Re: [ccp4bb] [ccp4bb] mmCIF files from PDB format for AlphaFill

Hi Nick I noticed this today when I was researching the differences between mmCIF and modelCIF - but thanks anyway. I haven't tried running it yet, but the important thing for me is to be able to convert my bare-bones PDB format files to something that AlphaFill will accept - and as the

Re: [ccp4bb] [ccp4bb] mmCIF files from PDB format for AlphaFill

Hi Harry, I did stumble upon this python mmCIF handler for modelCIF: https://github.com/ihmwg/python-modelcif/blob/main/examples/README.md Maybe this will have something of use to your efforts? Best, Nick Clark Nicholas D. Clark (He/Him) PhD Candidate Malkowski Lab University at Buffalo

Re: [ccp4bb] [ccp4bb] mmCIF files from PDB format for AlphaFill

Hi folks I’ve made considerable progress in getting to the bottom of this problem. From what I can gather, AlphaFold writes “modelCIF”, which is not quite the same as “mmCIF”, and just saying “CIF” is not unambiguous. So I guess I should have been more aware of this when posting my original

Re: [ccp4bb] [ccp4bb] mmCIF files from PDB format for AlphaFill

Hi Nick doesn’t look encouraging - > ~/maxit/maxit-v8.120-prod-bin-linux/bin/maxit-v8.01-O -i 1A9W_A.pdb -o 1 > Initial filter libaray failed No need to worry - since the pdb2cif from the pdb-redo team works, and they’re the ones who produce AlphaFill, they can always help out if (when)

Re: [ccp4bb] CCP4BB Digest - 21 Dec 2023 to 22 Dec 2023 (#2023-324) (out of office)

Thank you for your e-mail. I am out of office until January 2nd, 2024. I will respond to your e-mail as soon as possible upon my return. For urgent matters please contact: b...@boku.ac.at Thank you for your understanding. With kind regards, Elisabeth Laurent >>> CCP4BB automatic digest system

Re: [ccp4bb] [ccp4bb] Fragmented Chains after Automated Rebuilding

Surely in this day and age, one would just run AF2? - it’s clearly the best homology modelling program ever, finding homologies that other programs can’t reach. I would - we are - using it to supply another “best guess” for difficult-to-build structures. One could even use it as an input for

Re: [ccp4bb] CCP4BB Digest - 30 Nov 2021 to 1 Dec 2021 (#2021-335)

Subject: Re: High-order oligomers vs robust crystals - references? Hi Frank et al. Joining the discussion at this humorous stage... What about Janin's contributions on crystal packing versus oligomer interfaces? There are useful ideas in this assessment:

Re: [ccp4bb] [ccp4bb] A "funny" thing related to AlphaFold2 ....

Hi Jon Just checked an mmCIF file for one of the AlphaFold models - the model number is “1”, no sign of a model 0 that I can see… A quick “sed” script could sort them all out… Harry > On 10 Nov 2021, at 12:22, Jon Agirre wrote: > > It might be, because the mmCIF versions work fine with MG.

Re: [ccp4bb] [ccp4bb] A "funny" thing related to AlphaFold2 ....

It might be, because the mmCIF versions work fine with MG. On Wed, 10 Nov 2021 at 12:16, Harry Powell - CCP4BB < 193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote: > Hi folks > > Been a while, but I’ve been doing some work on checking that some files > are valid PDB files and went back to the

Re: [ccp4bb] [ccp4bb] A "funny" thing related to AlphaFold2 ....

Hi folks Been a while, but I’ve been doing some work on checking that some files are valid PDB files and went back to the documentation; as far as I can work out, the best solution to this is John Walker’s, because “MODEL 0” is not allowed in the standard (maybe it is for mmCIF…) - > On 27

Re: [ccp4bb] CCP4BB Digest - 14 Sep 2021 to 15 Sep 2021 - Special issue (#2021-265)

Hi Aaron, thank you for your tribute to an extraordinary scientist; It brought back happy memories. Jack Dunitz visited Australia in the late ‘80s, possibly for the IUCr meeting in Perth, and I can recall his razor wit and much hilarity when he, Sandy Mathieson, and Jim Morrison were

Re: [ccp4bb] [ccp4bb] AW: [ccp4bb] (R)MS

It’s also important to keep in mind that, in this equation, u is the component of the displacement *in the direction of the diffraction vector*. If you assume isotropic displacements and you know the mean-squared value of the overall xyz vector displacement, you have to divide that

