[ccp4bb] Computational crystallography in 2024
Dear all, I've been outside of the field for a few years (I have very fond memories of the 2008 Crystallographic Computing School, but did a lot of different stuff since then), but I'd love to come back and figured this would be the best place to ask - what are the go-to resources today for those who want to write code for crystallography? I remember back then the people involved in Phenix were developing open source libraries at the time. I'm aware Biopython does some stuff regarding coordinates, but as far as I'm aware not what I would need to, for example, writing simple 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 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] OT - Software articles / databases
I've been compiling a reference database and I've just noticed that it's quite difficult to automatically retrieve references for most articles on crystallographic software. Has anyone noticed that? It seems that, for some reasons, articles on the "Computer programs" 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 do momento no Yahoo! +Buscados http://br.maisbuscados.yahoo.com
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] 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 Yahoo! Mail, o único sem limite de espaço para armazenamento! http://br.mail.yahoo.com/
Re: [ccp4bb] Molecular replacement of a multidomain protein
I've had a very good experience with MrBump: http://www.ccp4.ac.uk/MrBUMP/ Not only because of the program itself, which was able to find an unexpected template for the problematic chain (the first one was straightforward in Phaser), but also because of great support from Martyn & 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 the asymmetric unit. > The structures of the individual domains are already > known from prokaryotes. > The sequence identity with the known structures are > about 30%. > I have tried molecular replacement using the two > parts as models > respectively with CNS, MOLREP, PHASER etc. However I > always get the solution > for one domain. I have also tried to fix that domain > and find the other one. > But none of the programs can find a solution. > I am trying to model build the correct sequence of > one domain using a > density modified (using CNS), NCS averaged (using > RAVE) map but the map does > not look very good. The side chains are not clear. > That might be due to the > fact that I am only having a partial model. > Any suggestion will be appreciated. > Thanks. > Ms. Anjali Mehta > Abra sua conta no Yahoo! Mail, o único sem limite de espaço para armazenamento! http://br.mail.yahoo.com/
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 <[EMAIL PROTECTED]> escreveu: > So - rather than repeat things that are obvious to > some people, would it > not be good to have a crystallography-FAQ that one > could point people > to? This should be part of a Wiki where "we > crystallographers" could > collect our wisdom. This would be much more > systematic, and less > volatile, than the postings of this mailing list > (which to me _is_ a > very valuable ressource). > > A Wiki is not difficult to set up. Maybe it could be > part of the CCP4 > pages? We set up a Wiki for our lab at the beginning > of the year, and it > was a great success, in particular because it works > the same way as > Wikipedia - anybody can contribute. There should be > some means of > controlling "write access", but that could simply be > granted to people > who are subscribed to the CCP4 mailing list. > > I'd at least volunteer in helping to get a Wiki > started. And one way to > get it filled with articles would be that those > people who used to write > a "summary" of responses would simply compose a new > Wiki article, and > report to the mailing list that this article exists, > which could then be > expanded by others. > > best, > > Kay > > > Anastassis Perrakis schrieb: > > Sorry for the cliche, but *the goal of refinement > is not to reduce R > > factors, but to produce a good model.* > > > > ARP/wARP uses the 'WEIGHT AUTO' option of REFMAC5 > to get a good geometry. > > You should set the weight to a value that produces > 1-2 and 1-3 distances > > rms deviations similar to the ARP/wARP job, > > to be able to compare. The fact that weight is 0.3 > says nothing. > > > > The correct weight can vary wildly from 0.02 to > 0.5, in my experience. > > for 2.0 data 0.3 sound loose, 0.15-0.2 is what I > am used to, > > depending on dataset. But, The only way to tell > what is right is > > inspecting the geometry and aim for a 'reasonable' > rms 1-2 distances > > deviation. > > > > What is 'reasonable', can cause yet another long > discussion, but my > > personal favorite for 1-2 distances rms deviation > is between 0.015-0.020. > > In Refmac these also give the lowest R factors, in > my hands. > > > > The invisible side chains is yet another long > discussion that you can > > retrieve from the ccp4bb archives. > > Again, my personal preference is to leave them in > and let them get very > > high B factors, as long as they do not > > get negative density in difference