Re: [ccp4bb] validating a homlology model

2018-03-03 Thread Ed Pozharski
Assuming that your homology model is that of a dimer, you could put it in a large unit cell (just add CRYST1 record).  The only interface you will get from pisa will be your dimer interface. If your homology model is a monomer, then pisa will not help, of course, and you would need to

Re: [ccp4bb] question related to MTZ file

2015-01-03 Thread Ed Pozharski
I suspect the question might be about converting intensities to anplitudes.  If so ctruncate is your friend. Happy Connecting. Sent from my Sprint Samsung Galaxy S® 5 Original message From: Eleanor Dodson eleanor.dod...@york.ac.uk Date:01/03/2015 3:42 PM (GMT-05:00) To:

Re: [ccp4bb] water at the same exactly position

2014-10-29 Thread Ed Pozharski
Why? Merging waters like that in coot is a user error, and it does not happen too often.  I realize you are talking about changeable settings, but it would be really annoying if a refinement program kept removing water molecules that were placed manually because it does not fit some internal

Re: [ccp4bb] Merge PDB chains

2014-10-23 Thread Ed Pozharski
Edit the ATOM records? Sent on a Sprint Samsung Galaxy S® III div Original message /divdivFrom: luzuok luzuo...@126.com /divdivDate:10/23/2014 6:51 AM (GMT-05:00) /divdivTo: CCP4BB@JISCMAIL.AC.UK /divdivSubject: [ccp4bb] Merge PDB chains /divdiv /divDear all, Sorry to

Re: [ccp4bb] I222 - P22121 space-group ambiguity

2014-10-13 Thread Ed Pozharski
Yes, having different crystal forms in the same crystallization conditions is, while clearly uncommon, not unheard of. I had a case once where at least four different crystal forms were observed in crystals harvested from identically prepared drops.  It may be that there is some major set of

[ccp4bb]

2014-08-19 Thread Ed Pozharski
Try refining your model both ways (with and without covalent link) and see if electron density maps give you an indication.  At this resolution there will be some model bias, so be critical.  Sent on a Sprint Samsung Galaxy S® III div Original message /divdivFrom: rohit kumar

Re: [ccp4bb] cc1/2 value in hkl2000

2014-08-15 Thread Ed Pozharski
Probably the only way is to take unmerged scalepack output to aimless. Sent on a Sprint Samsung Galaxy S® III div Original message /divdivFrom: Faisal Tarique faisaltari...@gmail.com /divdivDate:08/15/2014 9:40 AM (GMT-05:00) /divdivTo: CCP4BB@JISCMAIL.AC.UK /divdivSubject:

Re: [ccp4bb] CC-half value ??

2014-08-15 Thread Ed Pozharski
Same here.  Ultimately, the KD test must be used in the end to finalize the resolution (keeping in mind recently discussed issues of effective resolution given data completeness).  I just want to add that at least some versions of aimless report overestimated resolution based on CC1/2 cutoff

Re: [ccp4bb] thin shell Rfree set selection

2014-08-13 Thread Ed Pozharski
By all means, try it both ways and see whether the R-Rfree gap narrows with random vs thin shell selection. Depending on resolution and data quality, you may also consider imposing NCS restraints. Sent on a Sprint Samsung Galaxy S® III div Original message /divdivFrom: Xianchi

Re: [ccp4bb] The modified DNA could not be linked to the downstream DNA in the COOT?

2014-07-15 Thread Ed Pozharski
You may need to 1) modify _chem_comp.group to be DNA in the cif-file 2) import the resulting cif-file in coot Cheers Sent on a Sprint Samsung Galaxy S® III div Original message /divdivFrom: Wang, Wei wew...@ucsd.edu /divdivDate:07/15/2014 5:14 AM (GMT-05:00) /divdivTo:

Re: [ccp4bb] emergency substitute for RT loop cover?

2014-07-07 Thread Ed Pozharski
Try to put your crystal into oil drop?  Sent on a Sprint Samsung Galaxy S® III div Original message /divdivFrom: Frank von Delft frank.vonde...@sgc.ox.ac.uk /divdivDate:07/07/2014 12:32 PM (GMT-05:00) /divdivTo: CCP4BB@JISCMAIL.AC.UK /divdivSubject: [ccp4bb] emergency

Re: [ccp4bb] Kabat, insertion codes refinement

2014-06-16 Thread Ed Pozharski
There is no actual requirement to use Kabat numbering, you can avoid it alrogether.  Some argue that L27A is actually 28th amino acid in the protein sequence, and labeling it as L27A is simply incorrect.  I would suggest doing refinement with plain numbering (no insertion codes) and changing it

Re: [ccp4bb] metal ion dominating density!