Re: [ccp4bb] CCP4BB Digest - 25 May 2021 to 26 May 2021 (#2021-147)

For the NMR structure ensemble, you could calculate root mean square fluctuations (RMSFs) and put them into the B factor column. This is a fairly common analysis within molecular dynamics software. You could also use the ProDy Python API to do this. ProDy also has command line apps including

Re: [ccp4bb] CCP4BB Digest - 13 Feb 2021 to 14 Feb 2021 (#2021-51)

> On Feb 14, 2021, at 4:00 PM, CCP4BB automatic digest system > wrote: > > Date:Sat, 13 Feb 2021 20:24:07 -0500 > From:Nicholas Larsen > > Subject: Re: Bug in mmCIF handling of UNK residues? > > I hope this doesn't confuse the discussion, but

Re: [ccp4bb] CCP4BB Digest - 29 Dec 2020 to 30 Dec 2020 (#2020-345)

Hi Anamika, Just to be clear, the M13 ori is for production of ssDNA using a helper phage. Replication of that plasmid is more likely from another ColE1-derived origin elsewhere on the vector and also likely to give high copy numbers - which it seems it does. The p15 ori is indeed quite a low

Re: [ccp4bb] [ccp4bb] Up-to-date 3D stereo solution

Ah yes, fond memories of that mirrored contraption! There were also wooden contraptions to strap on one's head with image-merging mirrors in them. We had fun lining up equal-height friends and merging them. But both of those did have the downside that getting engrossed in electron density

Re: [ccp4bb] [ccp4bb] Up-to-date 3D stereo solution

the “best” I’ve found is stereo glasses and display side-by-side stereo. When I was a graduate student in the Steitz lab a WHILE ago, there was a frame built that fit over the Evans and Sutherland Ps2 and PS390 monitors (I said a while ago :)) that carried two mirrors at 45 degrees at your eye

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

Several people have mentioned lack of peer review as a reason to doubt the significance of the AlphaFold2 results. There are different routes to peer review and, while the results have not been published in a peer review journal, I would have to say (as someone who has been an assessor for two

Re: [ccp4bb] CCP4BB Digest - 28 May 2020 to 29 May 2020 (#2020-148)

Ta Now dear My deadline for this grant is on the second I will try to get a rewritten simplified version to you before tomorrow morning. When I do PLEASE look it over and see if you can write in anything else wrt modelling - at present its not written in year 1 Also general check and approval

Re: [ccp4bb] CCP4BB vs COVID19

g1,2 Nature (2013) Philippe Dumas De: "James Holton" À: "CCP4BB" Envoyé: Dimanche 22 Mars 2020 16:38:28 Objet: Re: [ccp4bb] CCP4BB vs COVID19 Thank you Patrick, RNA structure is still structural biology, so I think relevant here.  It seems to me that RN

Re: [ccp4bb] CCP4BB vs COVID19

*À: *"CCP4BB" mailto:CCP4BB@JISCMAIL.AC.UK>> *Envoyé: *Dimanche 22 Mars 2020 16:38:28 *Objet: *Re: [ccp4bb] CCP4BB vs COVID19 Thank you Patrick, RNA structure is still structural biology, so I think relevant here.  It seems to me that RNA as a thermometer would be an e

Re: [ccp4bb] CCP4BB vs COVID19

For what it’s worth, I’ve spent the last few days going over most of the existing COVID-19 related structures and rebuilding/re-refining wherever I considered necessary. The resulting models along with some basic explanatory notes are at

Re: [ccp4bb] CCP4BB vs COVID19

James, there are lots of quite simple experiments that would be could be done, but I can't get anyone to think seriously about the problem - let alone do the experiments. The attitude seems to be, "it can't be as simple as you suggest - someone would have noticed it". * Has anyone measured

Re: [ccp4bb] CCP4BB vs COVID19

umas De: "James Holton" À: "CCP4BB" Envoyé: Dimanche 22 Mars 2020 16:38:28 Objet: Re: [ccp4bb] CCP4BB vs COVID19 Thank you Patrick, RNA structure is still structural biology, so I think relevant here. It seems to me that RNA as a thermometer would be an easy hypothes

Re: [ccp4bb] CCP4BB vs COVID19

by Neisseria meningitidis Edmund Loh1*, Elisabeth Kugelberg2*, Alexander Tracy1, Qian Zhang2, Bridget Gollan2, Helen Ewles2, Ronald Chalmers3, Vladimir Pelicic2 & Christoph M. Tang1,2 Nature (2013) Philippe Dumas De: "James Holton" À: "CCP4BB" Envoyé: Dimanche 22 Mars