maps, that I > presume you are inspecting. > > I dont mind deleting them (but dont like it) and I > think mutating to ALA > > is worse since its misleading to users. > > > > Finally, given that you have 2.0 A data you should > try and model not > > only waters, but also: > > a. double conformations of side chains > > b. solvent and cryoprotectant molecules; glycerol, > SO4 etc should be > > different than waters and easy to model. > > > > ... and I still cant help wondering how people do > their phd's or > > post-docs in labs that no-one can explain > > such trivialities. Or why people prefer not to ask > their colleagues and > > supervisors, but to mail ccp4bb. > > Or why do I bother answering such emails on a > Saturday morning, and then > > complaining, > > only to have the likes of Dr. Walsh commenting > about my humor ;-))) > > I find all these really scary. > > > > Tassos > > > > On 21 Jul 2007, at 0:29, JOE CRYSTAL wrote: > > > >> Dear all, > >> > >> > >> I am refining a structure at 2.0 A. The water > molecules have been > >> added using arp/warp resulting Rwork/Rfree=21/26% > (about 370 HOH for > >> 360 residues). After 10 cycles of refmac > refinement (wt 0.3), > >> Rwork/Rfree went up about 1.5% to 22.5/27.5%. I > did some minor > >> adjustments and add/delete water in Coot followed > by 10 cycles refmac > >> refinement, but Rwork/Rfree are still around > 22.5/27.5%. I also > >> noticed a few side chains without density. Will > setting those atoms > >> to 0 occupancy or high B factor or mutating to > Ala help decrease Rfree > >> substantially? If not, is there any better > strategies to lower down R > >> factors? I will be very appreciative if you have > any suggestions or > >> comments to offer. Thank you in advance. > >> > >> > >> Best, > >> > >> > >> Joe > > > > > -- > Kay Diederichs > http://strucbio.biologie.uni-konstanz.de > email: [EMAIL PROTECTED] Tel +49 7531 > 88 4049 Fax 3183 > Fachbereich Biologie, Universität Konstanz, Box > M647, D-78457 Konstanz > > Flickr agora em português. Você cria, todo mundo vê. http://www.flickr.com.br/
[ccp4bb] SUMMARY: I vs. 2theta plot, image processing
Few, but very informative and useful responses about
2D to I vs. 2theta plot conversion and image
processing.
My original message was:
1) Some data collection and image processing files
have the options to show the intensity distribution
over a user-defined "line" in the image. Does any
program allow one to trace a line from the beam center
to
the detector edge and save this intensity distribution
to a file, so one could have I vs. 2theta data (or
even a I vs. pixel data file, which could be easily
converted to a I vs. 2theta file given the
experimental
setup)?
2) Is there a program which could convert image files
from common 2D detectors (Mar345, MarCCD, RaxisII...)
to a text file with the intensity on each pixel so one
could easily write programs to do things such as in
(1)?
3) If the answer to 2 is "No, you should learn how to
handle binary files and image data formats", is there
a tutorial on how to do this (I would prefer C/C++,
but Fortran is OK), or some well-documented open
source code I could study?
==
James Holton wrote:
I recommend Andrew Hammersley's program "FIT2D" for
doing this.
http://www.esrf.eu/computing/scientific/FIT2D/
You can integrate a 2-D image into a 1-D profile using
the "POWDER" command. You want to set up the image
geometry with the "GEOM" command first. Then you have
the option to get I vs 2theta in the output. You can
also go from a 1-D profile to a 2-D image with the
"SYMFUNC" command.
FIT2D can also interconvert a number of image file
formats. When it can't output the file format you
want, you can usually just export the image data as
"binary" and slap a new header on it. For example, if
you read in a Bruker image to FIT2D and want to make
it an ADSC-type image, then you can export the data
("OUTPUT") as binary integers ("BIN"), using the
filename binary.bin, then you can do this:
head -512c frame_001.img >! header
vi header
head -512c header >! newimage.img
cat binary.bin >> newimage.img
Here you are "stealing" a header from a pre-existing
image "frame_001.img". You can edit the header with a
text editor if you like, but make sure it stays as 512
bytes (you can run the saved text through "head -512c"
to truncate it). This will let you display the
Bruker data frame in ADXV. You might need to play
around with byte swapping in FIT2D to make it work.
To get binary data into text, I find it most
convenient to use the unix program "od" (octal dump).
The dump does not have to be octal and you can
arbitrarily set where in the file to start dumping and
what format
to dump it. For example, dumping a MarCCD image goes
something like this:
od -v -t u2 -w2 -j 4096 frame_0001.mccd
Will dump all the 2-byte words in the image, starting
with the first pixel in the image. The only problem
is if the pixels are byte-swapped. A quick-and-dirty
way to un-swap bytes is:
od -v -t u1 -w2 -j 4096 frame_0001.mccd | awk '{print
$2*256+$3}'
Will dump as single bytes, and then you convert them
into the equivalent 2-byte value with awk.
