Re: [ccp4bb] Message from the Uppsala EDS: "Morituri te salutant"

The replacement of the EDS might be an excellent opportunity to upgrade/include the newer EDSTATS metrics and make these raw data also downloadable/parse-able for analysis purposes (xml). A server option where you can send in your own PDB files (included in the validation server?) before submissio

Re: [ccp4bb] diffraction images simulator

Contact James Holton, he has MLFSOM and other goodies. James Holton (jmhol...@lbl.gov) Best, BR From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Daniele de Sanctis Sent: Friday, November 25, 2016 8:45 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] diffraction images s

[ccp4bb] Model parts rearrangement

Hi Fellows, I seek advice for a trivial but tedious problem: I have rebuilt, automatically and manually, several parts of a structure, which of course, are all over the place in different ASUs. I also have a reference model, where the parts form a correct ASU. Is the a program/script that can

Re: [ccp4bb] PAD images

click on the "Small Spots" radio button. This solves most of the "I can't interpret the spots" problems you describe. -James Holton MAD Scientist On 4/27/2015 3:31 PM, Bernhard Rupp (Hofkristallrat a.D.) wrote: > Hi Fellows, > > I wonder whether it's j

[ccp4bb] PAD images

Hi Fellows, I wonder whether it's just me and my eyesight failing (or excessive internal lubrication) It seems that the art of looking at diffraction patterns and being able to tell a lot about modulation, superstructures, extinctions, etc. becomes kind of useless old fart stuff when dealing

Re: [ccp4bb] 3BDN, 16.5% Ramachandran Outliers!!!!!

Once more to those who feel offended by the structures in discussion: I’d be very careful at judging low resolution structures. This is a tricky business requiring a lot more info than just the PDB validation report. The 3+ to 4 A resolution range is a particularly deceptive one: The crystal

Re: [ccp4bb] 3BDN, 16.5% Ramachandran Outliers!!!!!

Well, with full respect to your sensitivities as far as your own person is concerned: if you play rough (and 5 exclamation marks qualify by commonly accepted email etiquette as incipient flame, at least), you need to be willing to take a few as well... Best, BR --

Re: [ccp4bb] funding experiences - query

Hi Fellows, thanks to all who have responded to my query. The response were very elucidating, and at the same time (a) consistent and (b) depressing, even for my slightly cynical standards As no good deed goes unpunished, I wonder whether the respondents (and anyone else) have a reasonable

[ccp4bb] funding experiences - query

Hi Fellows, hopefully everyone has recovered from the Easter Egg coma & April jokes by now. Now something serious: for a commissioned opinion piece in a vanity journal, I seek to get a better understanding regarding improvement of review and funding decisions for crystallographic studies. U

Re: [ccp4bb] Picking water molecules at 4A structure.

> Now my query is, whether one should pick water molecules at this low > resolutions or it is totally unscientific to do so? Your question is justified in intent, but ill phrased. The question you are faced with is “How plausible would the assignment of a given electron density reconstructi

Re: [ccp4bb] Number of Molecules in Asymetric Unit

New kernel version http://www.ruppweb.org/mattprob/default.html Best, BR From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of amro selem Sent: Wednesday, April 01, 2015 8:45 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Num

[ccp4bb] Manuscript PRL

HI Fellows, just in time for some easy Easter reading, the first page regarding some new ideas about nucleation Link to full content is in the PDF document. Best regards, BR - Bernhard Rupp 001 (925) 209-7429 +43 (676) 571-0536

Re: [ccp4bb] Basic Anomalous Scattering Theory

A look at the term scheme might help to understand the absorption edge structure - pp 286 and Figure 6-30 BMC. Best, BR -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Keller, Jacob Sent: Wednesday, March 11, 2015 9:58 AM To: CCP4BB@JISCMAIL.AC.UK

