Re: [ccp4bb] Is there a bulletin board (similar to ccp4bb) for small molecule crystallography

Hi, In fact the problem was solved with the help of Ivica Dilovic from Zagreb who suggested some changes to the shelxl .ins file. After these modifications the cryptic error message was still there, but the modifications made me try to remove one card. That did it. So the part that is

Re: [ccp4bb] Is there a bulletin board (similar to ccp4bb) for small molecule crystallography

t remember (the Linux flavour here is Alma Linux 9, not Debian). Fred. On 12/03/2024 10:56, David Waterman wrote: Hi Fred, CCP4 distributes the shelxl binary on Linux. I've not checked yet, but perhaps it is also part of CCP4 on Windows? Cheers -- David On Tue, 12 Mar 2024 at 09:38, Fred Vellie

Re: [ccp4bb] Is there a bulletin board (similar to ccp4bb) for small molecule crystallography

did your input files come from? Cheers -- David On Tue, 12 Mar 2024 at 09:01, Fred Vellieux wrote: Hi folks, I have a simple question: is there an electronic bulletin board for small-molecule crystallography? I have checked the list of CCP projects and there is no CCP

[ccp4bb] Is there a bulletin board (similar to ccp4bb) for small molecule crystallography

Hi folks, I have a simple question: is there an electronic bulletin board for small-molecule crystallography? I have checked the list of CCP projects and there is no CCP-project for small molecule crystallography in the list. I am trying to run SHELXL, and it fails with the cryptic message

Re: [ccp4bb] Crystals with DNA

Hello, Overhanging "sticky" ends are mentioned frequently when it comes to obtaining infinite helices that are useful in crystallization. For example in https://home.ccr.cancer.gov/csb/nihxray/Tips-and-Tricks_Crystallization_Protein-DNA_updated.pdf . Cheers, Fred. On 09/02/2024 10:59,

Re: [ccp4bb] Solution to [ccp4bb] problem running ccp4mg: ugly and useless graphics

d). Just in case. Fred. On 17/01/2024 10:17, Frederic Vellieux wrote: Dear all, Perhaps a reader of the bb will have a solution for this problem. ccp4 is version 8.0 and is up to date. All graphics programs (coot, but also other non-ccp4 software such as chimeraX, Pymol...) run fine on the Alma

Re: [ccp4bb] problem running ccp4mg: ugly and useless graphics

al) https://moorhen.org/ (the program) Best wishes, Stuart On Wed, 17 Jan 2024 at 09:17, Frederic Vellieux wrote: Dear all, Perhaps a reader of the bb will have a solution for this problem. ccp4 is version 8.0 and is up to date. All graphics programs (coot, but also othe

[ccp4bb] problem running ccp4mg: ugly and useless graphics

Dear all, Perhaps a reader of the bb will have a solution for this problem. ccp4 is version 8.0 and is up to date. All graphics programs (coot, but also other non-ccp4 software such as chimeraX, Pymol...) run fine on the Alma-Linux 9.3 system. There is a problem however with ccp4mg: the

Re: [ccp4bb] CentOS 7 end of life (july 2024)

- From: CCP4 bulletin board on behalf of Fred Vellieux Sent: Friday, August 18, 2023 10:43:34 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] CentOS 7 end of life (july 2024) Hi, Other people on this BB may run into the same problem. CentOS 7 end of life is announced to happen in July 202

[ccp4bb] CentOS 7 end of life (july 2024)

Hi, Other people on this BB may run into the same problem. CentOS 7 end of life is announced to happen in July 2024. I have to migrate my Linux box to another Linux "flavour". I've had a look at the possibilities: - migrate to another RHEL (rpm-based) Linux, with "elevate-linux" and

[ccp4bb] Question about BIOVIA DiscoveryStudio 2021

Folks, apologies for the non-CCP4 software question. I have tried to contact the BIOVIA DiscoveryStudio support team, somehow my browser does not allow me to open their "contact form". I am trying to visualize and perform an analysis on a protein:smaller molecule complex. The smaller

Re: [ccp4bb] how to get mol files from PDB and restraint CIF?

