[ccp4bb] iNEXT-Discovery 2021 webinars

Dear all, I do hope that after a full week for recovery from the CCP4 “study weekend”, you might want to consider joining our iNEXT-Discovery webinar series! We have lined up a series of new talks on X-ray tomography, cryo-EM, NMR, and more! To see the full program and also register (even if yo

[ccp4bb] iNEXT-Discovery

state-NMR, and many more at: https://inext-discovery.eu/network/inext-d/home Best regards and best wishes for the holiday season, Tassos Prof. Dr. Anastassis Perrakis Group leader, Dept. of Biochemistry, Netherlands Cancer Institute Professor of Macromolecular Structures, University of Utrecht

Re: [ccp4bb] Finding partial occupancy monomer by MR ?

Dear Phil, What is the space group? Could it be that the 4th monomer makes also a trimer by symmetry, in an alternative SG? A. > On 10 Dec 2020, at 14:49, Phil Jeffrey wrote: > > Preamble: > I have an interesting crystal form with 3 monomers (~400aa) at full occupancy > and apparently one a

Re: [ccp4bb] AlphaFold: more thinking and less pipetting (?)

result of the Phaser run with the Alphafold model compare with a Phaser run using the Arcimboldo phased model as a probe? Boaz Boaz Shaanan, Ph.D. Department of Life Sciences Ben Gurion University of the Negev Beer Sheva Israel On Dec 4, 2020 00:32, Anastassis Perrakis mailto:a.perra...@

Re: [ccp4bb] AlphaFold: more thinking and less pipetting (?)

ss than 10%. Reza Reza Khayat, PhD Associate Professor City College of New York Department of Chemistry and Biochemistry New York, NY 10031 From: CCP4 bulletin board <mailto:CCP4BB@JISCMAIL.AC.UK> on behalf of Anastassis Perrakis <mailto:a.perra...@nki

Re: [ccp4bb] AlphaFold: more thinking and less pipetting (?)

AlphaFold - or similar ideas that will surface up sooner or later - will beyond doubt have major impact. The accuracy it demonstrated compared to others is excellent. “Our” target (T1068) that was not solvable by MR with the homologous search structure or a homology model (it was phased with Ar

[ccp4bb] What can iNEXT-Discovery do for us?

/webinar/register/WN_ZPGVwe7xR9GIyqESRS-dxA Best regards on behalf of the iNEXT-Discovery team, A. Perrakis Prof. Dr. Anastassis Perrakis, PhD Group leader, Dept. of Biochemistry, Netherlands Cancer Institute Professor of Macromolecular Structures, University of Utrecht Oncode Institute

[ccp4bb] iNEXT-Discovery: Access to facilities for structural biology research

access Anastassis Perrakis (Coordinator) To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1

Re: [ccp4bb] Macromolecular Crystallography workshop in South America 2020

Dear all, As this discussion is receiving so much deserving attention, I should say that being an organiser of crystallography events in the past and in the future, we always strive to *intentionally* achieve a good gender balance of speakers. Sometimes we did even well, albeit often not well e

[ccp4bb] PhD / PostDoc positions @NKI Amsterdam

We expect applications to be sent in by Monday 13th January and all positions are available asap. PhD candidate positions are for four years; post-doc positions can be for 1-4 years depending on qualifications and experience; the CAO salary levels apply according to the NKI collective agreemen

Re: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] Problem with structural alignment

Dear Herman et al, On Dec 16, 2019, at 17:52, Schreuder, Herman /DE mailto:herman.schreu...@sanofi.com>> wrote: Dear Ishan, A structural alignment should be independent of the software used. However, the residues being selected for the alignment can make a big difference and different programs

Re: [ccp4bb] Unusual dataset with high Rmerge and extremely low b-factors?