2014-06-05 Thread Ed Pozharski
Or, if for whatever reason sphere refine isn't an option, fix the metal and all of its ligands Sent on a Sprint Samsung Galaxy S® III div Original message /divdivFrom: Paul Emsley pems...@mrc-lmb.cam.ac.uk /divdivDate:06/05/2014 3:51 AM (GMT-05:00) /divdivTo:

Re: [ccp4bb] baverage: no tables were found in this file

2014-06-03 Thread Ed Pozharski
This may not work if a program implements its own algorithm for parsing command line parameters Sent on a Sprint Samsung Galaxy S® III div Original message /divdivFrom: Tim Gruene t...@shelx.uni-ac.gwdg.de /divdivDate:06/03/2014 8:27 AM (GMT-05:00) /divdivTo:

Re: [ccp4bb] baverage: no tables were found in this file

2014-06-03 Thread Ed Pozharski
Would a no-space symlink resolve this? Sent on a Sprint Samsung Galaxy S® III div Original message /divdivFrom: Mark J van Raaij mjvanra...@cnb.csic.es /divdivDate:06/03/2014 8:03 AM (GMT-05:00) /divdivTo: CCP4BB@JISCMAIL.AC.UK /divdivSubject: Re: [ccp4bb] baverage: no

Re: [ccp4bb] negative density around disulfide bond

2014-06-02 Thread Ed Pozharski
Try refining without disulfide bond - from the way density looks it might work.  Whether this is what happens in vivo is a different question entirely.  Sent on a Sprint Samsung Galaxy S® III div Original message /divdivFrom: Eze Chivi ezech...@outlook.com.ar

Re: [ccp4bb] (high) values of R-factors in outermost resolution shell

2014-06-02 Thread Ed Pozharski
My suggestion is to ignore Rmerge when making decisions about resolution cutoff.  While cc1/2 may still perhaps qualify for the recent discussion tag (is two years recent?), deeply flawed nature of the Rmerge concept is over a decade old. Sent on a Sprint Samsung Galaxy S® III div

Re: [ccp4bb] distinguish ligand binding sites within a protein

2013-11-20 Thread Ed Pozharski
there are other dedicated methods to do it that suffer less from side effects. Including the docking approach. Kind regards, Baerbel Quoting Ed Pozharski epozh...@umaryland.edu: If I understand the original post correctly, the binding sites in question are not chemically identical

Re: [ccp4bb] distinguish ligand binding sites within a protein

2013-11-19 Thread Ed Pozharski
are solid methods to determine some sort of relative affinities. I'd suggest to design mutants for either binding site and ITC measurements with the mutant proteins. This might also tell you if some sort of co-op exists between both sites. Baerbel Quoting Ed Pozharski epozh...@umaryland.edu

Re: [ccp4bb] Comparison of Water Positions across PDBs

2013-10-29 Thread Ed Pozharski
http://www.ccp4.ac.uk/html/watertidy.html On 10/29/2013 04:43 PM, Elise B wrote: Hello, I am working on a project with several (separate) structures of the same protein. I would like to be able to compare the solvent molecules between the structures, and it would be best if the waters that

Re: [ccp4bb] Is there someone work with Lipids?

2013-09-30 Thread Ed Pozharski
May I ask a question? This is a catch-22 situation. If you ask permission to ask a question, you are already asking a question. Answering this with no would probably create a wormhole. I'd also like to see a bulletin board where asking questions requires separate permission. When we

Re: [ccp4bb] Low 280 absorbance imidazole?

2013-08-22 Thread Ed Pozharski
On Thu, 2013-08-22 at 10:07 -0400, Bosch, Juergen wrote: Yes, I'm also surprised why people run gradients for the capturing step ? Because we can. Joking aside, I've seen some examples where protein eluted at relatively low imidazole and upon running the gradient there remains some (minimal)

Re: [ccp4bb] Low 280 absorbance imidazole?

2013-08-22 Thread Ed Pozharski
On Thu, 2013-08-22 at 13:58 -0400, Bosch, Juergen wrote: well if we hit the timer after lysis, say via cell disruptor then I have my eluted protein in less than 1 hour, including 40 minutes batch binding. then proceeds to wait six weeks for crystals to appear... :) Cheers, Ed. PS. There

Re: [ccp4bb] Low 280 absorbance imidazole?

2013-08-22 Thread Ed Pozharski
On Thu, 2013-08-22 at 14:22 -0400, Bosch, Juergen wrote: But when it sits and crystallizes it is cleaner - unless some opportunistic fungal contamination helps you trim off those nasty loops that you would have omitted anyhow from your model. Jurgen, Good point and admittedly I never

Re: [ccp4bb] Low 280 absorbance imidazole?