Re: [ccp4bb] CCP4BB vs COVID19

Thank you Patrick, RNA structure is still structural biology, so I think relevant here.  It seems to me that RNA as a thermometer would be an easy hypothesis to test?  Has anyone measured virulence vs temperature in cell culture? The 3D structure of the genome is no doublt important.  I

Re: [ccp4bb] CCP4BB vs COVID19

2020 15:41:17 *To:* CCP4BB@JISCMAIL.AC.UK *Subject:* Re: [ccp4bb] CCP4BB vs COVID19 James, this isn't conventional structural biology, but may be of interest, and I haven't been able get any mainstream virologists to think about it. The protein sequences are obviously of interest, but so

Re: [ccp4bb] CCP4BB vs COVID19

y very nicely, including that key position 84 https://www.biorxiv.org/content/10.1101/2020.03.04.977736v1 Best wishes Dan From: CCP4 bulletin board on behalf of Patrick Shaw Stewart Sent: 21 March 2020 15:41:17 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb]

Re: [ccp4bb] CCP4BB vs COVID19

___ > From: CCP4 bulletin board on behalf of Patrick Shaw > Stewart > Sent: 21 March 2020 15:41:17 > To: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] CCP4BB vs COVID19 > > > James, this isn't conventional structural biology, but may be of interest, > and

Re: [ccp4bb] CCP4BB vs COVID19

: 21 March 2020 15:41:17 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] CCP4BB vs COVID19 James, this isn't conventional structural biology, but may be of interest, and I haven't been able get any mainstream virologists to think about it. The protein sequences are obviously of interest, but so

Re: [ccp4bb] CCP4BB vs COVID19

James, this isn't conventional structural biology, but may be of interest, and I haven't been able get any mainstream virologists to think about it. The protein sequences are obviously of interest, but so are the RNA sequences at both ends of the Covid genome, which have conserved secondary

Re: [ccp4bb] CCP4BB vs COVID19

The best way against COVID19 is staying at home, staying at home, and staying at home. Nothing else. On Fri, Mar 20, 2020, 5:59 PM James Holton wrote: > You might think that as a structural biologist you won't be able to do > much about COVID-19 anytime soon, but that is not true. Yes,

Re: [ccp4bb] CCP4BB vs COVID19

Dear James, On Fri, Mar 20, 2020 at 03:59:01PM -0700, James Holton wrote: > ORF8 has only one homolog in the PDB: 5o32 with 25% identity over a stretch > of 60 residues.  This homologous region contains the S84L site (Val I544 in > 5o32).  I had a quick look and appears to be a cavity-filling

Re: [ccp4bb] CCP4BB vs COVID19

21, 2020 11:12:36 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] CCP4BB vs COVID19 Liz Tunbridge's lab at Oxford are offering PCR machines and expertise to help fill the testing shortfall in the UK (see https://www.wired.co.uk/article/coronavirus-uk-testing-key-workers<https://eu

Re: [ccp4bb] CCP4BB vs COVID19

To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] CCP4BB vs COVID19 Liz Tunbridge's lab at Oxford are offering PCR machines and expertise to help fill the testing shortfall in the UK (see https://www.wired.co.uk/article/coronavirus-uk-testing-key-workers<https://eur03.safelinks.protection.outlook.

Re: [ccp4bb] CCP4BB vs COVID19

Liz Tunbridge's lab at Oxford are offering PCR machines and expertise to help fill the testing shortfall in the UK (see https://www.wired.co.uk/article/coronavirus-uk-testing-key-workers). This is a worthy initiative, if it is accepted (logistics are the main problem). The structural biology

Re: [ccp4bb] CCP4BB Digest - 27 Feb 2020 to 28 Feb 2020 (#2020-61)

While we're at it, it would also be a great improvement if the PDB would list nominal resolution in all 3 directions for structures with significantly anisotropic data. I'm never 100% sure what to do in those cases. Thanks, Phoebe ~~~ Phoebe A. Rice Dept. of

Re: [ccp4bb] CCP4BB Digest - 27 Feb 2020 to 28 Feb 2020 (#2020-61)

Hi again, First, I wish to thank everyone for their responses. I hope that no one minds that I include them in my response letter to the Editor ? The idea of citing the Karplus and Diedrichs paper in Science has been essentially consumed already in our first response letter, which accompanied

Re: [ccp4bb] CCP4BB Digest - 24 Mar 2019 to 25 Mar 2019 (#2019-91)

Jan, you my wish to try MAIN as an alternative "http://www-bmb.ijs.si/;. The superimposition parameters obtained from either FatCat or MAIN directly are directly saved into the form that is used in map rotation and translation. Maps do not have to be in a unit cell (it may be simpler though).