Dear Michael, Exactly because the B factor is only 8, the intensity as function of resolution is droping really slowly, and thus the I/sigI 4.7 at low resolution drops so slowly to 1.0. I would almost bet you have a low solvent content. The data are fine imo. Best, Tassos On Nov 4, 2019, at

Re: [ccp4bb] Optimisation of 2D very thin plates to thick plates

Microseeding for new conditions? https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4118815/ On Sep 19, 2019, at 17:30, William Richardson mailto:william.richard...@nottingham.ac.uk>> wrote: Dear colleagues, I would like some advice on crystal growth optimisation. I have been trying to crystallis

Re: [ccp4bb] not solely pdb issue: need someone to officially settle the pdb dispute

If the structure has been deposited in the PDB and thus is public ally available, B (or F, G, Φ, Ξ, Δ, Α or whoever else) has every right to use it in a publication. “A” should follow the advice of Frank and do a happy dance for the usefulness of the work, or if not feeling like dancing she/he

Re: [ccp4bb] need someone officially settle a pdb dispute for a publication

Something is unclear to me in the original question. What does “has used his pdb for a publication” mean? Somebody used an entry already in the PDB? Somebody used a “.pdb” coordinates file for publication (without “.mtz”)? What was and is the relationship between A and B? In any case, assuming

Re: [ccp4bb] challenges in structural biology

I would wonder more if the biological questions you can *ask* with a (crystal) structure are sufficiently relevant to justify the resources. Sent from my iPhone > On 15 Jul 2019, at 22:08, Tim Grüne wrote: > > Dear James, > > 10) are the biological questions that you can answer with a (cryst

[ccp4bb] CCP4mg trouble making movies

Dear all, I am having some trouble with ccp4mg 2.10.10 and making movies on a Mac running OSX 10.13.6 I am trying now for a test a single-scene movie of 2sec “rock”. The movie previews fine. When I “make movie” the scene directory and the frames are created, and I get a window telling me: “Fo

Re: [ccp4bb] ORCID being mandatory for PDB depositions

I am wondering, are there any arguments that would suggest that ORCID is not in line with GDPR requirements? You are disclosing your name etc to the PDB anyway, does it matter if its through ORCID or not? Tassos > On Apr 9, 2019, at 14:04, V F wrote: > > Dear all, > Did anyone observe that

[ccp4bb] X-Ray Methods in Structural Biology @CSHL

Dear all, The June 15th deadline for applications to the CSHL X-ray Methods in Structural Biology Course to be held later this year, October 15 through October 30, 2019 is rapidly approaching. The official course announcement is here: https://meetings.cshl.edu/courses.aspx?course=C-CRYS&year=1

Re: [ccp4bb] coiled-coil "degree"

Dear Jorge, The “coiled coil” has a formal definition - not all interacting helices are coiled coils. I would refrain from expressions like "more or less "coiled-coiled"one to another”. I have found the program “socket” very useful for analysing such structures. http://coiledcoils.chm.bris.ac.

[ccp4bb] Deadline for the EM and the X-ray bundles of iNEXT extended to 24 April (midnight)

Dear all, The deadline for the EM and the X-ray bundles of iNEXT is now extended until 24 April (midnight, for all timezones …). For more information http://www.inext-eu.org/inext-em-and-x-ray-bundles/ and to submit a proposal https://www.structuralbiology.eu/submit-proposal/?t=inext Best rega

[ccp4bb] Reminder: iNEXT Bundles

Dear all, The single deadline for the iNEXT bundles for EM and X-ray projects “from purified molecule to high resolution data” is this Friday, 20th April. Dont miss it. https://www.structuralbiology.eu/submit-proposal/?t=inext Best regards, On behalf of the iNEXT team, Tassos

[ccp4bb] iNEXT EM and X-ray bundles!

Dear all, iNEXT, a European program to support access to research infrastructures for Structural Biology, is now welcoming applications for the “EM and X-ray bundles", to help people carry a project all the way from the starting sample to the initial structure determination, by EM or X-rays. T

[ccp4bb] Access to iNEXT!