2013-08-21 Thread Ed Pozharski
According to Qiagen Since imidazole absorbs UV radiation at 280 nm, an elution profile measured at 280 nm while purifying a 6xHis tagged protein by FPLC will show an increase in absorbance above the background signal allowing quantitation of your protein. The absorbance of imidazole can vary

Re: [ccp4bb] Problems with SANS data analysis

2013-08-07 Thread Ed Pozharski
This question may be better suited for more small-angle-oriented forum, e.g. http://www.saxier.org/forum/ On 08/07/2013 11:22 AM, Remec, Mark wrote: Dear CCP4bb, I have a few questions concerning SANS data recently collected that I'm having trouble analyzing. The data was collected at 2

Re: [ccp4bb] mmCIF as working format?

2013-08-07 Thread Ed Pozharski
On 08/07/2013 01:51 PM, James Stroud wrote: In the long term, the MM structure community should perhaps get its inspiration from SQL For this to work, a particular interface must monopolize access to structural data. Then maintainers of that victorious interface could change the underlying

Re: [ccp4bb] mmCIF as working format?

2013-08-07 Thread Ed Pozharski
On 08/07/2013 03:54 PM, James Stroud wrote: On Aug 7, 2013, at 1:06 PM, Ed Pozharski wrote: On 08/07/2013 01:51 PM, James Stroud wrote: In the long term, the MM structure community should perhaps get its inspiration from SQL For this to work, a particular interface must monopolize access

Re: [ccp4bb] mmCIF as working format?

2013-08-07 Thread Ed Pozharski
James, On 08/07/2013 05:36 PM, James Stroud wrote: Anyone can learn Python in an hour and a half. Isn't this a bit of an exaggeration? Python is designed to be easy to learn, but we probably talking about different definitions of learning and anyone. I.e. programs would look like this

Re: [ccp4bb] mmCIF as working format?

2013-08-07 Thread Ed Pozharski
On 08/07/2013 05:54 PM, Nat Echols wrote: Personally, if I need to change a chain ID, I can use Coot or pdbset or many other tools. Writing code for this should only be necessary if you're processing large numbers of models, or have a spectacularly misformatted PDB file. Again, I'll repeat

Re: [ccp4bb] ctruncate bug?

2013-06-21 Thread Ed Pozharski
On 06/21/2013 10:19 AM, Ian Tickle wrote: If you observe the symptoms of translational NCS in the diffraction pattern (i.e. systematically weak zones of reflections) you must take it into account when calculating the averages, i.e. if you do it properly parity groups should be normalised

Re: [ccp4bb] ctruncate bug?

2013-06-19 Thread Ed Pozharski
Dear Kay and Jeff, frankly, I do not see much justification for any rejection based on h-cutoff. FrenchWilson only talk about I/sigI cutoff, which also warrants further scrutiny. It probably could be argued that reflections with I/sigI-4 are still more likely to be weak than strong so F~0

Re: [ccp4bb] sigma value in structure file

2013-06-17 Thread Ed Pozharski
The only thing that seems to make sense is bonds rmsd - but you should ask the annotator for specifics directly. If it is bonds rmsd, this has been discussed many times - just google rmsd bonds ccp4bb and look for most recent entries. On Mon, 2013-06-17 at 12:11 +0530, Faisal Tarique wrote:

[ccp4bb] ctruncate bug?

2013-06-17 Thread Ed Pozharski
I noticed something strange when processing a dataset with imosflm. The final output ctruncate_etc.mtz, contains IMEAN and F columns, which should be the conversion according to FrenchWilson. Problem is that IMEAN has no missing values (100% complete) while F has about 1500 missing (~97%

Re: [ccp4bb] ctruncate bug?

2013-06-17 Thread Ed Pozharski
in the morning when I get into the lab and let you know. Jeff On Mon, Jun 17, 2013 at 5:04 PM, Ed Pozharski epozh...@umaryland.edu mailto:epozh...@umaryland.edu wrote: I noticed something strange when processing a dataset with imosflm. The final output ctruncate_etc.mtz, contains

Re: [ccp4bb] Concerns about statistics

2013-06-15 Thread Ed Pozharski
On 06/14/2013 07:00 AM, John R Helliwell wrote: Alternatively, at poorer resolutions than that, you can monitor if the Cruickshank-Blow Diffraction Precision Index (DPI) improves or not as more data are steadily added to your model refinements. Dear John, unfortunately the behavior of DPIfree

Re: [ccp4bb] Concerns about statistics

2013-06-13 Thread Ed Pozharski
On Thu, 2013-06-13 at 08:44 -0700, Andrea Edwards wrote: In this case, the author should report a correlation coefficient along with the other standard statistics (I/sigI, Rmerg, Completeness, redundancy, ect.)? Won't hurt. What about Rpim instead of Rmerg? and if Rpim is reported, what

