[ccp4bb] Computational crystallography in 2024

mple code that would read a PDB and mtz and calculate real space fit for an aminoacid, or generating symmetry neighbours from a asymmetrical unit PDB and its space group. How are people doing things like that in 2024? Cheers, Lucas Bleicher

[ccp4bb] Data reprocessing

en the PDB deposition and update the files? Or simply state in the publication that the data was reprocessed? I'm curious if there's a consensus on handling situations of this nature. Cheers, Lucas To unsubscribe

[ccp4bb] Volunteer for Science chats with children during lockdown (and beyond)

ase include a small photo of yourself, where you're based and a short paragraph about your research in layman's terms. You can see what other people have written on the website for inspiration. Thank you! Lucas Rudden SND Project Coordinator Email: outre...@scientist-next-door.org Face

[ccp4bb] Parseable residue-ligand and/or residue-nucleic acid interaction database?

Just so that we don't reinvent the wheel: is there any database or webservice on which one can parse the list of residue-ligand interactions for the entire PDB? I'd like to programmatically obtain information such as "in PDB 3hdl the Calcium 306 is in contact with Asp223 or in PDB 5gjb Arg388 is in

Re: [ccp4bb] Yet another "what's my blob" thread, part II

Oops, should have mentioned that - Cryoprotectant was PEG200, 20%.

Re: [ccp4bb] Verify 3D score

I had the same question long ago and I was directed to the Verify3D code, which is also not that easy to read these days. If you receive any feedback, let me know. Perhaps there are also more recent profile-based scores with available code somewhere? 2016-11-14 16:20 GMT-02:00, Hammond, Robert Gle

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

2016-11-09 3:56 GMT-02:00, kaiser : > Yeah, given Europe and Canada are obvious, I think Brazil and Japan are > actually viable alternatives if the first choices are getting too crowded. > They do have synchrotrons and "internets". We just had a president impeached, and the new one is forcing a la

[ccp4bb] Ligand relevance for bioinformaticians using PDB files

list most "usually biologically irrelevant" I could remember, but now I wonder if that is something someone has probably thought about doing before and there's some article/database dealing with it somewhere. Any suggestions? Lucas

Re: [ccp4bb] FW: [ccp4bb] PDB passes 100,000 structure milestone

2014-05-15 9:53 GMT-03:00 Colin Nave : > Of course exponential growth can’t go on forever – the hidden point behind > my question. > A nice example from another biological database is Swissprot. It had an exponential-like growth until 2009, and now it's somewhat linear: http://web.expasy.org/doc

[ccp4bb] Problematic PDBs

at can go wrong in a PDB construction. Best regards, Lucas

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

esponse addressing this issue is given here: http://www.michaeleisen.org/blog/?p=1439 Lucas

Re: [ccp4bb] The number of protein-protein complex in recent years

ns 14453 hits if I click "result count". Then you can add search criteria to refine your search - in your case, Deposition->Deposit Date and then select the desired timespan will return what you're looking for. Lucas 2013/3/13 Wei Feng : > Dear all, > I want to do a stat

[ccp4bb] [MX2] EPICS driver for Amptek MCA8000A

://www.aps.anl.gov/epics/modules/bus.php#RS%2d232). Since it is a pretty common device in the community, I believe there may be someone around with this guy running under EPICS. Thanks in advance for any help, Lucas Sanfelici Brazilian Synchrotron Light Laboratory (LNLS/Sirius) Brazilian Center for

Re: [ccp4bb] do you think it is interesting?

2012/6/18 Tim Gruene : > -BEGIN PGP SIGNED MESSAGE- > Hash: SHA1 > [...] >> of monomers is called a multimer, not a polymer. > [...] > shiver - what a terrible mixture of languages. 'multi-' has got latin > origin, whereas both poly and mer have got greek origin, and I don't > think one sho

Re: [ccp4bb] saxs on xtals

will be fine?", but it is a bit trickier than that. I am pretty sure they will be able to provide some hints to Anna's case, which seems very similar to a powder diffraction experiment. Lucas Bleicher

[ccp4bb]

i.nlm.nih.gov/pubmed/21382498 Lucas Bleicher 2011/11/26 REX PALMER : > Does anyone have an up-to-date account of protein structure anlysis from > powders? > > > Rex Palmer > http://www.bbk.ac.uk/biology/our-staff/emeritus-staff > http://rexpalmer2010.homestead.com

Re: [ccp4bb] Linux vs MacOS for crystallographic software

long time since I had that feeling for destroying the computer with a sledgehammer after trying the nth version of xorg.conf and still being unable to run coot. Lucas

[ccp4bb] OT - Software articles / databases

ot; section on Journal of Applied Crystallography (where the "official reference" for most of the software we use gets published) is not indexed on databases such as ISI Web Of Science, Pubmed, etc, but all other sections from that magazine are. Lucas Veja quais são os assuntos

[ccp4bb] Monochromator Stabilization

some company which still assemblies such system. It seems today's solution would be to integrate complementary peaces of hardware or even program them in software. Hope this message finds each of you well, Lucas Sanfelici Physicist Brazilian Synchrotron Light Source- LNLS (www.lnl

Re: [ccp4bb] looking for a program

By the way, is there a program (perhaps one of those cited on this thread) that would list all salt bridges and hydrogen bonds for residues in the same chain? Lucas Veja quais são os assuntos do momento no Yahoo! +Buscados http://br.maisbuscados.yahoo.com

[ccp4bb] Air Conditioning System for Optical Hutch

quirements. However at the present time I would like to just have a feeling of how much I would probably spend with a system like that. Someone who already had to commissioning one could give some idea? I hope you are all fine, Lucas Sanfelici Physicist Brazilian Synchrotron Ligth Source- LN

[ccp4bb] RES: [ccp4bb] Beamline Stability Issues

would be elucidative… Michele, thank you one more for your help. I’ll be pleased to inform you about our progress. Regards, Lucas.

