Re: [ccp4bb] buccaneer_pipeline failure (ccp4 6.2.0) (SOLUTION)

We discovered the problem: the file $CBIN/buccaneer_pipeline needs to be told to expand its lookup path, so we inserted in the 2nd line: sys.path.append("/usr/local/ccp4/6.2.0/ccp4-6.2.0/share/python/") We had this fix in our previous installation as well, but can't remember where we got

Re: [ccp4bb] IUCr committees, depositing images

Sure they will There is no irony in what I say FF Dr Felix Frolow Professor of Structural Biology and Biotechnology Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723

Re: [ccp4bb] IUCr committees, depositing images

What do you consider good ? r.m.s.d of 2.5 Å ? fatal for drug design. On Oct 18, 2011, at 12:19 PM, Enrico Stura wrote: Dear Peter, How many crystallographers does it take to transform bad data into good data? None, you need a modeller. Only a modeller can give you a structure with perfect geome

Re: [ccp4bb] newbie question about data processing

Thanks! That does it. Harry wrote: Hi Ed "reindex" is your friend here - reindex hklin jumbo.mtz hklout dumbo.mtz < I integrated data with mosflm using the lowest symmetry implied by the lattice- P4. Scaling with scala confirms that symmetry. Now I want to test P422, but scala doesn't seem to

Re: [ccp4bb] newbie question about data processing

Hi Ed "reindex" is your friend here - reindex hklin jumbo.mtz hklout dumbo.mtz < I integrated data with mosflm using the lowest symmetry implied by the lattice- P4. Scaling with scala confirms that symmetry. Now I want to test P422, but scala doesn't seem to have a SYMM or SPACE GROUP keyword. I

[ccp4bb] newbie question about data processing

I integrated data with mosflm using the lowest symmetry implied by the lattice- P4. Scaling with scala confirms that symmetry. Now I want to test P422, but scala doesn't seem to have a SYMM or SPACE GROUP keyword. I'm sure there is an obvious way to do this, which everyone else knows, but i don't

Re: [ccp4bb] Cell Params as a Function of Temperature

On Tue, Oct 18, 2011 at 5:01 PM, Jacob Keller wrote: > references studying variation in cell params > systematically as a function of temperature, with many points on the > curve (not just RT and 100K?) a well cited article, from 1992: Effects of temperature on protein structure and dynamics: x-

[ccp4bb] Cell Params as a Function of Temperature

Dear Crystallographers, is anyone aware of references studying variation in cell params systematically as a function of temperature, with many points on the curve (not just RT and 100K?) Jacob Keller -- *** Jacob Pearson Keller Northwestern University Medi

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

> Selecting a test set that minimizes Rfree is so wrong on so many levels. > Unless, of course, the only thing I know about Rfree is that it is the > magic number that I need to make small by all means necessary. By using a simple genetic algorithm, I managed to get Rfree for a well-refined model

Re: [ccp4bb] IUCr committees, depositing images

Phoebe, Just automate the archiving and come up with a reasonable scheme how to. Ours is that data sets are called: userid_yearmonth_projectid_# Userid is derived from the login into CrystalClear (oops, free advertizing), projectid is set by the PI (so she can remember 10 years from now what

Re: [ccp4bb] IUCr committees, depositing images

On Tue, 2011-10-18 at 18:17 +0100, Gerard Bricogne wrote: > it would be of the greatest value to that > investigator to be able to double-check how reliable some features of > that > structure (especially its ligands) actually are. Certainly, one could argue here that the current PDB policy that

Re: [ccp4bb] IUCr committees, depositing images

One more consideration: Since organization is not one of my greatest talents, I would be absolutely delighted if a databank took over the burden of archiving my raw data for me. Phoebe = Phoebe A. Rice Dept. of Biochemistry & Molecular Biology The Universit

Re: [ccp4bb] IUCr committees, depositing images

Dear Enrico, Frank and colleagues, I am glad to have suggested that everyone's views on this issue should be aired out on this BB rather than sent off-list to an IUCr committee member: this is much more interactive and thought-provoking. There would seem to be clear biases in some of t