Re: [ccp4bb] Concerns about statistics

2013-06-13 Thread Ed Pozharski
. This is based predominantly on Scala/Aimless. Cheers, Ed. On Thu, 2013-06-13 at 18:20 +0200, Tim Gruene wrote: On 06/13/2013 06:16 PM, Ed Pozharski wrote: [...] With that said, I am pretty sure that in vast majority of cases structural conclusions derived with I/s=2 vs CC1/2=0.5 vs DR

Re: [ccp4bb] Extracting .pdb info with python

2013-06-06 Thread Ed Pozharski
ATOM records have fixed format so you can (and should) use string slicing instead, like so (one-liner) serial, aname, altloc, resn, chid, resi, insCode, x, y, z, occ, b, element, q = line[6:11], line[12:16], line[16], line[17:20], line[21], line[22:26], line[26], line[30:38], line[38:46],

Re: [ccp4bb] Extracting .pdb info with python

2013-06-06 Thread Ed Pozharski
On Thu, 2013-06-06 at 14:41 +1000, Nat Echols wrote: You should resist the temptation to write your own PDB parser; that way lies pain and suffering. There are multiple free libraries for Python that can be used for this task - I recommend either CCTBX or BioPython (probably the latter if you

Re: [ccp4bb] use only companies that you know to purchase chemicals

2013-05-29 Thread Ed Pozharski
On Wed, 2013-05-29 at 12:30 -0400, Jeremy Stevenson wrote: In this particular case you can see the website was registered in September of 2012, which is a good indication that it was set up just to scam people. Just curious - why registration date indicates unsavory nature of Jieke? -- After

Re: [ccp4bb] To build ssDNA to base pair with the other strand of DNA in coot

2013-05-29 Thread Ed Pozharski
I am wondering whether there is a function I could use to build the missing bases in one strand of the DNA to base pair with the other strand of DNA which is complete... Calculate-Other modeling tools- Base pair... -- Coot verendus est

Re: [ccp4bb] Short contact between symmetry equivalents

2013-05-27 Thread Ed Pozharski
It is probably a wrong question to ask here. Pretty much everything is tolerated by PDB during deposition, the report you get is an advice, not instruction. I wonder whether anyone has an example of the RCSB/PDBe/PDBj ever turning down submitted structure. The right question is whether the

Re: [ccp4bb] Short contact between symmetry equivalents

2013-05-27 Thread Ed Pozharski
On 05/27/2013 11:27 AM, ka...@ssl.serc.iisc.in wrote: Sir, Ok. It is an acetate ion which interacts with its symmetry equivalent ion only one of its oxygen atoms is closer to its symmetry equivalent and not the entire ion. So do I need to give lower occupancy for this ion? Thank you Regards

Re: [ccp4bb] Short contact between symmetry equivalents

2013-05-27 Thread Ed Pozharski
On 05/27/2013 12:14 PM, Kavyashree Manjunath wrote: Later I tried with 0.8, 0.99 for which the map was normal and also validation did not report it as short contact. Is it ok if I give 0.99 occupancy? Validation most likely will not report any short contacts if occupancy is 1. If the distance

Re: [ccp4bb] cryo condition

2013-05-23 Thread Ed Pozharski
Matt, with this technique, how do you prevent crystal from drying up (other than doing it fast)? I know Thorne's group does this trick under oil. If you take no extra precautions, do you have an estimate of how often diffraction is destroyed by this? On the other hand, it's quite possible

Re: [ccp4bb] DNA version converter

2013-05-22 Thread Ed Pozharski
, Tim On 05/21/2013 10:40 PM, Ed Pozharski wrote: On 05/21/2013 04:35 PM, Francis Reyes wrote: Since you're using buster, have you tried global phasing's own pdbvconv tool? Naturally, but it leaves file unchanged. -- Edwin Pozharski, PhD, Assistant Professor University of Maryland

Re: [ccp4bb] DNA version converter

2013-05-22 Thread Ed Pozharski
On Wed, 2013-05-22 at 18:09 +0200, Tim Gruene wrote: the answers you received were correct with respect to the question you asked. If they are not satisfactory, you have not given sufficient information. Tim, Not sure when I expressed any dissatisfaction with replies I received. I asked

Re: [ccp4bb] DNA version converter

2013-05-22 Thread Ed Pozharski
and give a helpful answer. Regards, Tim On 05/22/2013 07:55 PM, Ed Pozharski wrote: On Wed, 2013-05-22 at 18:09 +0200, Tim Gruene wrote: the answers you received were correct with respect to the question you asked. If they are not satisfactory, you have not given sufficient