Dear all, iNEXT has been offering access to X-rays, electrons, magnets, and photons for a bit over than two years. iNEXT has pioneered the so-called “Structural Audit” access, where any user can mail-in their sample for initial characterisation by structural biology met

[ccp4bb] Helical bundles vs coiled coils

Dear all, I suspect that helical bundles and coiled coils would have different CD spectra? Are you aware of a paper that has shown that (or the opposite …). Would anyone know another experimental method (*) to check this quickly? Thanks A. (*) Other than solving the structure by crystallograp

Re: [ccp4bb] Crystal structure of an unknown protein

I wonder why you assume know there are "about 20 point mutation sites” if "this protein is an unknown protein”. It looks like you are comparing the sequence of a protein you do not know what it is to the sequence of a protein you dont really know what it is (1). I would consider it more likely,

Re: [ccp4bb] secondary structure prediction

Dear Zheng, You might want to try the tools at: https://ccd.rhpc.nki.nl Tassos On Dec 6, 2017, at 15:14, zheng zhou mailto:zhengzho...@gmail.com>> wrote: Dear CCP4 community, Sorry for the off-topic question. I am trying to design constructs for structure studies. It only has a homolog struc

[ccp4bb] Biophysical Characterisation of Macromolecules and Quantification of Biomolecular Interactions

Dear all, I would like to remind you that the deadline for applying to this course is 10 October 2017 https://www.structuralbiology.eu/events/biophysical-characterisation-of-macromolecules-and-quantification-of-biomolecular-interactions/ You can apply at: https://www.aanmelder.nl/96461/subscri

[ccp4bb] Master Your Proteins, NKI Amsterdam, 20-23 November 2017

Dear all, Applications for the Instruct-ERIC course on Biophysical Characterisation of Macromolecules and Quantification of Biomolecular Interactions are now open. The course aims to provide the theoretical background of popular biophysical methods that are often used in relation to Structural

[ccp4bb] Course: Bridging solution methods: from NMR to X-ray scattering and biophysics"

Dear all, Announcing in the mailing list for crystallography and in the era of the single particles EM resolution revolution, a course for solution methods? NMR, SAXS, calorimetry, fluorescent methods and modeling? Seriously? Well, yes! For many, many reasons, you should be at least curious, an

[ccp4bb] iNEXT access: NMR Extended Support and more!

Dear all, I should perhaps offer sincere apologies for posting the crystallography boards with NMR news ;-). However, I will not do that, as I sincerely hope you will see that in an era of integration of structural methods, such opportunities can offer the chance for excellent and exciting sc

Re: [ccp4bb] Superpose program in CCP4

Dear Wenhe, Besides this advice, have a look at the http://webapps.embl-hamburg.de/rapido/ server. Sometimes its goodo to re-think of what you want to do, and wonder why its not easily doable in software (perhaps because its not the right thing to do …)

Re: [ccp4bb] problem in space group!!

> On 15 Apr 2015, at 7:55, 高艺娜 wrote: > > Dear all, > Recentely I have got a dataset of 3.0A resolution and I have a big problem in > choosing space group because the crystal were found in both P4,P1and P222 > space groups,here are the figures of self rotation function on P4,P1 and P222 > per

Re: [ccp4bb] funding experiences - query

Dear Bernhard, I think you need to clarify the first question. “Denied funding’ means to me that a committee officially denied the proposal for these reasons, which is rare, as typically they are very careful, or at least that is my experience. However, its rather common that one of the referee

[ccp4bb] GRC/GRS Diffraction Methods

Dear all, I am sorry to send one more post to the already overloaded bb, but please let me remind you for the last time that the deadline for applications for the GRC and the GRS is approaching, and is only three days from now. http://www.grc.org/programs.aspx?id=11654 We are all looking forwa

[ccp4bb] GRC and GRS on Diffraction Methods in Structural Biology 7/27/2014 - 8/1/2014

Dear all, As I did give the full promotional message for why these are just outstanding meetings to attend, I will only invite you to look at the latest programs GRC (http://www.grc.org/programs.aspx?id=11654) GRS (http://www.grc.org/programs.aspx?year=2014&program=grs_diff).