Re: [ccp4bb] IUCr committees, depositing images

given that: - storage is becoming cheaper exponentially, - computer power is increasing exponentially, I think there is no reason to not store all images used for solving a structure - linked to the pdb entry and properly annotated with beam centre, lambda, pixel order and all other necessary pro

Re: [ccp4bb] Fixing cis peptides

What's wrong with cis-peptides? there are plenty of those in the PDB, independent of the presence of proline. If they fit the density better and neighbouring residues are happy, just go with it. The refinement suggests that this could indeed be the case. Boaz Boaz Shaanan, Ph.D. Dep

Re: [ccp4bb] Dennis Ritchie

On Tue, 2011-10-18 at 10:58 +0200, Miguel Ortiz Lombardía wrote: > Hi community, > > I have been waiting for someone more knowledgeable to write about the > passing away of Dennis Ritchie (8 October) especially after the recent > obituaries posted in the list. I confess I know little about him, ex

Re: [ccp4bb] Dennis Ritchie

> Are you saying that undergraduates do not learn to program any more, or that > they use a more "advanced" language than C where they don't really learn > what is going on? The latter. It's usually Java and .NET nowadays IIRC.

Re: [ccp4bb] Phenix building residues not found in input sequence file

Could you have an unexpected "small subunit" (or some other situation) giving additional density that Phenix is building into ? In other words, how sure are you of what is present in the crystal ? This is because I remember the enzyme methanol dehydrogenase where there was a small subunit which

Re: [ccp4bb] IUCr committees, depositing images

Dear Peter, How many crystallographers does it take to transform bad data into good data? None, you need a modeller. Only a modeller can give you a structure with perfect geometry. Data just introduces experimental errors into what would otherwise be a perfect structure. If you have good

[ccp4bb] Fixing cis peptides

Hi everybody, I am currently refining a 2.2 A crystal structure with a very mobile subdomain. The initial density for this subdomain was very weak, however, I was able to rebuild it using low resolution omit maps (and some perturbing of atomic coordinates). When I refine the structure, four of

Re: [ccp4bb] Dennis Ritchie

Le Mardi 18 Octobre 2011 16:36 CEST, Sabuj Pattanayek a écrit: Should I understand that Gérard Brigogne really meant that Ritchie's achievements were peanuts ? Yet, after so many years in England I thought Gerard mastered British humour rather well... Encore un effort Gérard Philippe Dum

Re: [ccp4bb] IUCr committees, depositing images

Sorry if this message reads a bit out of date, it has been sent two days ago without success, I am trying to sent it one more time. XDS 发件人: gsw...@pku.edu.cn 收件人: Felix Frolow , CCP4BB@JISCMAIL.AC.UK, x...@pku.edu.cn 已发送邮件: Tue, 18 Oct 2011 10:36:51 +0800 (CST) 主题: Re: [ccp4bb] IUCr committee

[ccp4bb] Phenix building residues not found in input sequence file

Hi everyone, Apparently my Phenix (1.6.3-473) is building in extra residues in the C-terminal region, which is not found in my input sequence file. It's trying to build a model which is longer than I expected. Phenix building 87 extra amino acids. Any clue what's wrong? I made sure that t

Re: [ccp4bb] IUCr committees, depositing images

Dear Enrico, Please don't get me wrong: what you are saying is not incorrect, but it is only half the story. On Tue, 2011-10-18 at 15:13 +0200, Enrico Stura wrote: > With improving techniques, we should always be making progress! Yes, of course! > If we are trying to answer a biological questio

Re: [ccp4bb] Dennis Ritchie

Dear Sabuj, Your opening remark made me worried that the facetious "what has he done since?" might be taken seriously ... . That was not what was intended! A variant of the joke was about a similar committee in charge of evaluating God's performance, and coming up with "Sure, he created the U

Re: [ccp4bb] Dennis Ritchie

The silence on this list was deafening. > group is saying: "OK, so he discovered fire and invented the wheel - but > what has he done since?". 1983 Turing Award 1990 IEEE Hamming medal 1999 National Medal of Technology 2011 Japan Prize for Information and Communications (while he was still alive