[ccp4bb] Twilight 2014 update

Dear All, Chris Weichenberger just released the 2014 update for TWILIGHT. It is available from my web site http://www.ruppweb.org/twilight/default.htm http://journals.iucr.org/d/issues/2013/02/00/issconts.html http://journals.iucr.org/f/issues/2013/02/00/issconts.html Please note: The

Re: [ccp4bb] Bulk solvent correction in Phaser MR LF

CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] de la part de Bernhard Rupp (Hofkristallrat a.D.) [hofkristall...@gmail.com] Envoyé : mardi 3 février 2015 14:49 À : CCP4BB@JISCMAIL.AC.UK Objet : [ccp4bb] Bulk solvent correction in Phaser MR LF Hi Fellows, I cannot find the proper reference for the im

[ccp4bb] Bulk solvent correction in Phaser MR LF

Hi Fellows, I cannot find the proper reference for the implementation of bulk solvent corrections in the Phaser Molecular replacement likelihood functions. For the unplaced model, it can only be a Babinet model to improve the scaling, and I believe that is implemented via a Babinet rescaled

[ccp4bb] [OT]:Typoglycemia

Today, after 6 years in circulation, John Tesmer kindly informed me about a labelling error in BMC figure 6-17 http://www.ruppweb.org/Garland/gallery/Ch6/pages/Biomolecular_Crystallograph y_Fig_6-17.htm I think the reason that nobody has noticed it until now is perhaps (in addition to the fac

Re: [ccp4bb] chloride or water

After reading this exchange, I think at the core of the dispute is the question what a structure model really is supposed to represent (a), and how to annotate/describe it (b). ad (a) In general, and forgive me for not disclosing all caveats and fine tune (I leave this to GB), we are in

Re: [ccp4bb] CCP4 Release 6.5

OK I tried this on a 3rd machine (6.4 to 6.5 w/o uninstall of 6.4 before 6.5 install). Same result. Window attached. Somehow it seems the shortcut icon does not properly update. Its command becomes C:\CCP4\TclTk84\bin\wish.exe "C:\CCP4\6.5\share\ccp4i\bin\ccp4i.tcl" Changing the command to C:\CC

[ccp4bb]

Also MATTPROB indicates 3 or 4 molecules/asu as likely solutions. http://tinyurl.com/pe2choc I do not understand why you propose 16 mol/asu? The entire unit cell would likely be only 8 molecules (2 tetramers) BR -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL

Re: [ccp4bb] Observations-to-parameter ratio in Refmac

Ethan is right. I also have compiled a few estimates how to get to this number pp638 ff 'Estimating the restraint count' in BMC Best, BR -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Ethan A Merritt Sent: Tuesday, June 03, 2014 11:44 AM To: CCP

[ccp4bb] BMC second edition - request for comments

Dear Fellows and faithful readers of BMC: Many thanks again to the members of the community who have contributed so generously to BMC either with original ideas and comments during its 60 month gestation period or by careful reading and correcting many mistakes and outright errors during pos

[ccp4bb] OT:Website help

Hi Fellows, please allow me this OT posting I would kindly ask to be continued by interested parties off-board. Summary: I am having serious trouble with my web hosting provider. Problem: My ruppweb/hofkristallamt site which has to a degree become a community resource is hosted on a windows NT s

Re: [ccp4bb] popular piece on X-ray crystallography

squared) probability distribution - after you have collected many photons - is your diffraction pattern. Chapter 6 introduction... Best, BR -Original Message- From: Tim Gruene [mailto:t...@shelx.uni-ac.gwdg.de] Sent: Friday, April 19, 2013 9:44 AM To: b...@hofkristallamt.org Cc: Bernhard Rupp

Re: [ccp4bb] popular piece on X-ray crystallography

However, a reviewer could reject the method on theoretical grounds - the explanation of X-ray diffraction as a multi-photon process is not correct BR -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Peter Artymiuk Sent: Friday, April 19, 2013 7:

[ccp4bb] Thx...