[ccp4bb] GRC Diffraction 2014 Instruct fellowships

Dear all, Unfortunately something went wrong in email archiving, and I recall receiving more applications from specific people, than what are now in my mailbox. May I kindly ask the people that did send an application, to re-send me their PDF file by reply to this email? Sorry again to everybo

[ccp4bb] GRC on Diffraction Methods: end July 2014

Dear all, We are getting closer and closer to the 2014 edition of my favorite Gordon Research Conference (https://www.grc.org/programs.aspx?year=2014&program=diffrac ) on Diffraction Methods in Structural Biology "Faster, Smaller, Better: Novel Technologies for Diffraction Experiments in Molec

Re: [ccp4bb] Can not see density map when I turn off normalization in PYMOL

Dear Hongshi - I cant help but to first suggest that as this is the CCP4bb, the first thing you should try is using CCP4mg, if you want to make pretty pictures. If you just want to look at the map and work with it, you should use Coot. If still for some reason you want to use Pymol, you should a

[ccp4bb] Gordon Conference on Diffraction Methods in Structural Biology

Dear all, The biannual Gordon Research Conference in Structural Biology, accompanied by the first Gordon Research Seminar, will take place in the last week of July at Bates College, New England, a few hours drive from the IUCr meeting that follows in the first week of August. The theme for the

Re: [ccp4bb] Sister CCPs

It is an interesting observation, Tim. The fact that people do not read tutorials or manuals, is somewhat related to the fact that many questions asked in the ccp4bb could be answered by a more experienced colleague, a supervisor, a manual, a wiki, St Google the revealer, not to mention the som

Re: [ccp4bb] About protein precipitation problem during dialysis

On 20 Nov 2013, at 21:56, Dhanasekaran Varudharasu wrote: > Dear Crystallographers, > > I dialysed a 30 kDa protein > (Recombinant protein which was eluted by 20 mM Tris, 500 mM NaCl, 120 mM > imidazole) against water for overnight. But it gets precipitat

Re: [ccp4bb] [ccp4bb] AW: [ccp4bb] uncertainites associated with intensities from twinned crystals; Sorry for HTML.

Dear Jens, That formula for error propagation is correct for independent measurements. Does this assumption stand true for Intensities in twinning? I am no expert, but I would think not. Tassos On 7 Nov 2013, at 7:53, Jens Kaiser wrote: > Fulvio, Tim, > error propagation is correct, but wron

Re: [ccp4bb] OT: "Who's Afraid of Peer Review?"

I could not resist but comment at the end ... (sorry for cleaning up the thread text) I agree with Roberto that the system is actually not that bad when you think of it. Or, it could be much worse. In my experience, the editors of many journals - professional or academic - try very hard, and m

[ccp4bb] 2014 Gordon Research Conference and Research Seminars on Diffraction Methods in Structural Biology

Dear all, In a bit more than a year from now, we will be running the Gordon Research Conference on Diffraction Methods in Structural Biology, this time preceded for the first time by a two-day Gordon Research Seminar, exclusively for young scientists and a few mentors. http://www.grc.org/progr

Re: [ccp4bb] Off-topic: NMR and crystallography

I would agree with Mark. It would be also good to state that neither of us is cross-trained, but are one-trick dogs as far as NMR vs X-rays goes. Still, I think that if you get any protein in good amounts, try to crystallize it (there are even good facilities for that these days, and funding t

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

Hi - You can use Xia2 or, you can use Pointless ("Find or Match Laue group") to combine the two datasets after Mosflm in one MTZ with common correct origin etc, and then use SCALA to scale them together. For more info: http://ccp4wiki.org/~ccp4wiki/wiki/index.php?title=Data_processing_with_C

Re: [ccp4bb] delete subject

Dear all, Let me start by apologizing for finally making this email longer than I intended - I did not have the time to make it shorter. I must say I am humbled by the amount of positive energy and constructive thinking that Bill has. That must explain also how he manages to keep up a fantasti