Re: [ccp4bb] IUCr committees, depositing images

For the record, the amount of disk storage space per unit cost has doubled every 14 months for the last 30 years. It's an exponential relationship: www.mkomo.com/cost-per-gigabyte So data generated at a very high rate today, will be trivial to store in the near future. That's not to say it is

[ccp4bb] CCP4 Study Weekend 2012 - Data Collection and Processing

Dear All, This is a reminder about this coming January's CCP4 Study Weekend taking place from the 4th - 6th of January at Warwick University in the UK. The topic for the 2012 meeting will be "Data Collection and Processing" and a provisional programme is now available. The meeting will cover al

Re: [ccp4bb] IUCr committees, depositing images

With improving techniques, we should always be making progress! If we are trying to answer a biological question that is really important, we would be better off improving the purification, the crystallization, the cryo-conditions instead of having to rely on processing old images with new so

Re: [ccp4bb] How can improve diffraction quality

Hello You can do dehydration of crystal to get better diffraction ...go through this reference Dehydration Converts DsbG Crystal Diffraction from Low to High Resolution Begoña Heras

Re: [ccp4bb] IUCr committees, depositing images

Hi Felix, Excuse my question, but what have you discovered about lysozyme that we haven't already known before which justifies all these efforts? After all, we're mostly after finding solutions to biological problems, aren't we? Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion

Re: [ccp4bb] How can improve diffraction quality

Silver bullet Additive screens Methylation Construct boundaries in situ proteolysis Have you got a ligand? Stick in in there! Do you have an expression tag? Cleave it/leave it on. What is in your protein buffer? Mess about with that? Temperature gradients How is your purity? How quickly are you

Re: [ccp4bb] How can improve diffraction quality

Hi You don't give any details of how you are collecting your data or what the protein is (small, medium, large, solvent content, unit cell etc etc). But at first glance your crystal is huge by "modern day standards". Very often large crystals are of poorer overall quality than smaller ones.

[ccp4bb] How can improve diffraction quality

 Dear ccp4 user I am facing one crucial problem regarding diffraction. Actually the size of my crystal is good enough 0.5mm but it  was diffracted only 4 A. The conditions of crystallization recipes are 4.5% PEG 1000, 0.1M Tris and 25mM Na citrate. I really need your suggestions regarding  ho

Re: [ccp4bb] IUCr committees, depositing images

I could not agree less. There is constant development of the software for refinement that allow to do things that were not possible or were not necessary in the past such as intelligent refinement of occupancies of mutually exclusive sites, entities and conformations. I frequently remeasure lyso

Re: [ccp4bb] IUCr committees, depositing images

Perhaps this kind of discussion that should be continued on the IUCr forums, once people have had a chance to register. However, to answer these particular points: On Tue, 2011-10-18 at 10:52 +, Chris Morris wrote: > Some crystals are hard to make, so storing all the data the best way to get

Re: [ccp4bb] Assay of enzyme from thermophile

You can do it without having to do an assay at high temperature, because the substrate stability would also change at higher temperature. What you could do is the following: 1. Use a PCR machine to heat the enzyme, and then cool it down. 2. Keep one fraction at 4C / RT separately. 3. Do the assays

Re: [ccp4bb] error message in scalepack

Solved. I run scalepack under C shell (csh) and seems it works fine. Fulvio Il giorno mar, 18/10/2011 alle 12.18 +0200, fulvio saccoccia ha scritto: > Dear ccp4bber, > I received the following message, during a run with scaling: > > forrtl: error (72): floating overflow > > does anyone know wh

Re: [ccp4bb] IUCr committees, depositing images

Some crystals are hard to make, so storing all the data the best way to get reproducibility. On the other hand, no one needs more images of lysozyme. So using the same standard for every deposition doesn't sound right. The discussion should be held on the basis of overall cost to the research b

[ccp4bb] Assay of enzyme from thermophile

Dear users, Pardon me for the non-crystallography related question, Can anyone provide some papers regarding the assay ofenzymes from hypertherphilic /thermophilic organisms? ie,assays at high temperatures..Thanking youWith RegardsM. Kavyashree -- This message has been scanned for viruses and dang