Re: [ccp4bb] : [ccp4bb] SO4 or PO4

Besides the anomalous difference peak which might be similar in height to the anom diff peak from an intrinsic sulfur found in cysteine or methionine, also consider hydrogen bonding. In general, a sulfate will not be donating a hydrogen bond. A phosphate probably will.

Re: [ccp4bb] CCP4BB Digest - 15 Feb 2019 to 16 Feb 2019 (#2019-53)

Hi! As suggested below sulfur/phosphorous anomalous difference Fourier density would be nice, but you might be able to figure out what's going without collecting more data. Have you investigated the direct interaction partners of your mystery oxyanion? Unless you are at extreme pH values,

Re: [ccp4bb] CCP4BB Digest - 11 Sep 2018 to 12 Sep 2018 (#2018-231)

It's 1/e. To some of us, that's a round number. -Original Message- From: CCP4 bulletin board On Behalf Of CCP4BB automatic digest system Sent: 13 September 2018 00:14 To: ccp4bb Subject: CCP4BB Digest - 11 Sep 2018 to 12 Sep 2018 (#2018-231) There is 1 message totaling 48 lines in

Re: [ccp4bb] [ccp4bb] Oxford University Press

AI researchers are boycotting Nature journals: http://www.sciencemag.org/news/2018/05/why-are-ai-researchers-boycotting-new-nature-journal-and-shunning-others May be there is something we can in our field? 2018-07-02 10:01 GMT+03:00 George Sheldrick : > Since neither I nor my university can

Re: [ccp4bb] [ccp4bb] Oxford University Press

Since neither I nor my university can afford Elsevier journals, I have no access to papers published in them. In view of their excessive profits, for some years I have not submitted papers to them and have declined all requests to referee for them. If everyone did that, they might reconsider

Re: [ccp4bb] [ccp4bb] Oxford University Press

: Sunday, July 1, 2018 7:13:44 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] [ccp4bb] Oxford University Press Jacob, This is a known thing in other circles - see e.g. https://arxiv.org/abs/1011.6590 "Extending ArXiv.org<http://ArXiv.org> to Achieve Open Peer Review and Publishing

Re: [ccp4bb] [ccp4bb] Oxford University Press

----- > Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von > Keller, Jacob > Gesendet: Samstag, 30. Juni 2018 00:00 > An: CCP4BB@JISCMAIL.AC.UK > Betreff: Re: [ccp4bb] [ccp4bb] Oxford University Press > > The one I don't get is why not pay reviewers? $1000

Re: [ccp4bb] [ccp4bb] Oxford University Press

IL.AC.UK] Im Auftrag von Keller, Jacob Gesendet: Samstag, 30. Juni 2018 00:00 An: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> Betreff: Re: [ccp4bb] [ccp4bb] Oxford University Press The one I don't get is why not pay reviewers? $1000 per review? If you look at publishers' profit mar

Re: [ccp4bb] [ccp4bb] Oxford University Press

@JISCMAIL.AC.UK Betreff: Re: [ccp4bb] [ccp4bb] Oxford University Press The one I don't get is why not pay reviewers? $1000 per review? If you look at publishers' profit margins, you will see that they can afford it. I actually think the scientific community should go on a "review strike&q

Re: [ccp4bb] [ccp4bb] Oxford University Press

not occur in the future. -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Petr Leiman Sent: Friday, June 29, 2018 4:47 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] [ccp4bb] Oxford University Press Indeed! Scientists in the Soviet Blo

Re: [ccp4bb] [ccp4bb] Oxford University Press

Indeed! Scientists in the Soviet Bloc got paid for publishing their scientific papers (and maybe for citations as well - not sure about that one)! We need to change the current system! Although these changes could be accompanied by many other pleasant virtues of the Soviet regime. Petr > On

Re: [ccp4bb] CCP4BB Digest - 24 Jun 2018 to 25 Jun 2018 (#2018-154)

Quoting CCP4BB automatic digest system : There are 6 messages totaling 891 lines in this issue. Topics of the day: 1. Postdoctoral position in ABC transporter-mediated polysaccharide secretion 2. refinement papers (3) 3. I used up all CCP4 projects ... seemingly ... (2)

Re: [ccp4bb] CCP4BB Digest - 13 May 2018 to 14 May 2018 (#2018-119)