Hi Fellows from the programming department(s), I just had the pleasure to work with the new update mechanism and Win CCP4 6.3 GUI. That you can get from the summary page directly to Coot (which also automatically updates) and that everything works as advertised is very impressive and I perhaps eve

Re: [ccp4bb] 3D alignment of points (atoms)

A brief description of the Kearsley implementation including F77 code is in the old (1993) computing tutorial: http://www.ruppweb.org/xray/comp/superpos.htm The example program only works with pairwise correspondence but still one gets the idea. Best wishes for 2013, BR -Original Message--

Re: [ccp4bb] vitrification vs freezing

Agreed. When we do not know what is actually happening upon cooling in a multi-component system like the crystal, avoiding well -defined terms referring to the state of matter, and instead restricting ourselves to a term describing the process appears less contentious. Thus, flash-cooling, cryo-

Re: [ccp4bb] usefulness of cacodylate?

Math may be frightening but cacodylate seems not... With a MW of 214 for the trihydrate a 70 kg clone needs at the 0.5 g/kg LD50 to consume about 35 g of it, which is 0.16M. Of a 0.1M solution you'd therefore have to drink 1.6 L or almost 4 pints. So, prost, cheers, gsuffa, bescheid, slantje,

Re: [ccp4bb] inflluence of pH for crystallization on protein 3-D structure

An example for how crystallization at non-physiological pH (and non-physiological concentrations and non-physiological environmental) may influence behavior of the protein is the Botulinum A LC protease. Under normal conditions (upon endocytosis of a few molecules at best into the nerve cell),

Re: [ccp4bb] PNAS on fraud

I think the real point here is that a difference exits between divergent interpretation of legitimate evidence - which is normal scientific epistemology - or whether the presented 'evidence' is in some fashion tampered with. The former is healthy procedure and (I hope) not subject of disagreement -

Re: [ccp4bb] PNAS on fraud

Randy Read just pointed out to me that in their case-controlled analysis paper http://journals.iucr.org/d/issues/2009/02/00/ba5130/index.html when considering lower resolution and other factors, the vanity journals seem to come out no worse than the rest. In any case I suspect any retractions a

Re: [ccp4bb] PNAS on fraud

Jeudi 18 Octobre 2012 19:16 CEST, "Bernhard Rupp (Hofkristallrat a.D.)" a écrit: > > I had a look to this PNAS paper by Fang et al. > I am a bit surprised by their interpretation of their Fig. 3: > they claim that here exists a highly signficant correlation between &

[ccp4bb] PNAS on fraud

Dear CCP4 followers, Maybe you are already aware of this interesting study in PNAS regarding the prevalence of fraud vs. 'real' error in paper retractions: Fang FC, Steen RG and Casadevall A (2012) Misconduct accounts for the majority of retracted scientific publications. Proc Natl Acad Sci U S A

Re: [ccp4bb] Question about weird diffraction map

lto:mfrank...@nysbc.org] Sent: Tuesday, July 24, 2012 7:08 AM To: b...@hofkristallamt.org Cc: Bernhard Rupp (Hofkristallrat a.D.); CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Question about weird diffraction map Hi Bernhard - Having the spots in regular lines indicates that this is a single cry

Re: [ccp4bb] Question about weird diffraction map

> you'll see that some of them are arranged in regular lines. I am not sure I understand what the line argument implies? >indicates a very small unit cell, with dimensions probably < 10 A Very indicative also the few strong and isolated high resolution reflections Cheers, BR

Re: [ccp4bb] linking PLP-Lys

Link statement? LINK NZ LYS A 72 C4A PLP A 500 1555 1555 1.30 There are many examples in the PDB this one 1hkv Best, BR From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Rajesh Kumar Sent: Monday, July 23, 2012 10:30 AM To: CCP4BB@J