Hello Frank, We have to convert betwen file formats very frequently (usually several times daily) and: 1) we didn't need any restraints CIF file for that; 2) the tools we are using are http://www.cheminfo.org/Chemistry/Cheminformatics/FormatConverter/index.html

Re: [ccp4bb] ISO model with large groups of atoms in alternative conformations

Hello Pavel, You may want to have a look at PDB structure 6YCR: the macrocyclic peptide inhibitor is modelled as two conformations. The entire peptide. HTH, Fred. On 8/24/22 00:02, Pavel Afonine wrote: Dear community, I’m looking for an example of a crystal structure where a large group

[ccp4bb] SUMMARY: displaying residues (as a surface perhaps) for one component of a p-p-i

5/31/22 08:12, Fred Vellieux wrote: Dear bb members, I am quite certain that someone must have needed to do this already. I looked at publications but no details were given concerning how figures were prepared. So here is the problem: Given a protein protein interface (with the 3D struc

[ccp4bb] displaying residues (as a surface perhaps) for one component of a p-p-i

looking for a method allowing me to identify and display the interface forming residues of one of the protein components. Plus a surface representation of that part, for the 3D structure. Thanks in advance for any tips. Regards, Fred. Vellieux -- MedChem, 1st F. Medicine, Charles University

Re: [ccp4bb] Regarding File conversion

Hi, Last time I needed to do this the most convenient for me was to use Coot, with a very large coordinate file. Coot pre v1 (v0 something) to read in coordinates in the mmcif format and write out coordinates in the PDB format. HTH, Fred. On 2022-04-19 14:01, Abhilasha Thakur wrote:

Re: [ccp4bb] [summary] Does anyone know of a "CHARMM bulletin board" ?

Hello, I am posting this summary in case anyone else encounters the same problem. Replies were received from David A. Case, Morpholino Peligro, Arunabh Athreya, Tushar R. and Walker Olivier (through Adriana Miele). The problem: how to get MD runs when you are not a specialist (first time

[ccp4bb] Does anyone know of a "CHARMM bulletin board" ?

Hi folks, Sorry about the non-ccp4 question. I don't know where to ask. I have to perform MD simulations but I am totally on my own here. The one program that appears to be free (in terms of license) seems to be CHARMM. GROMACS (testing with the examples found in the internet) did not work

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

Hi folks, I'm trying to run Ligplot on a PDB file that contains a residue with type UNL (Unknown Ligand). I hadn't been using LigPlot for perhaps 2 years now (which means that I had to reinstall, with an expired license, and get familiar with it again). I get the following error message

[ccp4bb] coot & other graphics programs draw too many bonds

Hello there, After running autodock vina on certain small molecules, the graphics software I am using (e.g. Pymol, Coot) draws far too many bonds on the docked small molecule. See enclosed screen capture. Is there any way to prevent this from happening? This isn't very satisfactory of you

Re: [ccp4bb] Suggestions to improve resolution of protein crystals

Hi, In addition to all that's been suggested so far: when I was facing such problems I always tried the (commercially available) additive screens (additive kits, whatever they are called nowadays). This means setting up quite a few crystallisation experiments (you already have conditions in

[ccp4bb] Help needed (input files)

Hello, I need to perform some MD calculations and then trajectories of some small molecules analyzed. What I have is 1. protein 2. cofactor (FAD) 3. small molecule (either single O2 atom or single Chlorine atom) 4. crystallographic waters The software I can access is either Gromacs (with yum

[ccp4bb] summary of replies, superimposition of 3D structures using the dsDNA part only

s to all who replied. Superposition using the nucleid acid part of complexes can be very informative. Have a nice day further, Fred. Vellieux -- MedChem, 1st F. Medicine, Charles University BIOCEV, Vestec, Czech Republic

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

is the "best" way of doing this. Your suggestions will be appreciated, thanks. Fred. Vellieux -- MedChem, 1st F. Medicine, Charles University BIOCEV, Vestec, Czech Republic To unsubscribe from the CCP4BB list, click the

Re: [ccp4bb] current location for the Superimposé web server ?

Hello, Follow up concerning my query to the bb (in case anyone is interested), reply received from Robert Preissner through Philip E. Bourne and Joel Sussman: The Superimposé server was stopped in May 2018. Fred. Vellieux On 2/28/20 7:47 AM, Fred Vellieux wrote: *Hello, I am looking

[ccp4bb] current location for the Superimposé web server ?

