[ccp4bb] Coot for Fedora Core 8?

hi, The subject tells it all. Is there somewhere a version of Coot that is suitable for Fedora Core 8? Thanks in advance, Fred.

[ccp4bb] wich program to test an alternative phaser solution

Dear all, We have a phaser output with 2 alternative solutions. Not differing much by the statistics. Phaser provides the solution with the highest LLG. However I am not convinced by that solution. What program should be used with the input PDB and the Euler angles and translation parameters

Re: [ccp4bb] Fwd: [ccp4bb] pdbset

नुसंधान कर्ता संरचनात्मक जीवविज्ञान प्रयोगशाला डी. एन. ए. फिंगरप्रिंटिंग एवं निदान केंद्र हैदराबाद, ५००, ००१ और राष्ट्रीय कोशिका विज्ञान केंद्र पुणे विश्वविद्यालय परिसर, गणेशखिंड पुना, ४११,००७ -- -- स्वस्तिक फुलेरा वरिष्ठ अनुसंधान कर्ता संरचनात्मक जीवविज्ञान प्रयोगशाला डी. एन. ए. फिंगरप्रिंटिंग

[ccp4bb] Phaser question

the planet you 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: undefined edensity blob at glutamine sidechain

(green): 3 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)

d to load module "canberra-gtk-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 r

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] Some advices on model modification

alway used 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

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

79) invoked from within "source [file join $env(CCP4I_TOP) bin ccp4i.tcl]" (file "/home/prog/ccp4-6.5/bin/ccp4i" 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 de

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

Re: [ccp4bb] model bias

ds, Aleks -- 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] Which Coot for Scientific Linux 6.3

rsion, 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 438785

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

/our-staff/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] 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

0.150 15 0.2121 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

[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

should be done 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-

Re: [ccp4bb] Twinned Data

ldorf -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

Re: [ccp4bb] Twinned Data - more information

PhD student Arbeitskreis Schmitt 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

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

ty_and_Research/ http://www.rsc.org/shop/books/2008/9780854042722.asp ---- -- 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...

where... With this I think we can close the discussion (I do not favour "ccp4bb wars"). And I am in favour of job ads being posted to the bb. Fred. Original Message Subject:Re: Date: Tue, 30 Oct 2012 10:55:18 + From: Nicholas Keep To: vellie

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] Problems with PDB validation

g them again after refinement, 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.,

Re: [ccp4bb] vitrification vs freezing

nvince journals to only accept articles 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] wrong space group or wrong refinement strategy

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

[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] perfect twin

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

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] need some suggestions for crystallization

You 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=28&sid=56&pid=56 Ganesh -- Fred. Vellieux (B.Sc., Ph.D., hdr) IBS / ELMA 41 rue Jul

Re: [ccp4bb] the matrix format

tors" in phenix GUI? > > Thanks a lot! > > Qixu Cai -- Jon Agirre, PhD Unit of Biophysics (CSIC-UPV/EHU) http://sourceforge.net/projects/projectrecon/ +34656756888 -- 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] Rfree flag

it mandatory to use the same reflections for Rfree 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

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

d from 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.

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

be done with existing Fortran 77 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-38

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

XMIN(I)= . 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

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

, Ian 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

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

mentation fault - 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

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

n, it may be removed with very 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] Is there an alternative to Java to view the (nice) plots in ccp4i ?

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 and

Re: [ccp4bb] qtrview command line options

Ed. -- "Hurry up before we all come back to our senses!" Julian, King of Lemurs -- 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] Resolution limit of index in XDS

ution 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.

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

the lower 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

[ccp4bb] Vote for crystallography

e as we practice it today. As macromolecular 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.

Re: [ccp4bb] molecular replacement problem.

tor in Neurology, Harvard 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

Re: [ccp4bb] Twinning problem

nks. Best, Liang -- 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

ut maybethis is not true. There is definitely value in sharing preliminary data, especially for junior people. To have such a function 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 -- F

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

a S. 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 Fa

[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 nee

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

Desmond - their installation is simple and they 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 t

[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. * ##

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] superimposition of 3D structures with the DNA part only

s 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, clic

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

Thanks 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] 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

Re: [ccp4bb] Crystypos [WAS: [ccp4bb] Mac OSX 10.7 Lion]

Well in fact, it all depends on the type of detector these small angels end up on and on the speed of this "godly" radiation. Only once you have considered both these elements can you say "poor little things". My 2p worth. Fred. Ed Pozharski wrote: The best X-ray related typo I ever seen was

Re: [ccp4bb] Structure problem

Hi there, In crystallography there are so many places where you can have problems (and need to solve these problems) that I cannot list them all. "There is no twinning in the data" - you probably mean "the data does not seem to indicate the presence of twinning but there might be twinning";

[ccp4bb] important information for scientists with samples travelling via Lyon or Grenoble airports

Could be of importance to those who have to use the Lyon or Grenoble airports (to ship in or out), check out the update from Sept. 27, 2011. http://www.ill.eu/users/user-guide/safety/important-instructions-for-biological-samples/ Fred.