Would you help me to place the following information? Thank you. Dear CCP4ers, Looking for collaborators to annotate articles relevant to your research If you have published any article indexed by PUBMED, we invite you to join the RELISH (relevant literature search) consortium, whereby

Re: [ccp4bb] [ccp4bb] tNCS problem

Hi, Phaser is pretty robust now if you have 2-fold tNCS (indicated by having only one large non-origin peak in the native Patterson map), and recent versions are better at dealing with higher order tNCS (i.e. 3 or more copies related by multiples of a single translation vector). However,

Re: [ccp4bb] [ccp4bb] Rmergicide Through Programming

> > (2) Rsym has just: > >> R sym value in percent. > > see > . > To be honest, if that is the official definition it does make me wonder what > it is doing in the dictionary at all. > >

Re: [ccp4bb] CCP4BB Digest - 10 Apr 2017 to 11 Apr 2017 (#2017-100)

Let's step back a little bit first: Do these 3 to 4 diffraction data sets (when kept separate) process nicely individually and have good Rmeas and other results when scaled separately from each other? If so, then do they also have the same unit cell dimensions? Jim Date:Tue, 11 Apr 2017

Re: [ccp4bb] CCP4BB Digest - 5 Apr 2017 to 6 Apr 2017 (#2017-95)

Dear all, Regarding the job submission in SLURM from CCP4i, I wanted to add that it is possible for ARCIMBOLDO jobs to do it directly from the interface, you need to specify the path to a configuration file containing the required informations. More info on this configuration file are found

Re: [ccp4bb] [ccp4bb] protein precipitation reg

Since I’m in full-on cranky old biochemist mode now, I think that vitriol is an old name for sulfuric acid. > On Mar 29, 2017, at 8:40 PM, Keller, Jacob wrote: > >> And if we are going to pour scorn and vitriol on Tris, why not mention its >> large dpKa/dT of 0.03 pH

Re: [ccp4bb] [ccp4bb] protein precipitation reg

>And if we are going to pour scorn and vitriol on Tris, why not mention its >large dpKa/dT of 0.03 pH units/deg ? Hah! That's what many people are doing when they make buffers: pouring vitriol (HCl) on TRIS! I prefer to pour concentrated HEPES, and get two buffers without adding any extra Cl-.

Re: [ccp4bb] [ccp4bb] protein precipitation reg

] On Behalf Of CRAIG A BINGMAN Sent: Thursday, 30 March 2017 8:54 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] [ccp4bb] protein precipitation reg > On Mar 29, 2017, at 4:15 PM, Chun Luo <c...@accelagen.com> wrote: > > In addition to price, the prevalence of Ni purification may be

Re: [ccp4bb] [ccp4bb] protein precipitation reg

> On Mar 29, 2017, at 4:15 PM, Chun Luo wrote: > > In addition to price, the prevalence of Ni purification may be another reason > for Tris popularity. Some His-tagged constructs don't bind to Ni well in > HEPES. I wonder if anyone has similar experience or comments. —Chun

Re: [ccp4bb] [ccp4bb] protein precipitation reg

@JISCMAIL.AC.UK] On Behalf Of Mark Wilson Sent: Wednesday, March 29, 2017 1:12 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] [ccp4bb] protein precipitation reg I heartily concur with Craig. Tris can be a dangerous buffer for many reasons, including those listed below. In addition, as a primary

Re: [ccp4bb] [ccp4bb] protein precipitation reg

I heartily concur with Craig. Tris can be a dangerous buffer for many reasons, including those listed below. In addition, as a primary amine, it can complicate work with metalloproteins and has moderate nucleophilicity. There is almost always a better buffer choice than Tris. Best regards, Mark

Re: [ccp4bb] [ccp4bb] protein precipitation reg

There are almost always better choices than Tris buffer. Mo Cleland used to call it “Trash” buffer. He is no longer with us, but today I will happily carry that flag in his honor. Tris may show up in your crystal structure, especially at carbohydrate binding sites. Tris may be a surprisingly

Re: [ccp4bb] CCP4BB Digest - 23 Mar 2017 to 24 Mar 2017 (#2017-83)

Dear Alex, try MAIN "http://www-bmb.ijs.si/; it has a two way interface to Ramachandran plot, you can either display “HIS_RAMA” of individual clicked residues in displayed 3D model and also the other way around, you can click on residues in Ramachandran plot and center on the residue in 3D

Re: [ccp4bb] CCP4BB Digest - 13 Jan 2017 to 14 Jan 2017 (#2017-15)