*Hello, I am looking for the Superimposé web server (from Charité, Berlin). * *This web server must have moved from the place where it is supposed to reside, farnsworth.charite.de , not found. Does anyone know where this web server resides now ? TIA, Fred. *

[ccp4bb] Summary: MD program suitable to compute trajectories of a very small molecule in a protein

y work reasonably well. ---> Jack Tanner (U. Missouri-Columbia): "You might want to review the literature on using MD to study diffusion of O2/CO in myoglobin." (I had started in fact) [---> Lorenzo Briganti: the reply seems to have been lost along the way]. Hoping this will be use

[ccp4bb] MD program suitable to compute trajectories of a very small molecule in a protein

Dear all, I need to run MD calculations in order to follow the trajectories of a very small molecule inside a protein. From previous calculations (not MD) I have starting positions for this small molecule that all seem in agreement with a possible path of motion inside the protein. Now I

[ccp4bb] summary: how to define connectivity, bond types... in PDB files

Dear all, These are the replies received so far: Daniel Rigden (U. of Liverpool) suggested to do the conversion using https://www.webqc.org/molecularformatsconverter.php . It didn't work for me, the small molecule may be too complex (error message when reading the .mol file); Petr Kolenko

[ccp4bb] Current "best" software for computing volumes of active sites

use Voidoo however I do not know where to download an initial (and fairly comprehensive) cavity.lib file which I'd modify if need be. The links on the USF web site appear to be broken. I am running Linux. Thanks for the advice, Fred

Re: [ccp4bb] Backup of whole synchrotrons

Hi, We already have problems with the volume taken by our standard backups (they take too much space and we haven't been able to push the walls outwards in the Institute - I don't know why they keep telling us that our data should be in some clouds up in the sky). Hence I was wondering about

Re: [ccp4bb] Experimental phasing vs molecular replacement

Hello, I think what you are alluding to is model bias in (macromolecular) crystallography. What you should consult are the publications associated with this topic, and those on the map coefficients used to compute electron density maps (e.g. SIGMAA weighting), OMIT maps, current refinement

Re: [ccp4bb] AW: [ccp4bb] [ccp4bb] Oxford University Press

"how to get grants without papers in Nature. anyone have a solution to that one?" Simple: Once all of us have reviewed enough papers (with the money placed in a common pot) we simply buy the Nature Publishing Group. All those having taken part get a Nature paper every 4 years to ensure grant

[ccp4bb] Announcement: Instruct/CIISB Fragment Screening course in Vestec (Prague area) on April 5 and 6 (arrival on April 4, departure on April 7)

a very good festive season. Fred. Vellieux (Ph.D., HDR) Centre of Molecular Structure Institute of Biotechnology Czech Academy of Sciences, BIOCEV Prumyslova 595 252 50 Vestec Czech Republic Tel +420 325 873 786 - Upozornení: Není-li v této zpráve výslovne uvedeno jinak, má tato E-mailová zprá

[ccp4bb] Reminder: Open position for a specialist in biological X-ray techniques, especially SAXS plus XRD and crystallisation

://www.structuralbiology.eu/jobs/specialist-in-biological-x-ray-techniques-especially-small-angle-x-ray-scattering-saxs-and-single-cr/ . Thank you in advance, Best regards, F. Vellieux Fred. Vellieux (Ph.D., HDR) Centre of Molecular Structure Institute of Biotechnology Czech Academy of Sciences, BIOCEV Prumyslova 595

[ccp4bb] Open position for a specialist in biological X-ray techniques (SAXS, X-ray diffraction, crystallisation)

Dear all, Could you pass the following announcement on to suitable candidates (including yourselves, of course) ? Thank you. Fred. Vellieux Fred. Vellieux (Ph.D., HDR) Centre of Molecular Structure Institute of Biotechnology Czech Academy of Sciences, BIOCEV Prumyslova 595 252 50 Vestec Czech

Re: [ccp4bb] Help needed finding hit condition

Hello, Such pH drifts are rather common with crystallisation screens. Have you tried to produce other precipitant solutions with ca. 47% PEG 1000, 80 mM Potassium bromide but having a pH of (say) 6.2 ? A pH rangle close to that where your crystals were obtained. This would mean changing

Re: [ccp4bb] AW: [ccp4bb] Rmergicide Through Programming

. From: James Foadi [mailto:james_fo...@yahoo.co.uk] Sent: Tuesday, July 11, 2017 10:03 AM To: Vellieux Frédéric <frederic.velli...@ibt.cas.cz>; CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] AW: [ccp4bb] Rmergicide Through Programming Hello Frederic. Interesting. Have you got some ref

Re: [ccp4bb] AW: [ccp4bb] Rmergicide Through Programming

Hello, I think this needs a little bit of crystarchaeology. Rmerge and Rsym used to be different. This was at a time when data sets were typically collected from several crystals. Pre-cryo cooling, with data recorded on photographic film (Arndt-Wonacott cameras). Rmerge = agreement R-factor

Re: [ccp4bb] Incorrect Structure in the PDB

Hello, I think it makes sense to have a look at the policy of the PDB concerning obsoleting structures: The publication is retracted. The associated PDB entry will be obsoleted if requested by the journal. If a request has not been received, the wwPDB will do its best to contact the depositor

Re: [ccp4bb] Why Does Detwinning Not Work?