Re: [ccp4bb] Pointless (P41) vs. Phaser (P43)

P4(1) and P4(3) are enantiomorphic space groups. The only difference is the helix (one way, or another). No difference in the diffraction pattern. Hence a program (or a crystallographer) cannot distinguish the 2 based on the diffraction pattern. Once you start phasing, e.g. by molecular replace

Re: [ccp4bb] MR - small coiled coil, 1.65A = 1.000 solutions, all of them wrong

Just to add to what has been "said" (written) before: coiled coiled or simply helices can be very problematic for M.R.. Human sacrifice has never given any positive result (as reported in the literature as far as I know), but "heavy atom sacrifice" could be attempted ("heavy atom" includes in

Re: [ccp4bb] Phenix building residues not found in input sequence file

Could you have an unexpected "small subunit" (or some other situation) giving additional density that Phenix is building into ? In other words, how sure are you of what is present in the crystal ? This is because I remember the enzyme methanol dehydrogenase where there was a small subunit which

Re: [ccp4bb] Biological assembly

Hi, What you must deposit is what is present in the asymmetric unit of the crystal. The HEADER cards (and the publication) can describe the most likely biological assembly. Why is that: there is no reason why the crystal should conform to the biological function (and associated quaternary stru

Re: [ccp4bb] Biological assembly

Hi, If, in your case, no possible asymmetric unit can contain A1-B2, then you deposit A1-B1 (or I suppose A2-B2...) and indicate to the PDB (like placing cards in the header cards) the operator to be used (and the subunit it applies to) in order to generate the most likely biological dimer. N

Re: [ccp4bb] raw data deposition

D Bonsor wrote: and allow someone else to have ago at solving the structure. I'd be careful there if there was a motion to try to implement a policy at SR sources (for academic research projects) to make it compulsory to publically release all data frames after a period (1 year ? 2 years ?

Re: [ccp4bb] raw data deposition

I must "say" that there were some emails exchanged between me and Gerard later, in which I pointed out that I wasn't against deposition of images (data frames). In fact, if SR sources kept user's data there would be one more structure from here in the PDB: HDD failure here, the data on a mirror

Re: [ccp4bb] [off topic] Control of crystals' direction and position in the drop.

Hi, Your email mentions "drop". What about trying another technique where you do not have "drops", such as the liquid interface diffusion method (in capillaries), or the use of dialysis ? Crystallisation under oil (injection of the 2 components under "oil") could also be tried. Fred > Messag

Re: [ccp4bb] Can I combine selenoMet data and MR model to solve the phase problem?

Hi, This hasn't been mentioned by the people who have answered so far so here we go: your molecular replacement solution and your SeMet solution to the phase problem are not necessarily using the same origin. There is a ccp4 program (is it phistats ? and there may be other programs around) tha

Re: [ccp4bb] Movements of domains

A mixture between mathematical significance and biological significance as a part of the reply: you should also take into account the thermal vibrations of the atoms present in that domain, i.e. the "thermal ellipsoids" when you have one of the representations of anisotropic temperature factor

Re: [ccp4bb] MERGING THREE DATASETS

There are several ways to skin a cat. If you have processed your data with XDS, XSCALE can also do the job (you have to think of the unit cell parameters of the merged data set though - the default may not necessarily what you wish to have), and I am certain other data frame processing suites w

Re: [ccp4bb] MAD

For those of you interested, the reply to Tassos' question can be found here: http://www.iucr.org/resources/commissions/crystallographic-computing/schools/school96/ccp4-program-system (on-line) as well as here, http://www.*ccp4*.ac.uk/manual.ps (a ps file). McLaughlin, Terry and Zelinka. And

Re: [ccp4bb] off-topic:schematic representations for secondary structure

I believe Procheck generates drawings such as those. It generates PostScript files, and if you need to have (eg) jpg files, a PostScript interpreter, screen capture and there you are (Gimp to select only the areas you're interested in) HTH, Fred. WENHE ZHONG wrote: Dear memebers, Thank yo