Re: [ccp4bb] Crystal Optimization

> Always give up. ...definitely not the kind of guy I want to sit up front in an airliner… Best regards, BR - Bernhard Rupp, ATP-B737, CFII-MEI Vienna Air International Professional Aviation Services 001 (925) 209-7429 +4

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

Ø enjoy that the U.N.'s declaration of the International Year of Crystallography comes in the form of a "resolution." ...which tells what a UN resolution is worth… BR From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Sampson, Jared Sent: Thursday, July 05, 2012 10:2

Re: [ccp4bb] The effect of His-tag location on crystallization

Google yields amongst others: His-tag impact on structure Acta Cryst. (2007). D63, 295–301 ...quäl dich. -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of weliu Sent: Tuesday, June 26, 2012 6:07 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] The eff

[ccp4bb] [OT]: The Ultimate Inferior Beings

This is to inform you that a well-respected member of the crystallographic community has published a totally hilariously absurdly funny Sci-Fi novel. I added a link on my web site, www.ruppweb.org , and no, I said 'well respected', so I did not write it, but maybe you can guess from the pseudonym.

[ccp4bb] FW: [PyMOL] Structural biologist job

FYI for the on-pymol readers. BR -Original Message- From: H. Adam Steinberg [mailto:a...@steinbergs.us] Sent: Tuesday, June 12, 2012 4:22 AM To: pymol-us...@lists.sourceforge.net Subject: [PyMOL] Structural biologist job Hi all, A friend of mine is looking to hire a structural biologist

Re: [ccp4bb] Fun Question - Is multiple isomorphous replacement an obsolete technique?

Given Cu, yes, the five M edges between 2.3keV and 3.6keV contribute a continuum transition signal of the 8e- you initially referred to. -Original Message- From: Jacob Keller [mailto:j-kell...@fsm.northwestern.edu] Sent: Wednesday, June 06, 2012 12:35 PM To: b...@hofkristallamt.org Cc:

Re: [ccp4bb] Fun Question - Is multiple isomorphous replacement an obsolete technique?

There is also a relevant point from the physics of the absorption spectra - the XANES white lines (near edge peaks higher than the continuum transition or edge step) depend on the chemical environment of the anomalous atom in terms of available unoccupied states (which n. b. is something entirely d

Re: [ccp4bb] Fun Question - Is multiple isomorphous replacement an obsolete technique?

Richard Dickerson's book is relevant and gripping reading http://www.amazon.com/gp/product/0878931686?ie=UTF8&tag=brscrystallot-20&lin kCode=as2&camp=1789&creative=9325&creativeASIN=0878931686 BR -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of a

Re: [ccp4bb] to determine missing atoms and residues in a PDB file

I do not seem to understand the meaning of ‘fixing’. Fixing something can mean a) repairing it, implying that something was broken or amiss. Lack of experimental information expressed as omission of atoms is not something that needs fixing. b) keeping it constant. Like in having on

Re: [ccp4bb] Covert Structure Factor to mtz

It would be desirable to actually HAVE the cell information in the cif file, if simply for assuring/checking consistency between model and data. Maybe something for the PDB to contemplate BR -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of m

Re: [ccp4bb] very informative - Trends in Data Fabrication

>You never know when a forgotten slip of the mouse when using AutoDep ten years ago will come back to haunt you. On the paper James refers to and found the data, added mystery was that the postdoc who may have slipped disappeared w/o much of trace and the PI died. Dan was the only survivor. Still

[ccp4bb] [OT] to CCP admin - CCP14 - who's in charge?