Re: [ccp4bb] refinement protein structure

I think it will be the first time in 15 years I will disagree with Tim. I personally found the posting of Tom van der Bergh irritatingly disrespectful in many levels. 1. It does not respect my mailbox capacity 2. It does not respect CCP4 developers posting output from phenix.refine 3. It does n

Re: [ccp4bb] Isothermal titration calorimetry

It might be worth to consider the question more in detail. Do you want to study thermodynamics of the interaction, or a KD would do? If the former, you need ITC. If the latter, and you want to study things at the level of KD only, maybe investing on a plate reader, thermophoresis, or some biose

Re: [ccp4bb] first use of synchrotron radiation in PX

And indeed this experiment was done properly ... in a suit and tie! http://www.embl-hamburg.de/aboutus/general_information/HH_about/history/HH-holmes.jpg A. PS The journal is indeed a bit obscure ... On 13 Mar 2013, at 20:22, DUMAS Philippe (UDS) wrote: > Jean Witz (now deceased) once told

Re: [ccp4bb] how to make protein topology figure based on its structure

) to see which one works, when > Partha can tell us that Pro-origami will do it and provide a link to the > description. Seems to be just what I've been looking for. Thanks, Partha! > > Anastassis Perrakis wrote: > > On 9 Mar 2013, at 12:11, Jon Agirre wrote: > > Espript

Re: [ccp4bb] how to make protein topology figure based on its structure

On 9 Mar 2013, at 12:11, Jon Agirre wrote: > Espript will do. http://espript.ibcp.fr > > Well, if you want a topology diagram, espipt will not do. Brilliant as it may be, it will annotate the topology linearly on top of a set of aligned sequences (and more!). As for a topology diagram, I co

Re: [ccp4bb] laboratory phage infection [SEC=UNCLASSIFIED]

We have suffered from that a lot at the NKI a few years back. What worked for us was a combination of strategies, that were all mentioned before but I will repeat: 1. Buy T1 phage-resistant strains, and also use an old incubator (and luckily an old building that was available at the time) to 'e

Re: [ccp4bb] Mac mini advice

We did work with a full blown OSX Server in 2004 - indeed many issues on NFS were Ok, but NIS was a problem - or we could not figure it out. We used it as server for developers, running X-grid, SVN, WebObjects servers for a couple of EC networks, but never deployed it fully as a departmental-leve

Re: [ccp4bb] protein solubility predictions

Indeed there are many web tools predicting solubility. My personal bias is that your brain is the best tool for ideas on how to design expression constructs. (since one question in a multi-domain protein, is which bit is interesting ...!) Many brains are better than one (talk to your colleagues -

Re: [ccp4bb] Mac mini advice

I am of the opinion that the truth lies somewhere in between ... Here are my two cents based on personal experience ... For example, I am happy myself using a MacBook Pro, which is sufficient for all my activities, and has all software and data that I need. Thus, I am myself on the 'new' paradig

[ccp4bb] Post-doc positions @Amsterdam

Post-doctoral positions are available in the Netherlands Cancer Institute in the groups of Anastassis (Tassos) Perrakis and Titia Sixma (http://xtal.nki.nl). The Netherlands Cancer Institute (http://www.nki.nl) is a center of excellence with a high standard of biological research and an interac

Re: [ccp4bb] a challenge

> I think the real challenge (and one that makes for an excellent > macromolecular crystallographer) is how well one can interpret a map with > poor phases. Let me disagree ... An excellent macromolecular crystallographer, is one that given some crystals can derive the best strategy to collect

Re: [ccp4bb] vitrification vs freezing

talking semantics, kruos (Κρυος), means just cold, not icy cold. Cold in Greece is not nearly icy. Unlike the Netherlands ... it only gets cold when its really icy ;-) Tassos On 15 Nov 2012, at 19:45, Ethan Merritt wrote: > From Greek kruos, icy cold

Re: [ccp4bb] Plate crystals

Also, saying that you have a. 4.0 data without defining the beam line b. plates without defining the dimensions is of limited use to get feedback, in my view. If you got 4.0 data at home, and your plates are at least a couple of micron thick, one of the few modern micro crystal beam lines is