Re: [ccp4bb] MTZ file

Hi, The refinement program generates an mtz file with map coefficients (including difference Fourier coefficients) so you should use that one for model rebuilding in coot; for the next refinement rounds, at the beginning of each round you should provide the initial mtz file coming from data pr

Re: [ccp4bb] Temp Fact Variance Analysis

Hi, You could try to lower the threshold used to contour the maps for these side-chains (middle mouse "button" if you have a 3 button mouse with a wheel in the middle). Quite often such side chains have lowish electron density that does not appear at (say) 1.0 or 1.5 sigma (in the 2mFo-DFc ma

Re: [ccp4bb] Temp Fact Variance Analysis

Typo (my fingers type faster than my brain...) Original Message Subject:RE: [ccp4bb] Temp Fact Variance Analysis Date: Thu, 1 Mar 2012 14:56:06 + From: Oganesyan, Vaheh To: Vellieux Frederic References: <4f4f8cb1.1070...@ibs.fr> Fred,

Re: [ccp4bb] Disulfide bonds

I'd google for "Bart Hazes" and "SSBOND" myself. There is (or was) a server, and the publication is Prot. Eng. 1988, 119, 25 (PMID 3244694). The server seems to be down or has moved. HTH, Fred. > Message du 04/03/12 05:07 > De : "Naveed A Nadvi" > A : CCP4BB@JISCMAIL.AC.UK > Copie à : > Objet

Re: [ccp4bb] Off-topic: Supplying PDB file to reviewers

Hi, I think this practice (requesting the data) is getting more and more common these days with some "scientists" having published fake structures. You are far more protected from scientific misconduct when you provide the data to referees (this takes place through an editorial system - you s

Re: [ccp4bb] phaser: high z score but no sol

Hi, If you have the correct solution, clashes may be due to loops. It may be an idea to clip these off for the molecular replacement calculations (loops might be shorter in the structure-to-be-solved than in the search model, they may have different conformations in the structure-to-be-solved

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.

Re: [ccp4bb] which Linux workstation for crystallography to buy?

Hi, Frankly, any vendor or assembler of PC's will do. Things to make sure to have on your PC: an NVIDIA graphics board in order to get nice graphics (their Linux drivers are fine; I don't know their current range of boards, here we buy middle-range boards, not the cheapest ones that are speci

Re: [ccp4bb] protein ligand energy

Rex Palmer wrote: Can anyone reccomend a free download program that will calculate the energy of a protein/ligand complex? The ligand has been modelled in. Thanks Rex Palmer Birkeck College Hi Rex, I think any refinement program such as CNS will do this - problem is, since these programs

Re: [ccp4bb] How to add water molecules..??

I am not sure that I understand your question perfectly... You can add/remove waters "automatically" during refinement using the proper options. After refinement, then you can also (i.e. you should also) take the output mtz file and use a graphics program (with PDB and MTW file) for modelling (i

Re: [ccp4bb] Refinement

I second that. Incorrect space group assignment usually causes this behaviour of having R and R-free stuck at very high values. It is useful to go back to the data processing stage and carefully consider all Bravais lattices (and associated space groups) that the autoindexing routine finds cons

Re: [ccp4bb] what package provides libg2c.so.0 on Ubuntu ?

Hi, For questions relating to a specific package (if it is in rpm format, I don't know what the Uuntu installation software uses as packages), you can use the rpm search web site http://rpm.pbone.net/ (in addition to http://www.rpmfind.net/ , can't search in rpmfind.net at the moment, it says

Re: [ccp4bb] refining structures with engineered disulfide bonds

Bart Hazes wrote a program (and published as well, Hazes & Dijkstra perhaps) called SSBOND I think. I cannot remember exactly what the computer program does, but it certainly has a data base of "possible" disulphide bond conformers. Hence I would myself certainly check your second didulphide to

Re: [ccp4bb] Regarding space group P1, P21

Dear Mohinder, What one should really do is to provide an accurate model (including the space group) of what is taking place in the crystal. For example, there was this case reported by Morales et al. (2000, Acta Cryst sect. D56, 1408-1412) of a complex of 2 proteins (i.e. identical situation

Re: [ccp4bb] Rules of thumb (was diverging Rcryst and Rfree)

I do not know if that's really cynical: I've had the case of a referee recommending manuscript rejection because the title of the manuscript was not appropriate. The editor followed the advice of the referee. A proper refereeing job would have been to suggest that the authors change the title o

Re: [ccp4bb] convert map coefficients to phases and FOM

In CNS v1.2, you have the input file called "model_fcalc.inp". So what I would do is to generate these Fc's from the model, then "insert" them into an mtz that contains your Fo's, and use SIGMAA to generate the Sigmaa figures of merit. Or use another program to generate e.g. Sim weights. HTH,