[ccp4bb] Beamline Stability Issues

! : ) Thanks for the help one more time and regards, Lucas. -Mensagem original- De: Michele Cianci [mailto:[EMAIL PROTECTED] Enviada em: segunda-feira, 28 de julho de 2008 04:26 Para: [EMAIL PROTECTED] Assunto: Re: [ccp4bb] Beamline Stability Issues Hi, I commissioned and made

[ccp4bb] Beamline Stability Issues

Dear Mark, thanks for your answer! Yes, there is an actual change in energy and I guess my problem does not have a single source! In the case you know someone who faced/have faced a similar problem around please tell me. Brazilian regards, LS. 1. Is the energy drift a change in flux or actual

[ccp4bb] RES: [ccp4bb] Beamline Stability Issues

Hey Andrew! Thanks for answering! Does someone have experience in minimize energy instabilities in beamlines? Are you sure it's an energy instability and not an intensity one? It's quite rare to see energy instabilities from a well calibrated monochromator. All monochromators should be in a clos

[ccp4bb] Beamline Stability Issues

uld I expect the heating of a non-cooled 2nd crystal affects energy? Does someone know cases of a few eVs drifts? Thanks in advance and regards, Lucas Sanfelici Physicist Brazilian Synchrotron Ligth Source- LNLS (www.lnls.br) Diagnostics Group PO Box 6192 Postal Code 13083-970 Campinas-SP Brazil

[ccp4bb] Model ensemble for x-ray crystallography

Some time ago I've heard about the idea of proposing an ensemble of models (as in NMR), instead of a single model for x-ray crystallography structures. If I remember correctly, this idea has been published somewhere. Can anyone tell me what article is that? Lucas Abra sua conta no

Re: [ccp4bb] Molecular replacement of a multidomain protein

Ron. It's definitely worth a try. Lucas --- Anjali Mehta <[EMAIL PROTECTED]> escreveu: > Dear All, > I am working with a Bifunctional protein of > molecular weight ~60 kDa. > I have a 3.3 angstrom native dataset. The matthews > number show there are 6 > molecules in th

Re: [ccp4bb] Suggestion: Wiki -- was:Re: [ccp4bb] need help--Rfree is not decreasing

That would be a great idea. In fact, I keep on my mailbox dozens of great postings (most of them summaries) in CCP4 which would be very useful to everybody if there's an online resource, with information organized in topics. I would gladly copy them to this wiki. Lucas --- Kay Diederichs &l

[ccp4bb] SUMMARY: I vs. 2theta plot, image processing

ut from the sequence. For example, if you have a 4096x4096 image, od -v -t u2 -w2 -j 4096 frame_0001.mccd | awk '{print x+0,y+0,$2;++x} x>4096{++y;x=0}' Will dump x,y,and I for every pixel in the image. This output file will be quite large and this is DEFINITELY not the fastest wa

[ccp4bb] I vs. 2theta plot, image processing

could study? Thanks, Lucas Bleicher __ Fale com seus amigos de graça com o novo Yahoo! Messenger http://br.messenger.yahoo.com/

Re: [ccp4bb] pdb-l: Sequence Location in Protein Tertiary Structure

ble code to assign residues to one of those "environments" and updated probabilities of finding amino acids in each one? Lucas Wei Huang wrote: > Hi all, > > Do someone know a tool which could identify the > location of the sequence in > tertiary structure known protei

Re: [ccp4bb] change the B-factor for a residue

ch. Does coot accept some kind of in-line command to do this, so I could automatically generate a script? Lucas __ Fale com seus amigos de graça com o novo Yahoo! Messenger http://br.messenger.yahoo.com/

[ccp4bb] change the B-factor for a residue

y b-factor" feature. I could write a script to directly parse and modify the PDB file, but things would be easier if I could just generate a script that used some program which would handle the B-factor assignment. Lucas __ Fale com seus amigos de g

[ccp4bb] Ordered His-tags

I remember reading once or twice people requiring examples of PDBs which contained ordered His-tags. Someone did a survey on this, which is on the latest Acta Cristallographica D: http://journals.iucr.org/d/issues/2007/03/00/en5203/index.html Lucas

Re: [ccp4bb] crytstallographic software

ng is quick. Cons: Impact factor is not so high (1.6 in 2005), and it's not a journal on which protein investigators would look for software. But I suppose that protein crystallography software could be properly reviewed and published there. Also, they demand the source code when the ar

[ccp4bb] Secondary structure assignment

-strand in Procheck). I understand that different criteria may exist to do this. Which one is actually used to determine the "HELIX" and "SHEET" lines in the header of a curated PDB? Lucas __ Fale com seus amigos de graça com o n