Re: [ccp4bb] PNAS on fraud

? Yes, that is what I am saying! 2% is good, 50% is bad. (btw, the 'worse' is close to 70% - any guesses?) A. > Or are you saying only 2% of structures are deposited in that journal ? > > Jürgen > > On Oct 18, 2012, at 3:24 PM, Anastassis Perrakis wrote: > >>

Re: [ccp4bb] PNAS on fraud

Just to add in the controversy, with a somewhat related issue: Current crystallographic ethic presumes that a structure is deposited just before the submission of the paper. In a survey we did, we found that while in one journal only 2% of structures are deposited after the paper submission date

Re: [ccp4bb] Do my SAXS data agree with the crystal structure?

If you main point is dimer vs monomer, Guinier plots is in fact all you would need, in my opinion according to what I have read so far... A. On 17 Jun 2012, at 13:01, David Briggs wrote: > Dear Xun, > > Regarding your monomer vs dimer, theoretical vs observed crysol plots > - yes - they are si

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

>> I still believe Prof. Dr. Hofkristallrat außer Dienst, is written as >> Bernhard - unless you are referring to some other guy with a >> french name >> Bernard. And the book indeed is a bible of xtallography. >>Jürgen ausser Dienst ... now I get it ... my German is a lot worse than just spelli

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

Reading the paper from Dr. Hofkristallrat a.D. and the editorial in ActaF, I must say that besides the rather reasonable demand for journals to include crystallography experts as referees, "Table 1" would have fooled me as referee. A validation report of the VTF style might not had helped either

Re: [ccp4bb] Envelope Phasing.

Hi David - I think you have four hurdles to overcome: 1. How good is a SAXS envelope 2. How will you place it in the right place 3. How will you extend from ~15-20 A to around 4 A 4. How will you extend from 4 A to beyond Steps 2 and 4 might be the easiest - albeit far from trivial. Point 1 can

Re: [ccp4bb] Help! weird thing

Hi - I agree with Garib that its likely a pseudo-translation issue. I also agree with that the advice he gives is correct, but ... ... since I am evidently less smart to follow all these steps, I like to use phenix.xtriage that will tell me if there is pseudo- translation or not, and will give

Re: [ccp4bb] Introducing an ELN

I think that all these points are interesting and valid. On Jan 25, 2012, at 10:37, Chris Morris wrote: Tassos reports: 1. None of the twenty test-users was satisfied with any of the two solutions - and each was annoyed for a different reason. This suggests that the choice of ELN is not the

Re: [ccp4bb] MAD

A, yes, inventor's names. Anyone reading who is less than 40 and knows what MTZ stands for? ;-) My favorite technique remains SADDAM - a side product of Gerard's War On Error, that never did catch-up with the masses - experimentally or as an acronym. A. On 19 Jan 2012, at 21:51, Petr Leiman w

Re: [ccp4bb] R/Rfree problem

Any crystal can be worked at as P1. What you know is that your crystal is not p212121 It can be P21212 P21221 P22121 P1121 P1211 P2111 P112 P121 P211 P1 And then there is twinning ... Suggestions: Use Pointless or Phenix.xtriage, feeding the unmerged p1 data to decide. Use the Zanuda serv

Re: [ccp4bb] Off-topic: ELNs

Hi - Here at the NKI, we had formed a committee to look at ELN solution two years ago. We had interviewed three vendors, and run two tests with twenty users. A brief description of the outcome: 1. None of the twenty test-users was satisfied with any of the two solutions - and each was anno

Re: [ccp4bb] Reference for Resolution Cutoffs

Also Nat Struct Biol. 1997 Apr;4(4):269-75. Improved R-factors for diffraction data analysis in macromolecular crystallography. Diederichs K, Karplus PA. But none of these are in any way 'discrediting' Rmerge, they are just proposing more statistically sound alternatives. That is not the same .