Hello Jacob, Quoting you, "Please let me know if you have a case where detwinning saved the day". Well you asked for it so here is one example where twinning saved the day: "Crystal structure of pb9..." by Flayhan et al. (2014), J. Virol. 88 (2), 820-828. Without detwinning I think there

Re: [ccp4bb] Off topic: textbook proteins for crystallization

Xylose Isomerase is another one. Cheers, Fred. -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of WENHE ZHONG Sent: Wednesday, April 20, 2016 11:39 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Off topic: textbook proteins for crystallization

Re: [ccp4bb] New crystallization technique

Hi Bernhard, We've been thinking along the same lines over here (but then our approach was far more "Sci Fi" like than yours, that is truly applicable in a real laboratory environment): we were devising ways here to crystallise in space, in black holes. Too bad, you beat us at it.

Re: [ccp4bb] cryo for crystals with CTAB as precipitant

Hi there, What about trying the ''olde'' method of a thin layer of oil around the crystal? No guarantee whatsoever that this will work but if you don't try it you won't know. Fred. From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of

Re: [ccp4bb] model bias

-- Fred. Vellieux (B.Sc., Ph.D., hdr) IBS / ELMA Campus EPN 71 avenue des Martyrs CS 10090 F-38044 Grenoble Cedex 9 Tel: +33 457428605 Fax: +33 476501890

Re: [ccp4bb] problems with ccp4-6.4.0 occurrences in ccp4-6.5

Hi there, Following your kind suggestions, logging out and logging in again solved the problem. Thanks ! Fred. On 23/01/15 18:07, vellieux wrote: Hello, I just installed ccp4-6.5 I get an error at run time (relating to $PATH I suppose, see below) that still contains occurrences of ccp4

[ccp4bb] problems with ccp4-6.4.0 occurrences in ccp4-6.5

line 12) and echo $PATH contains the following entry that shouldn't be there: /home/prog/ccp4-6.4.0/share/xia2/Applications Would anyone know how to deal with this ? Thank you in advance, Fred. -- Fred. Vellieux (B.Sc., Ph.D., hdr) IBS / ELMA Campus EPN 71 avenue des Martyrs CS 10090 F-38044

Re: [ccp4bb] Some advices on model modification

the whole model to mr. Could anyone give me some advice? what kind of software do you guys use? really need you help! Best regards, Allen -- Fred. Vellieux (B.Sc., Ph.D., hdr) IBS / ELMA Campus EPN 71 avenue des Martyrs CS 10090 F-38044 Grenoble Cedex 9 Tel: +33 457428605 Fax: +33 476501890

Re: [ccp4bb] coot error on a Scientific Linux box (32 bit)

to run coot through X11-forwarding of an ssh-connection which sometimes causes this error message, or you need to recompile your graphics driver, e.g. because your kernel was updated and the driver was not. Best, Tim On 12/10/2013 03:53 PM, vellieux wrote: Hi all, I was wondering if anyone had

Re: [ccp4bb] Fwd: undefined edensity blob at glutamine sidechain

rmsd​ -- *Priyank* -- Fred. Vellieux (B.Sc., Ph.D., hdr) IBS2 / ELMA Campus EPN 6 rue Jules Horowitz F-38042 Grenoble Tel: +33 457428605 (Fax: +33 438785494)

[ccp4bb] coot error on a Scientific Linux box (32 bit)

-module coot-exe: /home/prog/ccp4-6.4.0/bin/coot-real coot-version: /home/prog/ccp4-6.4.0/bin/coot-real platform: /bin/uname core: #f No core file found. No debugging This is not helpful. Please turn on core dumps before sending a crash report -- Fred. Vellieux (B.Sc., Ph.D., hdr) IBS2 / ELMA

[ccp4bb] Phaser question

sit). Fred. -- Fred. Vellieux (B.Sc., Ph.D., hdr) IBS2 / ELMA Campus EPN 6 rue Jules Horowitz F-38042 Grenoble Tel: +33 457428605 (Fax: +33 438785494)