Dear CCPx administrators: I just notice that on /www.ccp14.ac.uk/ccp/web-mirrors/llnlrupp/cvs/Rupp/rupp.html a deprecated web page from the early 2000s (!) that causes confusion exists on a mirror of the LLNL site dead since 2005. I cannot find a responsible contact for CCP14 since Lachlan's u

[ccp4bb] Refmac executables - win vs linux in RHEL VM

Something the developers might be interested in: The Refmac_5.6.0117 32-bit windows binaries run native on a win64 3-4x slower than those from the linux distribution run **in a RHEL6.2-64 VMware virtual machine hosted the same windows7/64 system.** VM/RHEL: Refmac_5.6.0117: End of Ref

Re: [ccp4bb] very informative - Trends in Data Fabrication

Ojweh > c) Discarding your primary data is generally considered bad form... Agreed, but it is a big burden on labs to maintain archives of their raw data indefinitely. Even IRS allows to discard them after some time. But you DO have to file in the first place, right? How long to keep is an

Re: [ccp4bb] very informative - Trends in Data Fabrication

I also don't really worry about the images as a primary means of fraud prevention, although such may be a useful side effect. These cases are spectacular but so rare that it indeed would not primarily justify the effort. That it can be a useful political instrument to make that argument and get fu

[ccp4bb] arp_waters still available?

Dear Developers, in some older scripts I still call the ccp4 version of arp_waters, which worked well for dummy atom picking. It does not seem to be included in recent 64 bit CCP4 packages. Does anyone perhaps have a precompiled 64 bit version of arp_waters that might run on RHEL62? Best regards,

Re: [ccp4bb] very uninformative

.org Cc: CCP4BB@jiscmail.ac.uk Subject: Re: [ccp4bb] very informative - Trends in Data Fabrication Thanks of your education. I got it. By the way, what does Orcus mean here? Regards, Kevin On Tue, Apr 3, 2012 at 5:11 PM, Bernhard Rupp (Hofkristallrat a.D.) wrote:

Re: [ccp4bb] very informative - Trends in Data Fabrication

Orcus, if you put yourself persistently into the face of guys who play hard, you need to learn to take a few hits and shake it off. Maybe a little retrospection on why your postings might perhaps possibly maybe perceived as somewhat self-promoting and ungracious could be helpful. The skil

Re: [ccp4bb] Who is using 64-bit Linux?

I have RHEL62-64 in a win 7-64 8GB desktop VMware installation. CCP4, ccp4i, coot, and shelxcde beta executables run fine. There were issues with the coot package installation due to unresolved dependencies and my ignorance thereof, but I think a working RHEL62-64 compatible package is available no

Re: [ccp4bb] Requested: Three-Day Data Fabrication Workshop

I wish to point out (because I remembered just now) that I offered a similar service after the Murthy scandal on this BB in August 2007: http://www.ruppweb.org/new_comp/frame_maker.html - and JK proposed a value-added contribution. See attached. Btw, Kim Henrick's analysis from

Re: [ccp4bb] very informative - Trends in Data Fabrication

[mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Bernhard Rupp (Hofkristallrat a.D.) Sent: Sunday, April 01, 2012 06:06 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] very informative - Trends in Data Fabrication >Hofkristallrat außer Dienst, is written as Bernhard - unless you are referring to some ot

Re: [ccp4bb] one datum many data? [was Re: [ccp4bb] very informative - Trends in Data Fabrication]

Guys, http://www.youtube.com/watch?v=CobZuaPMQHw second 9 in this 22 sec video -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Gerard DVD Kleywegt Sent: Monday, April 02, 2012 8:04 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] one datum

Re: [ccp4bb] very informative - Trends in Data Fabrication

orcus impudens From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Kendall Nettles Sent: Sunday, April 01, 2012 1:28 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] very informative - Trends in Data Fabrication What is the single Latin word for troll? Kendall On Apr

Re: [ccp4bb] very informative - Trends in Data Fabrication

Je pense donc je suis Kevin Cogito ergo erro. BR

Re: [ccp4bb] very informative - Trends in Data Fabrication

Btw, > "Table 1" would have fooled me as referee. Not if the bulk solvent parameters would be reported or validated. See recommendations. Best, BR