Re: [ccp4bb] Archiving Images for PDB Depositions

Dear Gerard Isolating your main points: but there would have been no PDB-REDO because the data for running it would simply not have been available! ;-) . Or do you think the parallel does not apply? ... have thought, some value. From the perspective of your message, then, why are the bene

Re: [ccp4bb] Archiving Images for PDB Depositions

To avoid misunderstandings, since I received a couple of emails already: Is it important to make such a resource available to developers? Absolutely? ? was a typo. I meant Absolutely! I think such data are essential for development of better processing software, and I find the development

Re: [ccp4bb] Archiving Images for PDB Depositions

Dear all, Apologies for a lengthy email in a lengthy chain of emails. I think Jacob did here a good job refocusing the question. I will try to answer it in a rather simplistic manner, but from the view point of somebody who might only have relatively little time in the field, but has enjoyed

Re: [ccp4bb] To archive or not to archive, that's the question!

Dear all, The discussion about keeping primary data, and what level of data can be considered 'primary', has - rather unsurprisingly - come up also in areas other than structural biology. An example is next generation sequencing. A full-dataset is a few tera bytes, but post-processing reduc

Re: [ccp4bb] should the final model be refined against full datset

> > > For structures with a small number of reflections, the statistical noise > in the 5% sets can be very significant indeed. We have seen differences > between Rfree values obtained from different sets reaching up to 4%. This is very intriguing indeed! Is there something specific in these

Re: [ccp4bb] is codon optimization worth it?

Well, codon optimization is not really trouble, it's money. The money are worth it usually anyway, since the optimized genes are easy to clone if you make many constructs out of one gene, as you better do anyway ... Compared with downstream expenses, optimized genes are these days almost always

Re: [ccp4bb] ARP/wARP install on 6.2.0 & RHEL 6?

My two cents: I am installing arp/warp on my Mac since ages and it works ;-) The only thing you need to make sure is that you grab ownership of the /usr/local directory to you as a user, if you installed ccp4 from dmg. If you do this by eg sudo chown -R me.mygroup $CCP4 Then install.sh should

Re: [ccp4bb] Peptide Crystallization

NMR ... synthesize with a few labeled aa according to taste of local NMR guru. If they cant do a15-aa peptide in a day, let the bb know, it will be entertaining ;-) A. On May 25, 2011, at 14:04, Buz Barstow wrote: Dear all, I am considering trying to crystallize a small peptide (around 15

Re: [ccp4bb] Ubiquitin E2-E3 co-crystallization

Dear Gett, Maybe you want to start by rephrasing the original question. What you need to know before anything else, is which E2 works together with your new E3, at least in vitro. Crystallizing with a random E2 sounds like a very bad idea - even if that works, why would it be interesting?

Re: [ccp4bb] how to remove part of data with bad signal to noise ratio

I think you are just confused. The solvent flattening is just a step to make your map clearer. You do not carry the modified phases from solvent flattening to refinement (and I sincerely hope you don't refine against the solvent flattened amplitudes but against the original data!) Herman's obse

Re: [ccp4bb] problem with pdb & its symmetry molecule

Yes, its surely possible. If there are no clashes start thinking if this dimer is the physiological molecule in solution. Check probability that this dimer is stable in solution in Pisa - ebiFold If so, check first with size exclusion columns if it behaves like dimer in solution, preferably us

Re: [ccp4bb] flex-wARP error

Hi - Yes, your suspicion is correct, and I think that bug has been silently fixed in the latest distribution. I am pretty sure Victor has now a job-dependent filename, if not we will try and fix it now as we prepare a new release. In that case, pleas email Gerrit telling him details about

Re: [ccp4bb] while on the subject of stereo

To add my two cents, I am not at all a fun of stereo for routine use, but I appreciate it if I have to look at a long ligand bent 90 deg in the middle to bury in my protein, and all that at 3.0-3.5 A resolution ... So, I must have both types of brain damage that Jan refers to. No surprises