Dear All, thanks for your replies. I tend to believe that it could be ATP some how copurified with the protein. Refinement with ATP, ADP+acetate, did not vary too much in the B factors. The main concern is, only one xtal was observed at this state ( mimicked like a ATP bound state and

Re: [ccp4bb] CCP4BB Digest - 24 Jan 2017 to 25 Jan 2017 (#2017-26)

On Thursday, 26 January 2017 11:03:12 PM Claire Smith wrote: > Hello, > > I would like to ask a question related to a recent thread regarding > bad/missing density. > > I have used SAD to solve the structure of a protein at about 2.6Å > resolution. Phenix build a good portion of it (about 50%)

Re: [ccp4bb] CCP4BB Digest - 24 Jan 2017 to 25 Jan 2017 (#2017-26)

Hello, I would like to ask a question related to a recent thread regarding bad/missing density. I have used SAD to solve the structure of a protein at about 2.6Å resolution. Phenix build a good portion of it (about 50%) and the density in this region is good. However, we cannot see ther rest

Re: [ccp4bb] CCP4BB Digest - 18 Jan 2017 to 19 Jan 2017 (#2017-20)

Hi, everyone, I think I found the cause and solution. It was due to the project folder of CCP4i,which was set by me to E:/***/** p reviously, based on which imosflm automatically set its processing folder also as E:/***/. Because disk E: used to be the flash disk on my computer, when I unplug

Re: [ccp4bb] CCP4BB Digest - 13 Jan 2017 to 14 Jan 2017 (#2017-15)

To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] CCP4BB Digest - 13 Jan 2017 to 14 Jan 2017 (#2017-15) Remember that 2xADP can disproportionate into ATP + AMP > On 19 Jan 2017, at 20:54, Panneerselvam, Saravanan > <saravanan.panneersel...@desy.de> wrote: > > Dear All, > Sor

Re: [ccp4bb] CCP4BB Digest - 13 Jan 2017 to 14 Jan 2017 (#2017-15)

Remember that 2xADP can disproportionate into ATP + AMP > On 19 Jan 2017, at 20:54, Panneerselvam, Saravanan > wrote: > > Dear All, > Sorry for the little bit off topic. Is there a possibility for covalent > bond formation between beta phosphate of ADP and

Re: [ccp4bb] CCP4BB Digest - 13 Jan 2017 to 14 Jan 2017 (#2017-15)

On 1/19/17 3:54 PM, Panneerselvam, Saravanan wrote: We observed additional density around ADP that fits perfectly like a gamma phosphate Hello Saravanan At 1.4 Angstrom resolution wouldn't that suggest that you've somehow got ATP in there ? I don't think I understand the other option - were

Re: [ccp4bb] CCP4BB Digest - 13 Jan 2017 to 14 Jan 2017 (#2017-15)

Dear All, Sorry for the little bit off topic. Is there a possibility for covalent bond formation between beta phosphate of ADP and acetate molecule both are coordinated by divalent metal ions? I am working on a Kinase structure which was crystallized with ADP and in presence of 1M sodium

Re: [ccp4bb] CCP4BB Digest - 10 Jan 2017 to 11 Jan 2017 (#2017-12)

Hi Claire, Isn’t the simplest answer just that the EDS server is calculating the completeness for a different amount of data (high res limit of 1.92 Å), whereas in your Depositor data it was only calculated to a high res limit of 2.1 Å? This would probably be the result of you measuring

Re: [ccp4bb] [ccp4bb] Remittance advice - Invitation to edit

my point exactly. Andy > On Dec 12, 2016, at 2:49 AM, Laura Spagnolo > wrote: > > Isn't this mailing list moderated? > Laura > > Sent from my iPhone > > On 11 Dec 2016, at 17:48, Bonsor, Daniel >

Re: [ccp4bb] CCP4BB Digest - 26 Nov 2016 to 27 Nov 2016 - Special issue (#2016-322)

Picture of electron density didn’t come through, but three planar fused rings sounds like a flavin - is your protein involved in redox reactions and is it coloured when concentrated ? The only four ring molecules that spring to mind are steroids, but these wouldn’t be all that flat and you

Re: [ccp4bb] [ccp4bb] Fwd: [ccp4bb] just out of totally idle curiosity ...

Sorry - didn't realise that was going out to the whole list, and just made a liar out of myself. Will bow out now. On 2016-11-10 10:20, Tristan Croll wrote: Hi Elton, I certainly didn't say I agreed with their choice or thought it was a good one. But as someone who grew up in a low-income,

Re: [ccp4bb] [ccp4bb] Fwd: [ccp4bb] just out of totally idle curiosity ...