[ccp4bb] DNA version converter

2013-05-21 Thread Ed Pozharski
Does anyone have a script to convert pdb file with DNA atom records from v3 back to v2? I can certainly right my own and asking only if you already have it written. Strictly speaking, this is not ccp4-related - apparently, buster expects the old format. Cheers, Ed. -- Oh, suddenly

Re: [ccp4bb] DNA version converter

2013-05-21 Thread Ed Pozharski
On 05/21/2013 04:35 PM, Francis Reyes wrote: Since you're using buster, have you tried global phasing's own pdbvconv tool? Naturally, but it leaves file unchanged. -- Oh, suddenly throwing a giraffe into a volcano to make water is crazy? Julian,

Re: [ccp4bb] question about CCP4 scripts

2013-05-09 Thread Ed Pozharski
At this point you do have the scalepack2mtz output file (BTW, imosflm/aimless is wholeheartedly recommended by this convert), and you can easily extract all the info from there. There is mtzdmp, of course, but it's easier to parse the actual mtz file (hey, the records are actually text). Like

Re: [ccp4bb] Program or server to predict Kd from complex structure

2013-04-18 Thread Ed. Pozharski
Don't believe such program/server does exist.   Notice that you are asking for something that *can* predict Kd.  One can *try* making such predictions and they may even be routinely in the ballpark, assuming that you are satisfied with being routinely off by, say, an order of magnitude.  One

Re: [ccp4bb] salt or not?

2013-04-15 Thread Ed. Pozharski
Protein-DNA complex crystal with channels too small for the dye is *extremely* unlikely, imho. Original message From: Ulrike Demmer ulrike.dem...@biophys.mpg.de Date: 04/15/2013 8:48 AM (GMT-05:00) To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] salt or not? Dear

Re: [ccp4bb] DNA structures superimpose

2013-04-12 Thread Ed. Pozharski
Doesn't lsqkab work? It just needs proper atom matching.  Coot definitely does superimpose DNA.  One problem is that simple-lsq works on a single chain, but you can trick it by changing chain id and renumbering the other strand. As for helix rotation, you can derive it from rotation reported

Re: [ccp4bb] CCP4 Update victim of own success

2013-04-12 Thread Ed Pozharski
On 04/12/2013 06:03 PM, Nat Echols wrote: On Fri, Apr 12, 2013 at 2:45 PM, Boaz Shaanan bshaa...@exchange.bgu.ac.il mailto:bshaa...@exchange.bgu.ac.il wrote: Whichever way the input file for the run is prepared (via GUI or command line), anybody who doesn't inspect the log file at the

Re: [ccp4bb] Building ideal B DNA model in Coot

2013-04-06 Thread Ed Pozharski
On 04/04/2013 04:51 PM, 李翔 wrote: Hi everyone, I met a problem when trying to build ideal DNA model in Coot. The calculated DNA looks less than 10.5 bp/ turn, probably is about 10 bp/ turn. Is there a way for me to change the pitch to make it 10.5 bp/turn in Coot? Thanks for your kind

Re: [ccp4bb] COOT usage for structure comparison

2013-04-04 Thread Ed Pozharski
On 04/04/2013 04:29 AM, Tim Gruene wrote: Dear --, Are we, the ccp4bb community, recently on the hunt to find new and exciting ways to make sure people stop asking questions? Gentleman from Moscow has clearly disclosed his full name and affiliation, but perhaps I am wrong and subtle

Re: [ccp4bb] Rfree reflections

2013-03-26 Thread Ed. Pozharski
As I recall, number of reflections set aside for cross-validation also affects stability of sigmaA estimates.  With 500 reflections and 20 resolution shells you are down to 25 reflections per shell, which may be a bit too low. Original message From: Robbie Joosten

Re: [ccp4bb] Isothermal titration calorimetry

2013-03-26 Thread Ed. Pozharski
This might have changed, but in the past file formats were different.   Microcal files are text, while TA's are binary.  I do have the actual description of TA's format if anyone is interested, but it must be easier to use native text export than write a converter.  Original message

Re: [ccp4bb] How to convert file format from CNS to CCP4

2013-03-23 Thread Ed Pozharski
On 03/23/2013 09:59 AM, Wei Feng wrote: Can you help me to check out why these maps can not be converted by sftools? sftools is not for manipulating map files. Mapman from uppsala software factory would be a good choice. xdlmapman, a gui frontend to it, used to be part of ccp4. -- Oh,

Re: [ccp4bb] Philosophical question

2013-03-19 Thread Ed Pozharski
On 03/19/2013 02:41 PM, Jacob Keller wrote: I don't understand this argument, as it would apply equally to all features of the theoretical LUCA No it won't. Different features would have different tolerance levels to modifications. Philosophically, one is wrong to expect that living

Re: [ccp4bb] Philosophical question

2013-03-19 Thread Ed Pozharski
Jacob, So you'd have to explain why the codon convention is so intolerant/invariant relative to the other features--it seems to me that either it is at an optimum or there is some big barrier holding it in place. Because altering codon convention will result in massive translation errors.