Re: [ccp4bb] Dennis Ritchie

Dear Miguel, Your list of two astounding achievements by Ritchie reminds me of an old satire of mutual assessment within academia, in cartoon form, showing a group of cavemen talking intensely and secretively to each other about another one who is standing anxiously in the distance. One of th

[ccp4bb] error message in scalepack

Dear ccp4bber, I received the following message, during a run with scaling: forrtl: error (72): floating overflow does anyone know what does it means and how can I overcome it? I am trying to scale 900 frames, with data integrated to 3.3 A resolution. Thanks in advance Fulvio Saccoccia, PhD s

[ccp4bb] IUCr discussion forum on diffraction data deposition

Thanks to John Helliwell for introducing the new IUCr forum at http://forums.iucr.org on diffraction data deposition. The Diffraction Data Deposition Working Group (DDDWG) has been established by the IUCr to address the growing calls within the crystallographic community for the deposition of prim

Re: [ccp4bb] buccaneer_pipeline failure (ccp4 6.2.0)

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 And you do have read access to /usr/local/ccp4/6.2.0/ccp4-6.2.0/share/python/CCP4pipeline.py (on our installation, the mode is actually 755, but I suppose 644 should be sufficient). You can set PYTHONVERBOSE to 1 or higher in the shell you start ccp4i

Re: [ccp4bb] buccaneer_pipeline failure (ccp4 6.2.0)

Mine reads: /usr/local/ccp4/6.2.0/ccp4-6.2.0/share/python:/usr/local/ccpnmr/ccpnmr1.0/python That should work, right? Where else can I look, for the failing import? This is a lettuce-fresh install, pulled straight off web and installed with all defaults. Cheers phx. On 18/10/2011 08:38, T

Re: [ccp4bb] Dennis Ritchie

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Miguel, There are a couple of well-written obituaries: http://www.wired.com/wiredenterprise/2011/10/dennis-ritchie/ http://edition.cnn.com/2011/10/14/tech/innovation/dennis-ritchie-obit-bell-labs/ To acknowledge his work, you might start you li

[ccp4bb] Head of Crystallography, Vertex

Posted on behalf of Vertex Pharmaceuticals (please do not reply directly to me!) Link for applicants: http://bs.serving-sys.com/BurstingPipe/adServer.bs?cn=tf&c=20&mc=click&pli=3398538&PluID=0&ord=[timestamp ] Head of Crystallography Oxfordshire Vertex creates new possibilities in medicine.

[ccp4bb] Dennis Ritchie

Hi community, I have been waiting for someone more knowledgeable to write about the passing away of Dennis Ritchie (8 October) especially after the recent obituaries posted in the list. I confess I know little about him, except: 1/ He created the C language ( and together with Brian Kernighan wro

Re: [ccp4bb] IUCr committees, depositing images

Dear Colleagues, Following on from my posting to the CCP4bb of yesterday an IUCr Forum has been set up for Public input on the diffraction data deposition future. Thus this Forum will record an organised set of inputs for future reference. Instructions on how to register at this Forum can be found

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

Just to add to what has been "said" (written) before: coiled coiled or simply helices can be very problematic for M.R.. Human sacrifice has never given any positive result (as reported in the literature as far as I know), but "heavy atom sacrifice" could be attempted ("heavy atom" includes in

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

Dear Napoleão, we solved this type of problem in a paper of 2004 (J. Mol. Biol. (2004) 342, 275–287) with the using of EPMR which use a evolutionary search algorithm, I will send you the paper later. It was 36aa dimeric coiled-coil and we had a lot of molecular replacement problems with other teste

Re: [ccp4bb] buccaneer_pipeline failure (ccp4 6.2.0)

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi Frank, it may not be the python binary itself but the PYTHONPATH which is incorrectly set. After initialising ccp4, mine reads tg@slartibartfast:~$ echo $PYTHONPATH /xtal/Suites/CCP4/ccp4-6.2.0/share/python: which is modified around