Hi Elton, I certainly didn't say I agreed with their choice or thought it was a good one. But as someone who grew up in a low-income, low-employment environment myself this has the ring of truth to it. I totally agree with you (and worry just as much) regarding the proliferation of

Re: [ccp4bb] [ccp4bb] Fwd: [ccp4bb] just out of totally idle curiosity ...

Hi Tristan, I’m afraid I don’t get the logic in the article you sent. In this case the farmers who are crying for the attention of the people in shiny palaces have voted for one who lives in golden mansions. For me the really worrying thing here is how can so many people be misled by a false

Re: [ccp4bb] [ccp4bb] Fwd: [ccp4bb] just out of totally idle curiosity ...

From letters in yesterday’s Guardian:- today is 9/11 Make America grate again > On 10 Nov 2016, at 08:00, Marjolein Thunnissen > wrote: > > Dear Bill, > > I fully agree with you, awareness has to be spread and one should not ignore > politics completely,

Re: [ccp4bb] [ccp4bb] Fwd: [ccp4bb] just out of totally idle curiosity ...

Dear Bill, I fully agree with you, awareness has to be spread and one should not ignore politics completely, especially when there are so strong anti-intellectual (anti-science) statements out there. best regards Marjolein On 10 Nov 2016, at 04:17, William G. Scott

Re: [ccp4bb] [ccp4bb] on NCS restraint

Hi, The purpose of NCS is to reduce the degrees of freedom in order to avoid over refinement -not only to expedite refinement. Strict or restrained NCS should be applied at lower resolutions (2.7Å) or data completeness. Forgo NCS If you have a complete and better than 2.5Å dataset. Also, you

Re: [ccp4bb] CCP4BB Digest - 1 Apr 2015 to 2 Apr 2015 (#2015-92)

Shane, After you define which segments share proper or improper all NCS their parameters in MAIN environment, they will be calculated and stored in such macro files. $ cat mol_A_to_B.com ! SAVING RMS FIT DATA: set matrix MAT_ROT number - 0.959598 -0.031620 -0.279592 - -0.029443

Re: [ccp4bb] CCP4BB Digest - 1 Apr 2015 to 2 Apr 2015 (#2015-92)

...@well.ox.ac.uk Tel: (+44) - 1865 - 287783 Original message Date: Fri, 3 Apr 2015 08:44:59 +0200 From: CCP4 bulletin board CCP4BB@JISCMAIL.AC.UK (on behalf of dusan turk dusan.t...@ijs.si) Subject: Re: [ccp4bb] CCP4BB Digest - 1 Apr 2015 to 2 Apr 2015 (#2015-92) To: CCP4BB

Re: [ccp4bb] CCP4BB Digest - 25 Mar 2015 to 26 Mar 2015 (#2015-86)

Dear Herman, I am not sure what you really want. Maybe this can help you. You can get the following numbers out of MAIN 1. comparing a pair of selections. It makes sense only if they are equivalent. rms b-val select my_selection_1 end select my_selection_2 end 2. Show command does

Re: [ccp4bb] CCP4BB Digest - 28 Feb 2015 to 1 Mar 2015 (#2015-61)

Instead of Br which has a weak signal at its K edge, why not use Iodide at some wavelength (or energy) where it gives a stronger signal? The longer wavelength used will help with spot spatial resolution as well. One may be fighting radiation damage, too. One may be fighting a moving (vibrating?)

Re: [ccp4bb] CCP4BB Digest - 5 Feb 2015 to 6 Feb 2015 (#2015-40)

Fred, as you know discontinuous lattice is not physically possible. Therefore first make sure to exclude your and deposition errors like a wrong space group and cell constants. However, it may be that some molecules are disordered and therefore absent in the structure solution. If there are

Re: [ccp4bb] CCP4BB Digest - 20 Dec 2014 to 21 Dec 2014 (#2014-38)

Please remove me from your mailing list. On 12/21/14, 7:00 PM, CCP4BB automatic digest system lists...@jiscmail.ac.uk wrote: There are 2 messages totaling 244 lines in this issue. Topics of the day: 1. Cross-validation when test set is miniscule 2. non-specific disulfide bonds in

Re: [ccp4bb] CCP4BB Digest - 13 Aug 2014 to 14 Aug 2014 (#2014-220)