Re: [ccp4bb] very informative - Trends in Data Fabrication

>Hofkristallrat außer Dienst, is written as Bernhard - unless you are referring to some other guy with a french name Bernard. As one may extrapolate given my recent paper, I have been called names a lot worse…. Ø And the book indeed is a bible of xtallography. Enough of this - it

Re: [ccp4bb] very informative - Trends in Data Fabrication

This is an unresolved problem, and no real satisfactory solution exists, because the underlying reasons for zero occupancy can be different. For people who understand this and look at electron density, it is not a problem. For users who rely on some graphics program displaying only atom coordina

Re: [ccp4bb] very informative - Trends in Data Fabrication

Hi Fellow BBers, I wish to point out that a) this is not an April fool’s joke, b) but on the other hand it shows (a little buried in the recommendations, and misspelled AFTER proofing) that people who properly do catalogue and preserve images actually can fix deposition errors (comp

Re: [ccp4bb] REFMAC5 residues with bad geometry

edu] Sent: Tuesday, March 27, 2012 5:14 PM To: b...@hofkristallamt.org Cc: CCP4BB@jiscmail.ac.uk Subject: Re: [ccp4bb] REFMAC5 residues with bad geometry On Tuesday, March 27, 2012 04:35:40 pm Bernhard Rupp (Hofkristallrat a.D.) wrote: > >phenix.refine allows any number of alternate c

Re: [ccp4bb] REFMAC5 residues with bad geometry

>phenix.refine allows any number of alternate conformers. Hmm. quoting our old friends from the validation circuit: Where freedom is given, liberties will be taken BR

Re: [ccp4bb] Refining Against Reflections?

As you observe, radiation damage is local, but the effect is - to different extent - on all Fs i.e. global (all atoms and their damage contribute to each hkl). So one would need additional local parameters (reducing N/P) if you want to address it as such, your use of occupancy is an example (even

Re: [ccp4bb] Matthews coeff. from model

> I can't imagine the results would be very different for protein-DNA vs. > protein-RNA. The reason protein-nucleic acids is an extra category in mattprob is largely due to poorer statistics resulting from limited sample size and hence no reliable resolution dependence can be computed. In add

Re: [ccp4bb] Water

Ø Some of these 'water' have more than 4 contacts, I would consider them as 'false'. How about bifurcated hydrogen bonds? BR

Re: [ccp4bb] Desalting columns

Ø in 2004. Of the 1000 entries that listed [protein], 46 proteins were crystallized below 3.1 mg/ml. That is not necessarily the success rate for low concentrations, which we actually would like to have. We would need negatives for < 3 for to give a correct answer. I guess even occurrence

Re: [ccp4bb] Desalting columns

Why, in the first place, do you feel an urge to concentrate your protein above 3 mg/ml ? For crystallization, the concentration needs to be a) high enough to achieve supersaturation, meaning close enough to the maximum solubility in a given buffer so that the precipitant can drive the s

Re: [ccp4bb] Aggregated protein for crystallization

> You might get lucky by setting up crystallization plates, but chances are you won't get very useful information from them, especially if your aggregated protein is soluble. I seem to fail to understand how crystallization plates would give information in the not-special case of protein aggregate

Re: [ccp4bb] Aggregated protein for crystallization

Well, depends on what 'aggregated' really means. If it implies reasonably weak oligomerization interaction - and it might not be too strong given that the oligomers remain soluble - a chaotropic crystallization agent (on the extreme end certain high salts, consult Hofmeister for chaotropicity) ma

Re: [ccp4bb] Bond Length Outliers (correction)

Btw, re other sources of deviation: Molprobity does not report geometry deviations beyond CB. The RUN500 command from CCP4i does. BR -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Dale Tronrud Sent: Thursday, February 16, 2012 10:56 AM To: CCP4B

Re: [ccp4bb] surface residue mutation

http://services.mbi.ucla.edu/SER/ but no space group predictions are possible. BR From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Prem Kaushal Sent: Tuesday, February 14, 2012 3:36 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] surface residue mutation Hi W