Re: [ccp4bb] Fwd: [ccp4bb] pdbset

पुणे विश्वविद्यालय परिसर, गणेशखिंड पुना, ४११,००७ -- Fred. Vellieux (B.Sc., Ph.D., hdr) ouvrier de la recherche IBS / ELMA 41 rue Jules Horowitz F-38027 Grenoble Cedex 01 Tel: +33 438789605 Fax: +33 438785494

Re: [ccp4bb] delete subject

as part of CCP4 might be a very good suggestion, but I agree with you that perhaps it should not land in its full glory in everyone's mailbox. Mark -- Fred. Vellieux (B.Sc., Ph.D., hdr) ouvrier de la recherche IBS / ELMA 41 rue Jules Horowitz F-38027 Grenoble Cedex 01 Tel: +33 438789605 Fax

Re: [ccp4bb] process data from two crystals in-house data

. Thiyagarajan Centre of Excellence in Bioinformatics School of Biotechnology Madurai Kamaraj University Madurai - 625021 Ph: +91-9159224881 (cell) -- Fred. Vellieux (B.Sc., Ph.D., hdr) ouvrier de la recherche IBS / ELMA 41 rue Jules Horowitz F-38027 Grenoble Cedex 01 Tel: +33 438789605 Fax: +33

Re: [ccp4bb] Twinning problem

. Vellieux (B.Sc., Ph.D., hdr) ouvrier de la recherche IBS / ELMA 41 rue Jules Horowitz F-38027 Grenoble Cedex 01 Tel: +33 438789605 Fax: +33 438785494

Re: [ccp4bb] molecular replacement problem.

Medical School Research Associate, Brigham and Women's Hospital Visiting Research Scholar, Brandeis University -- Fred. Vellieux (B.Sc., Ph.D., hdr) ouvrier de la recherche IBS / ELMA 41 rue Jules Horowitz F-38027 Grenoble Cedex 01 Tel: +33 438789605 Fax: +33 438785494

[ccp4bb] Vote for crystallography

crystallographers, what is our view of the importance of X-ray crystallography as an important innovation ? Perhaps it is the time to vote for our fav ? Only two days to go before the poll closes. Thank you, Fred. -- Fred. Vellieux (B.Sc., Ph.D., hdr) ouvrier de la recherche IBS / ELMA 41 rue Jules

Re: [ccp4bb] Scaling with SCALA high and low resolution data sets

resolution images varying between approximately 30 and 200! Do we need to pay attention to some particular options for running the program(s)? Thank you, Kyriacos e-mail: petra...@imbb.forth.gr -- Fred. Vellieux (B.Sc., Ph.D., hdr) ouvrier de la recherche IBS / ELMA 41 rue Jules Horowitz F

Re: [ccp4bb] Resolution limit of index in XDS

the resolution limit for index step in XDS? I only found a keyword INCLUDE_RESOLUTION_RANGE, but it looks to be a definition of resolution range after index step as it says: INCLUDE_RESOLUTION_RANGE=20.0 0.0 !Angstroem; used by DEFPIX,INTEGRATE,CORRECT Thanks! Niu -- Fred. Vellieux (B.Sc., Ph.D., hdr

Re: [ccp4bb] qtrview command line options

. Vellieux (B.Sc., Ph.D., hdr) ouvrier de la recherche IBS / ELMA 41 rue Jules Horowitz F-38027 Grenoble Cedex 01 Tel: +33 438789605 Fax: +33 438785494

[ccp4bb] Is there an alternative to Java to view the (nice) plots in ccp4i ?

in advance, Fred. -- Fred. Vellieux (B.Sc., Ph.D., hdr) ouvrier de la recherche IBS / ELMA 41 rue Jules Horowitz F-38027 Grenoble Cedex 01 Tel: +33 438789605 Fax: +33 438785494

Re: [ccp4bb] Is there an alternative to Java to view the (nice) plots in ccp4i ?

does not work for you? The viewer (QtRView) was released in 6.3.0-010 already integrated with ccp4i. Eugene On 8 Mar 2013, at 12:56, vellieux wrote: Hello, I think the Subject line tells it all. Former Linux box, Java was installed within a couple of browsers and I could view the (nice

Re: [ccp4bb] compiling Fortran 77 code on a Linux box (using gfortran ?)

little impact on performance. Cheers, Jon -- Fred. Vellieux (B.Sc., Ph.D., hdr) ouvrier de la recherche IBS / ELMA 41 rue Jules Horowitz F-38027 Grenoble Cedex 01 Tel: +33 438789605 Fax: +33 438785494

[ccp4bb] compiling Fortran 77 code on a Linux box (using gfortran ?)

code in order to get it to compile and run with gfortran ? Otherwise any idea which compiler should be used to compile Fortran 77 code ? Thanks in advance, Fred. -- Fred. Vellieux (B.Sc., Ph.D., hdr) ouvrier de la recherche IBS / ELMA 41 rue Jules Horowitz F-38027 Grenoble Cedex 01 Tel: +33

Re: [ccp4bb] compiling Fortran 77 code on a Linux box (using gfortran ?)