Re: [ccp4bb] Strange density in solvent channel and high Rfree

2013-03-15 Thread Ed Pozharski
Check for translational NCS And you are way too conservative with resolution. Even those holding onto the Rmerge-dictated past would probably acquiesce to lower I/sig cutoff. If you are using aimless, follow its recommendations based on CC1/2, it's good for you. Cheers, Ed. On Fri,

Re: [ccp4bb] statistical or systematic? bias or noise?

2013-03-13 Thread Ed Pozharski
Pete, Actually, I was trying to say the opposite - that the decision to include something in the model (or not) could change the nature of the error. Duly noted Pete PS - IIUC := ? IIUC - If I Understand Correctly -- Bullseye! Excellent shot, Maurice.

Re: [ccp4bb] [ccp4b] statistical or systematic? bias or noise?

2013-03-13 Thread Ed Pozharski
Adam, OK, seems like you are going with it's always statistical error we just don't yet know what it is option. Ed. On Tue, 2013-03-12 at 16:15 +, Adam Ralph wrote: Hi Ed, You can have both types of error in a single experiment, however you cannot determine statistical

Re: [ccp4bb] statistical or systematic? bias or noise?

2013-03-13 Thread Ed Pozharski
Kay, the latter is _not_ a systematic error; rather, you are sampling (once!) a statistical error component. OK. Other words, what is potentially removable error is always statistical error, whether it is sampled or not. So is it fair to say that if there are some factors that I either do

Re: [ccp4bb] statistical or systematic? bias or noise?

2013-03-13 Thread Ed Pozharski
the other uncontrollable errors. Cheers -- Ian On 11 March 2013 19:04, Ed Pozharski epozh...@umaryland.edu wrote: Ian, thanks for the quick suggestion. On Mon, 2013-03-11 at 18:34 +, Ian Tickle wrote: Personally I tend to avoid

Re: [ccp4bb] statistical or systematic? bias or noise?

2013-03-13 Thread Ed Pozharski
OK. Other words, what is potentially removable error is always statistical error, whether it is sampled or not. Clarification - what I meant is potentially removable by proper sampling and reducing standard error to zero with infinite number of measurements. Not removable by better

Re: [ccp4bb] statistical or systematic? bias or noise?

2013-03-13 Thread Ed Pozharski
Ian, On Wed, 2013-03-13 at 19:46 +, Ian Tickle wrote: So I don't see there's a question of wilfully choosing to ignore. or not sampling certain factors: if the experiment is properly calibrated to get the SD estimate you can't ignore it. So perhaps I can explain better by using the same

[ccp4bb] qtrview command line options

2013-03-11 Thread Ed Pozharski
Is there some way of opening a log file (specifically, the pointandscale.log that imosflm bridge to scala generates) with qtrview from command line? I tried, of course, this qtrview pointandscale.log but it opens empty, no log-file. I tried qtrview -h and qtrview --help and man qtrview but

[ccp4bb] statistical or systematic? bias or noise?

2013-03-11 Thread Ed Pozharski
Salve, I would like to solicit opinions on a certain question about the relationship between statistical and systematic error. Please read and consider the following in its entirety before commenting. Statistical error (experiment precision) is determined by the degree to which experimental

Re: [ccp4bb] statistical or systematic? bias or noise?

2013-03-11 Thread Ed Pozharski
Tim, On Mon, 2013-03-11 at 18:51 +0100, Tim Gruene wrote: I don't share your opinion about a single measurement translating into a systematic error. I would call it a poorly designed experiment in case you were actually iterested in how accurately you determined the protein concentration.

Re: [ccp4bb] statistical or systematic? bias or noise?

2013-03-11 Thread Ed Pozharski
Ian, thanks for the quick suggestion. On Mon, 2013-03-11 at 18:34 +, Ian Tickle wrote: Personally I tend to avoid the systematic vs random error distinction and think instead in terms of controllable and uncontrollable errors: systematic errors are potentially under your control (given a

Re: [ccp4bb] statistical or systematic? bias or noise?

2013-03-11 Thread Ed Pozharski
Pete, On Mon, 2013-03-11 at 13:42 -0500, Pete Meyer wrote: My take on it is slightly different - the difference seems to be more on how the source of error is modeled (although that may dictate changes to the experiment) rather than essentially depending on how the experiment was

Re: [ccp4bb] [Err] Re: [ccp4bb] statistical or systematic? bias or noise?

