S. Cheers -- Ian -Original Message----- From: Cle

[ccp4bb] PhD Position in Protein Biochemistry

protein crystals available. Please send your application including a letter of interest, curriculum vitae, academic certificates and the names and contact details of two referees to: Dr. Clemens Grimm e-mail: [EMAIL PROTECTED] Institut für Biochemie Biozentrum der Universität Würzburg Am

Re: [ccp4bb] Reducing Agents and pH

TCEP is often sold as hydrochloride salt and therefore reacts highly acidic. We usually titrate the concentrated solution *before* we add it to our proteins. This can be done within small volumes by dropwise addition of a saturated TRIS solution, check pH by pipetting a drop on a pH test s

Re: [ccp4bb] temperature after 30 minutes using microscopes ?

We have tested the Zeiss LED plate with hanging and sitting drop trays and found it it unsuitable for looking at crystals. The reason is the really low contrast with this kind of diffuse illumination. Obviously, contrast is generated by refraction at crystal/mother liquor interfaces and thi

[ccp4bb] Phasing at Low Resolution

Dear all, after the SeMet phasing discussion, what would be -in general- the best technique to phase low resolution data (<=4A) of large complexes (>=150 kDA) - in terms of - derivatization compounds (is there something like the 'golden five' HA compounds for these cases), - data colle

Re: [ccp4bb] Phasing at Low Resolution

9 at 09:35:28AM +0200, Clemens Grimm wrote: Dear all, after the SeMet phasing discussion, what would be -in general- the best technique to phase low resolution data (<=4A) of large complexes (>=150 kDA) - in terms of - derivatization compounds (is there something like the 'golden five

[ccp4bb] crystool

Dear all, is the Rupp & Segelke CRYSTOOL still accessible somewhere? The old link http://www-structure.llnl.gov/crystool/crystool.htm seems not to work anymore. Or are there alternatives? Thanks Clemens

Re: [ccp4bb] Phantom Crystals

Zitat von George DeTitta : I'd appreciate it if people could tell me their experiences with what I would call "phantom crystals", or "ghost crystals". These are objects that display the seeming morphology of crystals (clear facets, sharp edges) ... There is also a second type of "ghost crysta

[ccp4bb] PhD Position in Structural Biology, Wuerzburg, Germany

, curriculum vitae, academic certificates and the names and contact details of two referees to: Dr. Clemens Grimm e-mail: clemens.gr...@biozentrum.uni-wuerzburg.de Institut für Biochemie Biozentrum der Universität Würzburg Am Hubland D-97074 Würzburg Germany web: www.biozentrum.de

Re: [ccp4bb] Test of cryoconditions without X-rays or cryostream

Checking Cryo-Conditions under the microscope can actually be very useful. Even if you have access to a X-ray beam, simple pre-tests can be very informative. This can be done as follows: A 24well plate cover is placed on a stereo microscope open side down, a second one on top of it the oth

[ccp4bb] PhD Position in Structural Biology, Wuerzburg, Germany

, curriculum vitae, academic certificates and the names and contact details of two referees to: Dr. Clemens Grimm e-mail: clemens.gr...@biozentrum.uni-wuerzburg.de Institut für Biochemie Biozentrum der Universität Würzburg Am Hubland D-97074 Würzburg Germany web: www.biozentrum.de

[ccp4bb] Batch Queing of ccp4i Jobs

Dear all, has anybody set up successfully a batch queue for ccp4i under SUSE linux? Regards, Clemens

Re: [ccp4bb] Sokalan cp 42 as a cryoprotectant

nb.csic.es -- Dr. Clemens Grimm Institut für Biochemie Biozentrum der Universität Würzburg Am Hubland D-97074 Würzburg Germany e-mail: clemens.gr...@biozentrum.uni-wuerzburg.de phone : +49 0931 31 84031 -

Re: [ccp4bb] Crystallisation optimisation query

6481 c.fyf...@research.gla.ac.uk -- Dr. Clemens Grimm Institut für Biochemie Biozentrum der Universität Würzburg Am Hubland D-97074 Würzburg Germany e-mail: clemens.gr...@biozentrum.uni-wuerzburg.de phone : +49 0931 31 84031 -

[ccp4bb] PhD and Postdoc Positions in Structural Biology

Grimm e-mail: clemens.gr...@biozentrum.uni-wuerzburg.de Lehrstuhl für Biochemie Biozentrum der Universitaet Wuerzburg Am Hubland D-97074 Wuerzburg -- Dr. Clemens Grimm Institut für Biochemie Biozentrum der Universität Würzburg Am Hubland D-97074

[ccp4bb] EMAN e2proc2d mrcs conversion issue

0 particles Versions tested are EMAN 2.21a final and EMAN 2.2 final. Are we doing something wrong or is this a bug? Any help appreciated. Clemens -- Dr. Clemens Grimm Institut für Biochemie Biozentrum der Universität Würzburg Am Hubland D-97074

Re: [ccp4bb] cannot reproduce crystals

'oil separation and light ppt' is not necesserily an indicator that something is wrong with your crystallization condition. Actually, there are quite a few proteins that only crystallize in conditions with oil/water-like phase separation. Some crystals even appear WITHIN the oily drops (e.