The x-y coordinate of the pixel can be worked out 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 way in the world to do
this.
-James Holton
MAD Scientist
==
Graeme Winter wrote:
Hi Lucas,
There is a C++ library called DiffractionImage which
may help with #3 if you get that far:
http://www.ccp4.ac.uk/newsletters/newsletter45/articles/DiffractionImage.html
If you get in touch with Francois Remacle I'm sure
he'll send you everything you need.
Cheers,
Graeme
==
Jon Wright wrote:
Fit2d is perhaps the 'gold standard' for making powder
diagrams:
http://www.esrf.eu/computing/scientific/FIT2D/
See also:
http://www.datasqueezesoftware.com/
For source code try:
http://cctbx.sourceforge.net/current_cvs/python/iotbx.detectors.html
Good luck,
Jon
==
Thanks a lot,
Lucas Bleicher
Novo Yahoo! Cadê? - Experimente uma nova busca.
http://yahoo.com.br/oqueeuganhocomisso
[ccp4bb] I vs. 2theta plot, image processing
1) Some data collection and image processing files have the options to show the intensity distribution over a user-defined "line" in the image. Does any program allow one to trace a line from the beam center to the detector edge and save this intensity distribution to a file, so one could have I vs. 2theta data (or even a I vs. pixel data file, which could be easily converted to a I vs. 2theta file given the experimental setup)? 2) Is there a program which could convert image files from common 2D detectors (Mar345, MarCCD, RaxisII...) to a text file with the intensity on each pixel so one could easily write programs to do things such as in (1)? 3) If the answer to 2 is "No, you should learn how to handle binary files and image data formats", is there a tutorial on how to do this (I would prefer C/C++, but Fortran is OK), or some well-documented open source code I 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
By the way, I'll extend that question: the validation software Verify3D assigns not only buried state but also polar fraction and secondary structure, using the probability of finding given residues in the different "environment" defined when combining all this information to calculate a "score" of protein regions, which could identify, for example, sequence misthreading. The program is rather old (1991) and, aside from the automated validation site at UCLA (which just let you upload a PDB and get the scores), I haven't found a web page for it. Is there available 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 protein, that is the > sequence is on the surface or > in the > core? Usually we use visualization tools, such as > RasMol, VMD, to identify this > by our eyes. But I don't know whether there are > tools that we could input PDB > file and the sequence only, then the computer > tells us the sequence is on the > surface or in the core. __ Fale com seus amigos de graça com o novo Yahoo! Messenger http://br.messenger.yahoo.com/
Re: [ccp4bb] change the B-factor for a residue
--- Juergen Bosch <[EMAIL PROTECTED]> escreveu: > How about Coot ? Click the residue you want to > change and hit Resdiue > Property. That's how I used to do it, but things start to become boring when one needs to do it with more than one pdb file with about 200 residues each. 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
Is there a program in CCP4 with a command to change the B-factor of a single residue? I checked the documentation for pdbset and it seems to assign B-factors only for the whole molecule. What I'd like to do is plot a given residue property in a graphic software using the "color by 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 graça com o novo Yahoo! Messenger http://br.messenger.yahoo.com/
[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 __ Fale com seus amigos de graça com o novo Yahoo! Messenger http://br.messenger.yahoo.com/
Re: [ccp4bb] crytstallographic software
--- Marius Schmidt <[EMAIL PROTECTED]> escreveu: > Dear colleagues, > I was wondering whether someone of you has > reported/published > new or improved crystallographic software somewhere > else than Acta Cryst. It would be nice if you could > share your experience with me. Topics might be: > - quality of the journal > - rapid publication > - literate peers > - ... Aside from the given suggestions, another possibility is Computer Physics Communications from Elsevier. Pros: they will host your software in their website, response from editors and reviewing 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 article is accepted for publication. Lucas __ Fale com seus amigos de graça com o novo Yahoo! Messenger http://br.messenger.yahoo.com/
[ccp4bb] Secondary structure assignment
When I was checking a structure and preparing figures for an upcoming article, I found out that Procheck and Pymol use different criteria to assign secondary structure for residues in a PDB (i.e.: some residues that appeared as loops in the cartoon representation in pymol were assigned as beta-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 novo Yahoo! Messenger http://br.messenger.yahoo.com/