. XMAX(I)=-. 5 CONTINUE C C OPEN INPUT FILE C WRITE (*,10) 10 FORMAT(///,25X,'*', . /,25X,'* *', -- Fred. Vellieux (B.Sc., Ph.D., hdr) ouvrier de la recherche IBS / ELMA 41 rue Jules Horowitz F-38027

Re: [ccp4bb] SOLVED [ccp4bb] compiling Fortran 77 code on a Linux box (using gfortran ?)

Clifton and Bernhard Rupp for their suggestions. Fred. On 06/03/13 10:48, vellieux wrote: Hello, For those who still know the Fortran language and its Fortran 77 variant, I used to have a g77 compiler here (Linux box), and now on the new box it's no longer g77 but gfortran. When compiling

Re: [ccp4bb] SOLVED [ccp4bb] compiling Fortran 77 code on a Linux box (using gfortran ?)

- invalid memory reference. Backtrace for this error: #0 0x12244B #1 0x122A9C #2 0x473907 #3 0x1BD238 #4 0x1CB4BF #5 0x80486E2 in MAIN__ Segmentation fault Without that flag it compiles runs without error. So you may want to try it just without that flag. Cheers -- Ian -- Fred. Vellieux

[ccp4bb] example script to run SCALA while excluding films (frames)

the processing. If SCALA cannot remove data frames one can write a specific jiffy program to exclude specific rotation ranges from the XDS_ASCII.HKL file, but I'd prefer to use an existing program if it allows to do what I want to do. Thanks in advance, Fred. -- Fred. Vellieux (B.Sc., Ph.D., hdr

Re: [ccp4bb] Rfree flag

calculations of a ligand bound data as that of its native? Thank you With Regards Kavya -- Fred. Vellieux (B.Sc., Ph.D., hdr) IBS / ELMA 41 rue Jules Horowitz F-38027 Grenoble Cedex 01 Tel: +33 438789605 Fax: +33 438785494

Re: [ccp4bb] the matrix format

. Vellieux (B.Sc., Ph.D., hdr) IBS / ELMA 41 rue Jules Horowitz F-38027 Grenoble Cedex 01 Tel: +33 438789605 Fax: +33 438785494

Re: [ccp4bb] need some suggestions for crystallization

could try the Glucose Isomerase supplied by Hampton. It crystallizes under a number of conditions, details of which you can find in their manual. http://hamptonresearch.com/product_detail.aspx?cid=28sid=56pid=56 Ganesh -- Fred. Vellieux (B.Sc., Ph.D., hdr) IBS / ELMA 41 rue Jules Horowitz F

Re: [ccp4bb] refmac5 vs phenix refine mixed up

-- ---x With regards Rajesh K. Harijan Phd Researcher Department of Biochemistry, University of Oulu, Oulu, Finland- 90014 Off Phone: +358 85531174 Mob: +358 400408258 -- Fred. Vellieux (B.Sc., Ph.D., hdr) IBS / ELMA 41 rue Jules Horowitz F-38027 Grenoble Cedex 01 Tel: +33 438789605 Fax

Re: [ccp4bb] perfect twin

. Thanks Lisa -- Fred. Vellieux (B.Sc., Ph.D., hdr) IBS / ELMA 41 rue Jules Horowitz F-38027 Grenoble Cedex 01 Tel: +33 438789605 Fax: +33 438785494

[ccp4bb] another piece of sad news

Mill Hill, London will write a eulogy. I just want to say that I will miss him. Fred. -- Fred. Vellieux (B.Sc., Ph.D., hdr) IBS / ELMA 41 rue Jules Horowitz F-38027 Grenoble Cedex 01 Tel: +33 438789605 Fax: +33 438785494