2013-03-11 Thread Ed Pozharski
By the way, am I the only one who gets this thing with every post? If anyone can ask Jin Kwang (liebe...@korea.ac.kr) to either clean up his mailbox or unsubscribe, that would be truly appreciated. Delete button is easy and fun to use, but this has been going on for quite some time. On Tue,

Re: [ccp4bb] compiling refmac5 on Ubuntu 12.04

2013-03-06 Thread Ed Pozharski
On 03/04/2013 10:02 AM, Marcin Wojdyr wrote: It also puzzled me, but I haven't done more careful benchmarking yet. What did you get after compiling refmac? My numbers are not as impressive, but I also get quite detectable improvement, from 35s to 27s (ccp4-6.3.0 vs compiled from source). This

Re: [ccp4bb] compiling refmac5 on Ubuntu 12.04

2013-03-06 Thread Ed Pozharski
checking by running the tests provided with the suite. Aggressive optimization can be a source of bugs. Best regards Thierry -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Ed Pozharski Sent: Monday, March 04, 2013 8:55 AM To: CCP4BB@JISCMAIL.AC.UK

Re: [ccp4bb] compiling refmac5 on Ubuntu 12.04

2013-03-04 Thread Ed Pozharski
Adam, On Mon, 2013-03-04 at 09:56 +, Adam Ralph wrote: One of the first routines called by CCP4 progs is ccp4fyp. This initialises the CCP4 environment. I think you might have missed in my original post that I get an error when I *do* source ccp4 environment. Does the error occur with

Re: [ccp4bb] compiling refmac5 on Ubuntu 12.04

2013-03-04 Thread Ed Pozharski
Indeed, the problem goes away when -static flag is omitted. Interestingly, the resulting binary dependencies do not include any ccp4-related libraries. For those interested, I was able to track the segfault down to the close() operator - so basically it fails when closing a file opened with

Re: [ccp4bb] compiling refmac5 on Ubuntu 12.04

2013-03-04 Thread Ed Pozharski
On Mon, 2013-03-04 at 11:37 +, Marcin Wojdyr wrote: Running times were, correspondingly, 32.2s, 35.1s and 18.7s. Numbers are almost too impressive to believe :) How does it compare with ifort (which I thought should be the fastest option on intel processors and thus unavailable (not free)

Re: [ccp4bb] compiling refmac5 on Ubuntu 12.04

2013-02-28 Thread Ed Pozharski
Adam, I am not compiling CCP4, just refmac. IIUC, all that sourcing ccp4.setup does is it sets $CLIB for refmac makefile to find libccp4c and libccp4f. And presumably lapack and libblas, but that's a separate issue. On Thu, 2013-02-28 at 10:28 +, Adam Ralph wrote: Hi Ed, It looks

[ccp4bb] compiling refmac5 on Ubuntu 12.04

2013-02-27 Thread Ed Pozharski
I am trying to compile refmac from source on a machine running Ubuntu 12.04. In a nutshell, after some troubleshooting I end up with executable that generates a segmentation fault. Log-file states that CCP4 library signal ccp4_parser:Failed to open external command file (Success)

Re: [ccp4bb] Link problem with Refmac.

2013-02-21 Thread Ed. Pozharski
We might have just found a new recurring discussion - what to do with insertion codes! I am sure the opinion split is close to 50/50. Personally, I don't think insertion codes make sense in the first place. Are catalytic triad residues always the same distance from the N-terminus? No. The

Re: [ccp4bb] Renumbering and retaining state information pdb file

2013-02-14 Thread Ed. Pozharski
There should be many ways to do this.  You can split the file, renumber with pdbset, and then reassemble it.  This may be useful http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Useful_scripts_(aka_smart_piece_of_code) Cheers,  Ed Original message From: Amar Joshi

Re: [ccp4bb] S-nitrosylation protein

2013-02-13 Thread Ed. Pozharski
Maybe you can try different energies hoping that damage is wavelength dependent.  It must be dose dependent though, so you may consider merging short sweeps from multiple crystals. Original message From: Uma Ratu rosiso2...@gmail.com Date: To: CCP4BB@JISCMAIL.AC.UK

Re: [ccp4bb] refmac5 MMA bug

2013-02-11 Thread Ed Pozharski
On Mon, 2013-02-11 at 09:56 +0100, Robbie Joosten wrote: This is a 'compatability' option in Refmac that internally renames atoms. If you comment out 'MMA .C7 CM' in your mon_lib_list.cif file, the problem will disappear. Robbie, thanks a lot - this fixes it. Is this