Unsubscribe Sent via the Samsung GALAXY S®4, an ATT 4G LTE smartphone div Original message /divdivFrom: CCP4BB automatic digest system lists...@jiscmail.ac.uk /divdivDate:08/14/2014 6:00 PM (GMT-06:00) /divdivTo: CCP4BB@JISCMAIL.AC.UK /divdivSubject: CCP4BB Digest - 13 Aug

Re: [ccp4bb] [ccp4bb] Twinning in space group Pc

Dear, Indeed,. Pc is not compatible with chiral molecules,. my mistake. I’m trying to process/solve the structure in P1 now and see how far I get. Thank you very much for pointing things out. Regards Kristof On 13 Aug 2014, at 13:58, herman.schreu...@sanofi.com wrote: Dear Kristof,

Re: [ccp4bb] CCP4BB Digest - 6 Aug 2014 to 7 Aug 2014 (#2014-213)

Hi Remie, PyMOL by default sorts atoms based on their identifiers (segment, chain, residue number). Could it be that your file has segment identifiers? Try this after loading your file: PyMOLalter all, segi= PyMOLsort Cheers, Thomas On 07 Aug 2014, at 19:08, CCP4BB automatic digest system

Re: [ccp4bb] [ccp4bb] phaser issue MR

Dear Almudena, We actually have a tutorial that goes through the process of defining a solution step by step: http://www.phaser.cimr.cam.ac.uk/index.php/MR_using_keyword_input. The .sol file is a small text file that just contains the description of how a defined ensemble should be rotated

Re: [ccp4bb] [ccp4bb] map manipulation questions

Oh no, I’ve been meaning to update that page for a while! It’s much easier to cut out density now than it was when I wrote that. In CCP4, Kevin Cowtan has the program cmapcut, and in Phenix Tom Terwilliger has the program phenix.cut_out_density. For most purposes, I think you’ll find those

Re: [ccp4bb] [ccp4bb] Symmetry problem

Hi, Monika, It sounds like you got the two domains separately in the asymmetric unit. You could do the symmetric operation for one of the domains in pymol by generating the symmetric mates (say 10 Å). Then you should see several same ones there. Select the one you need, and save the coordinates,

Re: [ccp4bb] CCP4BB Digest - 22 Nov 2013 to 23 Nov 2013 (#2013-332)

Dear Nazia, Glad you are trying your hand at a membrane protein. You need to have detergents (like ldao, octylpoe ) in your refolding and purifcn buffer. Best wishes Krishnaswamy Mku On 24 Nov 2013 05:32, CCP4BB automatic digest system lists...@jiscmail.ac.uk wrote: There are 6 messages

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

Dear all, thank you for your reply. I would summarize my concerns and opinions, so far: 1) for QTLS (non-merohedral twinning - non intersecting lattices) I think one should consider the variables as independent and random and it is possible to recover the true intensities of a unique

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

Fulvio, First, to your point 2): Iobs(h1) and Iobs(h2) as well as Itrue(h1) and Itrue(h2) are /not/ correlated! The Iobses are /related/ to the Itrues by alpha (and the twin law), but the Itrues are totally uncorrelated to each other, and so are the Iobses, in my opinion (even though those will

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

Tassos, I'm no expert either, and there are caveats for using this formula on correlated magnitudes. But I would assume that the intensities of twin related reflections should be independent from each other (that's my understanding of the sigmoid cumulative intensity distribution of twins).

Re: [ccp4bb] [ccp4bb] Molecular Replacement using low sequence identity templates

Hi Eleanor, Yes, the initial LLG scores in Phaser are highly dependent on the assigned sequence identity, which is translated into an initial estimate of the effective RMSD of the model. However, the latest versions of Phaser refine the RMSD estimate at the end of the job and, assuming that

Re: [ccp4bb] [ccp4bb] Molecular Replacement using low sequence identity templates

I guess my experience is out of date - please ignore comments on LLG! Eleanor On 21 October 2013 15:40, Randy Read rj...@cam.ac.uk wrote: Hi Eleanor, Yes, the initial LLG scores in Phaser are highly dependent on the assigned sequence identity, which is translated into an initial estimate of

Re: [ccp4bb] CCP4BB Digest - 11 Oct 2013 to 12 Oct 2013 (#2013-289)

Dear Dilip Badjugar, Perhaps it may be good to take a look at the unmodelled blobs and see if there is any large densities left unexplained. Also how does the Rmerge vary with the resoln ? Is your data good upto 1.7A? Regards and wishes Krishnaswamy On 13 Oct 2013 04:33, CCP4BB automatic digest

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