Re: [ccp4bb] wrong space group or wrong refinement strategy

this mean this is not the right solution or maybe some problems with the space group?Any suggestions for next step? Thanks very much. -- Fred. Vellieux (B.Sc., Ph.D., hdr) IBS / ELMA 41 rue Jules Horowitz F-38027 Grenoble Cedex 01 Tel: +33 438789605 Fax: +33 438785494

Re: [ccp4bb] vitrification vs freezing

written in French - not sure, this will improve their quality, though, comparing my level of French with my level of English ;-) Lovely discussion, Tim -- Fred. Vellieux (B.Sc., Ph.D., hdr) IBS / ELMA 41 rue Jules Horowitz F-38027 Grenoble Cedex 01 Tel: +33 438789605 Fax: +33 438785494

Re: [ccp4bb] Problems with PDB validation

, but the problem doesn't disappear. I have spent a few weeks looking at this and trying every possible solution to this problem. Just wondering what else I can try to fix the issues reported! Thanks in advance. Regards, KS -- Fred. Vellieux (B.Sc., Ph.D., hdr) IBS / ELMA 41 rue Jules Horowitz F

Re: [ccp4bb] Problems in crystallization

University BioCity, Tykistökatu 6A FI-20520 Turku Finland -- Fred. Vellieux (B.Sc., Ph.D., hdr) IBS / ELMA 41 rue Jules Horowitz F-38027 Grenoble Cedex 01 Tel: +33 438789605 Fax: +33 438785494

Re: [ccp4bb] Faculty positions at Molecular Biophysics Unit, IISc, Bangalore

-- Fred. Vellieux (B.Sc., Ph.D., hdr) IBS / ELMA 41 rue Jules Horowitz F-38027 Grenoble Cedex 01 Tel: +33 438789605 Fax: +33 438785494

[ccp4bb] Fwd: email received from Nick Keep...

To: vellieux frederic.velli...@ibs.fr CC: n.k...@mail.cryst.bbk.ac.uk Dear Fred, Sorry did not mean to send a personal post, it was meant to go to the list which it has now. I think some discussion of career issues is not a bad thing for ccp4bb particularly as we allow job adverts. The discussion

Re: [ccp4bb] Twinned Data

-13577 -- Fred. Vellieux (B.Sc., Ph.D., hdr) IBS / ELMA 41 rue Jules Horowitz F-38027 Grenoble Cedex 01 Tel: +33 438789605 Fax: +33 438785494

Re: [ccp4bb] Twinned Data - more information

Institut für Biochemie Geb. 26.32.03.21 Heinrich-Heine-Universität Düsseldorf Universitätsstr. 1 40225 Düsseldorf -Germany- Tel: 0049-211-81-13577 -- Fred. Vellieux (B.Sc., Ph.D., hdr) IBS / ELMA 41 rue Jules Horowitz F-38027 Grenoble Cedex 01 Tel: +33 438789605 Fax: +33 438785494

[ccp4bb] Only su (root) can get ccp4i to run

out there knows what to do in order to solve this problem ? Ta. F.V. -- Fred. Vellieux (B.Sc., Ph.D., hdr) IBS / ELMA 41 rue Jules Horowitz F-38027 Grenoble Cedex 01 Tel: +33 438789605 Fax: +33 438785494

Re: [ccp4bb] Only su (root) can get ccp4i to run

in the same setup-file). Cheers, Tim On 10/09/2012 09:58 AM, vellieux wrote: Hi folks, on my SL6.3 box, only su (root) can lauch and run ccp4i. For other users I get this cryptic message, /home/prog/ccp4-6.3.0/bin/ccp4i: line 4: /wish: No such file or directory /home/prog/ccp4-6.3.0/bin/ccp4i

Re: [ccp4bb] Professor Dame Louise Johnson

A very nice picture of Prof. Louise Johnson can be found on http://www.flickr.com/photos/wellcomeimages/5814718414/ The picture was taken at Diamond's IO2 beam line. Condolences to her family and friends. Fred.