Re: [ccp4bb] problem with coot install

It might be worthwhile to follow the thread of similar problems on the coot mailing list and a generic solution on the coot-wiki, like http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Coot#Example:_in stalling_a_64bit_nightly_CentOS5_binary_build_on_64bit_SL6.1 BR -Original Messa

Re: [ccp4bb] Choice of wavelength

For MIR, you also need to weigh your options. If you want to use anomalous signal for SIRAS/MIRAS, you may want to be above the most prominent or at least a useful edge of your HA. On the other hand, being above an HA edge increases you chance of serious radiation damage. Sometimes you may need

Re: [ccp4bb] Molecular Transform Superimposed on a Dataset

), the real part is always centrosymmetric, while the complex (phase) part is not. Probably needs some tweaking to be really useful for presentation purpose. BR -Original Message- From: Bernhard Rupp (Hofkristallrat a.D.) [mailto:hofkristall...@gmail.com] Sent: Friday, January 06, 2012

Re: [ccp4bb] B_sol from EDS

On Mon, Jan 30, 2012 at 11:10 AM, Bernhard Rupp (Hofkristallrat a.D.) wrote: Dear All, when I plot bulk solvent B and K extracted from EDS, an improbable and bimodal distribution appears. In the B_sol vs k_sol PDF a sharp line of values with B-sol of 70 appears (B-axis left to right, 0-200). h

[ccp4bb] B_sol from EDS

Dear All, when I plot bulk solvent B and K extracted from EDS, an improbable and bimodal distribution appears. In the B_sol vs k_sol PDF a sharp line of values with B-sol of 70 appears (B-axis left to right, 0-200). http://www.ruppweb.org/images/b_sol_contour.jpg http://www.ruppweb.org/images/b_

Re: [ccp4bb] MAD

For the history buffs and crystallographers needing some R&R and chill-out, an interesting historic fiction read about the era of Newton and Leibnitz and the foundation of the Royal Society is the Baroque cycle by Neil Stevenson. http://en.wikipedia.org/wiki/The_Baroque_Cycle Cryptonomicon, althoug

[ccp4bb] CCP4 win dev

Dear ccp4 win developers: I would like to compile Ian's EDSTAT program using my windows7/64 ifort compiler. I have a few questions re library linking and win-compliable source distribution - wonder who I may kindly harass off-board. Best regards, BR ---

Re: [ccp4bb] on the electronic density of several maps

You might want to look at some images of side chain electron density. http://www.ruppweb.org/garland/gallery/Ch2/index_2.htm BR From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Dialing Pretty Sent: Friday, January 13, 2012 2:22 PM To: CCP4BB@JISCMAIL.AC.UK Subject:

Re: [ccp4bb] NMR review

] NMR review Dear Bernhard, Am 12.01.12 10:30, schrieb Bernhard Rupp (Hofkristallrat a.D.): > Dear All, > > I read an interesting statement in an NMR review: > > " regions of a protein or > DNA / RNA molecule that are ?exible in the crystal do not provide > coherent

[ccp4bb] NMR review

Dear All, I read an interesting statement in an NMR review: " regions of a protein or DNA ⁄ RNA molecule that are flexible in the crystal do not provide coherent X-ray scattering and hence do not contribute to the final electron density map. Thus, for all intents and purposes, they can effectiv

Re: [ccp4bb] Molecular Transform Superimposed on a Dataset

This may give some idea: Illustration of a molecule and its cosine transform: http://www.ruppweb.org/garland/gallery/Ch6/pages/Biomolecular_Crystallograph y_Fig_6-16.htm and sampled by lattice points http://www.ruppweb.org/garland/gallery/Ch6/pages/Biomolecular_Crystallograph y_Fig_6-01_PART3.h