Re: [ccp4bb] relationship between B factors and Koff

I can direct you to PDB entry 1EWY, where the average isotropic temperature factor for the major component of the complex is ca. 47 A**2 and that for the smaller component is ca. 69 A**2. Similar values than the ones you are reporting. I am assuming some sort of "disorder", or if you prefer, "w

Re: [ccp4bb] Problem with finding of spots

Hi, I agree with what has been mentioned about "fuzzy spots". But what seems obvious as well is that the resolution for spot picking should be limited (to 3.5 or 4 A resolution). It is difficult to judge from an image of a diffraction pattern, but it seems to me from this image that the spots

Re: [ccp4bb] Tough 'shell' on disturbed drop

Hi, In our hands, the crystallisation droplets of glycosomal pyruvate phosphate dikinase had a 'skin' of what I thought was denatured protein at the surface of every crystallisation droplet. We had to learn to use the crystal microtools (such as a microknife, or a micro-needle can't remember wh

Re: [ccp4bb] Structure based and motif based sequence alignment

Muhammed bashir Khan wrote: Dear All; I have structures of two protein one full-length while the other truncated at the c-terminus(one from prokaryote while the other from eukaryotes). Now I want to do the sequence alignment of these two proteins from all species in such a way that the structure

Re: [ccp4bb] diffcult MR case

Hi, How sure are you of the space group ? What are the data processing Rsym values (which if high may indicate mis-indexing due to an incorrect choice of detector origin for example) ? There are many places where things can go "wrong" before reaching the molecular replacement calculation stage

Re: [ccp4bb] Rfrees

I can't see any problem switching from Refmac to Phenix refinement. You just provide Phenix with the current model (if you have refined using TLS there is an "additional" step, using I believe tlsanl to generate the "proper" PDB file as you would for data deposition with the pdb), the initial m

Re: [ccp4bb] Space group vs. gap between Rwork and Rfree?

Hi Petr, Usually IDXREF suggests more than one Bravais lattice that is consistent with your diffraction images; hence it is (sometimes) worthwhile trying to INTEGRATE in all possible Bravais lattices and this allows you to eliminate a number of possibilities (poor profiles during integration,

Re: [ccp4bb] If it is a new structure?

Hi, Last couple of times I asked myself the same question ("what does it look like?") I used ssm (or PDBeFold as seems to be called now). http://www.ebi.ac.uk/msd-srv/ssm/ HTH, Fred. wrote: The structure of my protein is as shown as the purple one. Another one ,as shown as green,is homolo

Re: [ccp4bb] Mg2+ or water

James Stroud wrote: On Dec 20, 2010, at 1:53 PM, Jacob Keller wrote: what is the .odp file extension? http://tinyurl.com/mjokqs A .odp file is an "open document presentation". It is the open version of a power point presentation. http://en.wikipedia.org/wiki/OpenDocument An .odp fi

Re: [ccp4bb] heavy atom clusters

Hi, I suggest that you check out the lanthanide compounds investigated by a number of people including Richard Kahn. Papers can be found using the iucr web site (and its search function). Commercially available. Fred. > Message du 31/01/11 17:02 > De : "Jan Rashid Umar" > A : CCP4BB@JISCMAIL.

[ccp4bb] adding gaussian noise to an mtz data column

Before re-inventing the wheel... Is there anywhere some software (freely available software, I mean) that can add some Gaussian noise to data. The data is currently stored in a data column in an mtz (not phase data, but "amplitudes", "sigma values"...) but can be exported to another format if

Re: [ccp4bb] adding gaussian noise to an mtz data column

lumn with label Fsimulated which contains the value of column Fcalc plus 10 times a random number from a Gaussian distribution with average = 0 and variance = 1 Cheers -- Ian On Fri, Feb 4, 2011 at 12:40 PM, Vellieux Frederic wrote: Before re-inventing the wheel... Is ther

Re: [ccp4bb] CNS and protein structure refinement

Hi Rex, There will be small differences in particular due to the different ways of treating the solvent. How large of a difference are you talking about? Normally the difference should not be very large... And if this related to solvent effects, it will affect the low resolution reflections w

Re: [ccp4bb] MR problem in determining the number of identical molecules in ASU

Ting-Wei Jiang wrote: Dear experts, Sorry for a simple question but confusing me so much! Does it make bad effects on determining the number of identical molecules in ASU by choosing low symmetry space group. For example,If I choose lowest symmetry(p4) instead of higher one(p43212). Does it

  1   2   3   4   >