[ccp4bb] refmac5 MMA bug

2013-02-10 Thread Ed Pozharski
I see a strange issue with a model that includes O1-methyl-mannose (three letter code MMA). Basically, refmac fails and says that C7 is missing in the model while CM is absent from the library. The problem is that there is no CM atom in the pdb file, while C7 is right there. This happens

Re: [ccp4bb] protein crystals or salt crystals

2013-02-08 Thread Ed. Pozharski
Patrick, Something related: http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Conditions_prone_to_salt_crystallization Truth be told, we recently had a major breakthrough with the peg/fluoride condition I came to consider a useless salt crystal generator.  So tables like these are

Re: [ccp4bb] protein crystals or salt crystals

2013-02-08 Thread Ed Pozharski
On Fri, 2013-02-08 at 09:13 -0500, Edward A. Berry wrote: I like to take a 5-sec 180* oscillation which gives plenty of spots in a nice pattern for a salt crystal Second that It also confuses bystanders really well - what a strange diffraction pattern - half salt (small unit cell) / half

Re: [ccp4bb] protein crystals or salt crystals

2013-02-08 Thread Ed Pozharski
On Fri, 2013-02-08 at 14:53 +0400, Evgeny Osipov wrote: Protein crystals behave rather as gelatine and not as solid I'd have to disagree on that. Protein crystals are fragile but not soft. If your crystals are like gelatine it's unusual. It has been demonstrated that elastic properties of

Re: [ccp4bb] protein crystals or salt crystals

2013-02-08 Thread Ed Pozharski
On Fri, 2013-02-08 at 09:57 -0500, Jacob Keller wrote: do you have a reference quickly on hand http://www.ncbi.nlm.nih.gov/pubmed/8129868 and references therein http://www.sciencedirect.com/science/article/pii/S0022024801010922 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1300955/ The last

Re: [ccp4bb] protein crystals or salt crystals

2013-02-08 Thread Ed Pozharski
On Feb 8, 2013, at 9:23 AM, Ed Pozharski wrote: On Fri, 2013-02-08 at 14:53 +0400, Evgeny Osipov wrote: Protein crystals behave rather as gelatine and not as solid I'd have to disagree on that. Protein crystals are fragile

Re: [ccp4bb] gedit on mac terminal

2013-01-26 Thread Ed. Pozharski
Try this http://www.mac-forums.com/forums/os-x-apps-games/239657-gedit-command-not-found-terminal.html Original message From: LISA science...@gmail.com Date: To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] gedit on mac terminal Hi all, I installed gedit on my mac

[ccp4bb] engh huber

2013-01-14 Thread Ed Pozharski
To what extent modern geometric restraints have been upgraded over original EnghHuber? And where I can find a consensus set of values (with variances)? For example, Fisher et al., Acta D68:800 discusses how histidine angles change with protonation, and refers to EnghHuber when it says that

Re: [ccp4bb] engh huber

2013-01-14 Thread Ed Pozharski
Article in the Tables is the answer to my question about the latest EnghHuber parameters. These still don't match Fig.6 from Fisher, but I am OK with using Tables for my internal purposes. Thanks to Mitchell and Dale for prompt response. Cheers, Ed. -- After much deep and profound brain

Re: [ccp4bb] How to merge data from 2 separate sections of same crystal

2012-12-10 Thread Ed Pozharski
On 12/10/2012 08:45 PM, Yuri Pompeu wrote: hello everyone, I have collected data on a problematic crystal. (first mistake...) Images spanning phi angles 45-80 look ok and usable, also images 229-279 are usable (index well and merge well too). How can I combine the 2 separate .mtz files from

Re: [ccp4bb] thanks god for pdbset

2012-12-05 Thread Ed Pozharski
Francois, I did not realize Phil Evans is god (perhaps a minor one as he did not yet earn a capital G). I do concur that insertion code is evil. I had to re-refine an old antibody structure recently and it messes up coot sequence window and breaks refmac bond restraints. Evil, evil,.evil.

Re: [ccp4bb] thanks god for pdbset

2012-12-05 Thread Ed Pozharski
On Wed, 2012-12-05 at 17:02 +0100, Robbie Joosten wrote: Does 128A come before or after 128? Robbie, shouldn't it simply depend on which residue record comes first in the pdb file? Ed. -- Oh, suddenly throwing a giraffe into a volcano to make water is crazy?

Re: [ccp4bb] Mg++ interactions

2012-11-30 Thread Ed Pozharski
On Tue, 2012-11-27 at 21:46 -0800, William G. Scott wrote: Are Mg++ ions ever observed to chelate primary amines? MESPEUS reports, for example, 13 structure where magnesium is coordinated by a lysine. 7 with arginines and a bunch of asn/gln side chains as well. It does not prove, of course,

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