Re: [ccp4bb] AW: [ccp4bb] Phenix: heavy atoms

n the file with heavy atoms and the origin of coordinates of the molecular model? Thank you! Natalia - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen phone: +49 (0)551 39 22149 GPG Key ID = A46BEE1A ---

Re: [ccp4bb] cryo condition

iences JNU -- Dr. Clemens Grimm Institut für Biochemie Biozentrum der Universität Würzburg Am Hubland D-97074 Würzburg Germany e-mail: clemens.gr...@biozentrum.uni-wuerzburg.de phone : +49 0931 31 84031 -

Re: [ccp4bb] disulfide engineering

are to assist with this? Best Careina -- *** Jacob Pearson Keller, PhD Postdoctoral Associate HHMI Janelia Farms Research Campus email: j-kell...@northwestern.edu *** ------

Re: [ccp4bb] stereo monitor for DELL T7600

will be highly appreciated. Thanks so much in advance! Jl ------ Dr. Clemens Grimm Institut für Biochemie Biozentrum der Universität Würzburg Am Hubland D-97074 Würzburg Germany e-mail: clemens.gr...@biozentrum.uni-wuerzburg.de phone : +49 0931 31 84031 -

Re: [ccp4bb] [ccpem] Topaz picking in Relion

I figured out that setting 'Particle diameter' from default=-1 to a positive value results in single picks. Zitat von Clemens Grimm : Dear Developers and Users, after picking with a model trained with a pre-classified particle set, I get the following situation (see attach

[ccp4bb] A postdoctoral and a PhD position funded by the Volkswagen Foundation in Wuerzburg

directly: Utz Fischer (utz.fisc...@uni-wuerzburg.de) or Clemens Grimm (clemens.gr...@uni-wuerzburg.de) To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1

[ccp4bb] PhD position at the University of Wuerzburg

protein constructs and complexes for structural studies. Please send your application including a letter of interest, curriculum vitae and academic certificates to: Dr. Clemens Grimm e-mail: clemens.gr...@biozentrum.uni-wuerzburg.de Lehrstuhl für Biochemie Biozentrum der Universitaet Wuerzburg Am

[ccp4bb] PhD and Postdoc Position in Structural Biology (Cryo Electron Microscopy and X-ray Crystallography)

. Clemens Grimm e-mail: clemens.gr...@biozentrum.uni-wuerzburg.de Lehrstuhl für Biochemie Biozentrum der Universitaet Wuerzburg Am Hubland D-97074 Wuerzburg -- Dr. Clemens Grimm Institut für Biochemie Biozentrum der Universität Würzburg Am Hubland D

[ccp4bb] PhD and Postdoc Positions in Structural Biology

Grimm e-mail: clemens.gr...@biozentrum.uni-wuerzburg.de Lehrstuhl für Biochemie Biozentrum der Universitaet Wuerzburg Am Hubland D-97074 Wuerzburg -- Dr. Clemens Grimm Institut für Biochemie Biozentrum der Universität Würzburg Am Hubland D-97074

[ccp4bb] Open positions for one Postdoc and one PhD student

Biochemistry. For further information, please contact Utz Fischer utz.fisc...@uni-wuerzburg.de Tel.: +49 931-3184029 or Clemens Grimm clemens.gr...@uni-wuerzburg.de Tel.: +49 931-3184031 To

[ccp4bb] AW: [ccp4bb] 3D/Stereoscopic hardware options in 2025?

There will be no alternative to quad-buffered OpenGL if you want broad support of all stereo-capable software. In fact, quad-buffered OpenGL is part of the OpenGL specification since the beginning. The Acer website says that the SpatialLabs displays require an additional, dedicated driver. It se

[ccp4bb] AW: [ccp4bb] 3D/Stereoscopic hardware options in 2025?

Dear All, Nvidia dropped active stereo (3Dvision) in their drivers a few years ago - which is a shame because it worked great. There is still the option to send quadbuffered stereo output to two monitors. It seems that Nvidia then leaves it up to you how to pass the two images to your two eyes.

[ccp4bb] AW: [ccp4bb] symmetry of symmetry (equivalent of "Cheshire group" for point groups)

the point group symmetry nomenclature is often referred to as "Schönflies notation", do you mean that name? Von: CCP4 bulletin board im Auftrag von Stefano Trapani Gesendet: Montag, 24. März 2025 10:44 An: CCP4BB@