Re: [ccp4bb] refmac low resolution REMARK

> So what's new? Alzheimer's and late night senile dementia :-) BR PS: nice site! -Original Message- From: Ian Tickle [mailto:ianj...@gmail.com] Sent: Monday, January 02, 2012 4:34 AM To: b...@hofkristallamt.org Cc: CCP4BB@jiscmail.ac.uk Subject: Re: [ccp4bb] refmac low resolution RE

[ccp4bb] refmac low resolution REMARK

Dear Developers, it seems to me that at least Refmac 5.6.0117 does not report the actual lowest resolution used in refinement, but instead the lowest resolution of the hkl index range generated by the default cif import script instead. REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION

Re: [ccp4bb] refmac Bsol

Dear Garib, thank you for the quick response despite (or because of) the holidays. I’ll try to summarize because I am not sure I understand yet, and it might be useful for all : Ø Partial structure mask bulk solvent parameters. Mask bulk solvent B value is in addition to protein B value.

[ccp4bb] refmac Bsol

Dear Refmac developers group, I am trying to understand a small detail in the refmac log listing. In the bulk solvent section just below the restraint table (I use monitor MANY in general): - Overall : sca

[ccp4bb] cif_mmdic.lib

Dear Developers, A few observations during data import/export ccp4i win 64 installed from ccp4-6.2.2.msi a) cif2mtz 6.2 says: CCIF signal CCIF_FOPEN (severity: SEVERE ERROR/FATAL) (Raised in zzs_undump) Cannot open file C:\CCP4\6.2\lib\data\cif_mmdic.lib for reading! This fi

[ccp4bb] OT: LN2 autofill

Hi Fellows, I am looking for some advice re LN2 autofill. I want to automatically refill an open special-use foam Dewar on the crystal harvesting robot from an unpressurized secondary storage Dewar. We found this system http://www.norhof.com/fillingexample.html and it seems to do what we need an

Re: [ccp4bb] bias removal server

I am not sure this service is maintained anymore, but given that with automated model building pretty much the same can be achieved nowadays (pus benefit of a model), the ARP/wARP server in Hamburg is a well-working and up-to-date alternative. BR From: CCP4 bulletin board [mailto:CCP4BB@JI

[ccp4bb] Vote for Bill !

Hi Fellows, here is your chance to vote for a crystallographer in the People's Choice education program contest: http://us2.campaign-archive2.com/?u=3e43dd9d1724b97d2bc286881&id=485f01c36b&; e=76452e4682 Best regards, BR - Bernhar

Re: [ccp4bb] Movements of domains

> If the difference in likelihood is quite small then you cannot distinguish between a RB shifted model and one w/o the shift and that shift must be insignificant (in a statistical sense.) If the likelihood is better when the shift is allowed then the shift is significant. That of course is corre

Re: [ccp4bb] weight matrix and R-FreeR gap optimization

> What is your resolution? The gap is usually wider at lower resolution. Here a figure displaying distribution gap stats: http://www.ruppweb.org/garland/gallery/Ch12/pages/Biomolecular_Crystallograp hy_Fig_12-24.htm Cheers, BR -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@

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

If for example your presumed coil is differently bent than your search probe, overall rmsd is high and MR will likely fail. But maybe ARCIMBOLDO with helix fragments might do at 1.65A? George or Isabel will have a better answer. Good luck, BR PS: And may San Matheus de las Coefficientes listen t

Re: [ccp4bb] IUCr committees, depositing images

Ø Not if you are interested in scattering that falls between reciprocal lattice maxima, or if you want to preserve the possibility of applying future data reduction packages. Yep, this is exactly what I expressed in my original statement: “diffuse solvent contributions, commensurate and

Re: [ccp4bb] IUCr committees, depositing images

Ø Do you mean to reprocess determination of I and sig(I) from the diffraction images automatically??? Or just to get an access to the raw data? Reprocessing the images with the to-be-developed new software that will process the information in the data in full, and then using the new-and-improv

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