Re: [ccp4bb] First images of proteins and viruses caught with an X-ray laser

Anyway, I thought that was a cool idea, but like so many other cool things, it had to be cut from the Nature paper. Admittedly, the problem has not actually been solved yet. This is why we used REFMAC in TWIN mode. Is that a hint on the: a. wisdom of the editor b. wisdom of 'the third

Re: [ccp4bb] Solubilization refolding percentage efficiency

How: 1. measure total protein before refolding (eg by absorbance at 280) 2. Purify refolded fraction by gel filtration in FPLC 3. measure total protein after refolding 4. calculate efficiency ... Why? I don't see the reason to know the efficiency. If after refolding I would get enough in a de

Re: [ccp4bb] Problem of Refinement and density map

Although there might be space group and twining trouble from the sound of it, running ARP/wARP starting from your molrep solution, at that resolution should really do whatever can be done and reduce R/RFree while building the vast majority of the model. If Rfree stays high, start looking at

Re: [ccp4bb] Merging data to increase multiplicity

... but, back to the main point, my advice would be to only limit the mosaicity, to get better completeness by avoiding overlaps. Its not ideal, in the sense that you would be over-estimating the partial fraction of most partial reflections, and thus systematically underestimating intensities

[ccp4bb] Post-doctoral positions at the NKI /Amsterdam to work on Autotaxin

Dear all, Post-doctoral positions are available in the Netherlands Cancer Institute in the group of Tassos Perrakis (http://xtal.nki.nl). Our group, together with that of Wouter Moolenaar and of Huib Ovaa, have a long-standing interest and lively collaboration in the function and structu

Re: [ccp4bb] brute force MR

If the two molecules are related by translational symmetry, at least Phaser is not happy. Since in the second rotation function it removes contribution from the first orientation, if the orientation/rotations of the two molecules in identical, it will fail to see the second rotation applies.

Re: [ccp4bb] Problems with auto-indexing

please please please attachments are bad enough, but so far at least we had small ones. now we have a new record, 2.5 MB! There are a gadzillion sites in the web to put your image and give us a link to it. As an additional remark, I would had been tempted to ask the assistant professor in m

Re: [ccp4bb] diffcult MR case

Dear Xiuwen, First, I cant see how the space group is C2221 with a beta of 92.3 Maybe you need to clear the symmetry confusion before getting additional pseudo-symmetry suggestions. A. On Nov 29, 2010, at 14:16, xiuwen zhang wrote: Dear colleages, Currently I met problem in a MR ca

Re: [ccp4bb] Citations in supplementary material

e. Other chalenging cases are where they include a lot of maths. That said peer review does its best but can occasionally fail; this level of failure can be measured by the number of criticism articles or formal retractions. These are also very few, but it is true, not zero. Yours sincerely, John

Re: [ccp4bb] Citations in supplementary material

I like the online methods sections with e.g. Nature papers that also come with the pdf - they also count for citations, the citations are not within the manuscript allowance on numbers, they get peer reviewed and they actually leave quite a lot of space for readers to understand the experim

Re: [ccp4bb] Citations in supplementary material

On Nov 18, 2010, at 11:18, James Stroud wrote: The future of publishing will be (1) Publish your own work (2) Peer review by the entire community Although I have been remarkably bad at predicting the future, I still like attempting to do so ...! This will not happen ...! ;-) To be honest

Re: [ccp4bb] expression of Cys-rich small protein

>>> We are trying to express for structural studies a 257 AA eukaryotic intracellular [...] <

Re: [ccp4bb] Question on calculation of RMSD

My favorite tools for doing this are: http://webapps.embl-hamburg.de/rapido/ and/or http://www.theseus3d.org/ Reading some of the associated papers will not hurt inchoosing when to apply which one! A> On Nov 14, 2010, at 22:52, E rajakumar wrote: Dear All I have two structures of homo-d

Re: [ccp4bb] High Rmerge with thin frames

In the Pilatus mode these are "open-shutter" experiment, where the Pilatus integrates over different times - all these exposure times are slower than the frequency of the detector, as far as I understand the setup. So, the crystal gets the 'full blast' in all cases, and the blast is the sam

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