Re: [ccp4bb] ideal rms bond length

0.2593 0.804228480. 12456.9 0.0188 0.939 2.190 0.995 0.150 -- Regards Faisal School of Life Sciences JNU -- Fred. Vellieux (B.Sc., Ph.D., hdr) IBS / ELMA 41 rue Jules Horowitz F-38027 Grenoble Cedex 01 Tel: +33 438789605 Fax: +33 438785494

Re: [ccp4bb] Off Topic: help locating CNS data

/emeritus-staff http://rexpalmer2010.homestead.com -- Fred. Vellieux (B.Sc., Ph.D., hdr) IBS / ELMA 41 rue Jules Horowitz F-38027 Grenoble Cedex 01 Tel: +33 438789605 Fax: +33 438785494

Re: [ccp4bb] Which Coot for Scientific Linux 6.3

, and the version of Coot for Fedora core 12 runs and provides me with a proper graphics windows. I thought I'd keep the bb informed. F.V. -- Fred. Vellieux (B.Sc., Ph.D., hdr) IBS / ELMA 41 rue Jules Horowitz F-38027 Grenoble Cedex 01 Tel: +33 438789605 Fax: +33 438785494 email: frederic.velli

Re: [ccp4bb] diagram of dsDNA

of Pathogen Biology, CAMSPUMC. Building No.7, Bei Gong Da Ruan Jian Yuan, Beijing BDA, 100176, Beijing, China. Email: cuisheng2...@yahoo.com.cn Tel. +86 10 67828669 Fax. +86 10 67855012 -- F.M.D. Vellieux (B.Sc., Ph.D., hdr) IBS / ELMA 41 rue Jules Horowitz 38027 Grenoble Cedex 01

Re: [ccp4bb] NADP binding protein without Rossmann fold.

-classical Rossmann fold bearing proteins? Thanks, Sudipta. Sudipta Bhattacharyya. Senior Research Fellow, Department of Biotechnology, Indian Institute of Technology Kharagpur, India. -- F.M.D. Vellieux (B.Sc., Ph.D., hdr) IBS / ELMA 41 rue Jules Horowitz 38027 Grenoble Cedex 01 France Tel

[ccp4bb] question about DM

Hi all, Just a (naive?) question: how does one manage to introduce (and deal with) improper non-crystallographic symmetry in DM ? Or does one has to go to DMmulti for that (because, by definition, going from one crystal form to another crystal form is improper NCS) ? Ta, F. Vellieux

Re: [ccp4bb] Regarding refinement in Refmac5

Hi there, Not much information provided. How was the initial model refined ? Phenix ? It could be a problem with the Refmac refinement protocol (difficult to say with so little information) if you switched from Phenix to Refmac. How certain are you 1 - of the space group; 2 - that the

[ccp4bb] information received through the AFC: iycr2014

Dear colleagues, Information just received here through the AFC channels: the UN general assembly has declared that 2014 will be the international year of crystallography. Their statement (in French) as an attachment (sorry about including an attachment). F. Vellieux IYCr-FR.pdf

Re: [ccp4bb] information received through the AFC: iycr2014

The press release in English: http://www.un.org/News/Press/docs/2012/ga11262.doc.htm Boaz: perhaps the crystallography congresses and events taking place in 2014 will be attended by UN peacekeeping force members as well (with their blue helmets) ? F.V. Boaz Shaanan wrote: Et alors, what

Re: [ccp4bb] information received through the AFC: iycr2014

Do you mean we should crush the helmets and solve the structure of the resulting powder blue coloured powder by crystallographic methods ? Sounds like a good proposal to be put forward to the UN to help them get rid of their used helmets ! David Schuller wrote: On 07/04/12 08:03, Vellieux

Re: [ccp4bb] how to get phase of huge complex

-ray.com/products/catalogue_consum_CSM002.html HTH, Fred. F.M.D. Vellieux (B.Sc., Ph.D., hdr) Institut de Biologie Structurale J.-P. Ebel CEA CNRS UJF LBM/ELMA 41 rue Jules Horowitz 38027 Grenoble Cedex 01 France Tel: +33 (0) 438789605 (direct line), +33 (0) 663482891 (mobile phone) Fax: +33 (0

Re: [ccp4bb] P321 space group reindex problem

Hi there, I am not certain that the thread is P321 space group reindex problem any more. But: trigonal (and hexagonal) space groups are (usually?) polar. The cell axis c can go up or can go down, and in order to get a consistent indexing you need to check both indexing systems when you

Re: [ccp4bb] P321 space group reindex problem

:55, Vellieux Frederic frederic.velli...@ibs.fr wrote: Hi there, But: trigonal (and hexagonal) space groups are (usually?) polar. The cell axis c can go up or can go down, and in order to get a consistent indexing you need to check both indexing systems when you scale additional data

Re: [ccp4bb] question about a dataset with pseudotranslational symmetry

Hello,   Which version of Phaser are you using ? As you must be aware, not all versions of Phaser deal in the most appropriate manner with cases of translational NCS if this is what you mean by pseudo translational symmetry. Personally I'd go for the latest version of Phaser...   HTH,   Fred.

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