Re: [ccp4bb] To archive or not to archive, that's the question!

Dear Gerard K, Many thanks indeed for this. Like Gerard Bricogne you also indicate that the location option being the decentralised one is 'quite simple and very cheap in terms of centralised cost'. The SR Facilities worldwide I hope can surely follow the lead taken by Diamond Light Source and P

Re: [ccp4bb] Seeded rescreening with robot?

By popular request here's my favorite version of the in-screen seeding. We use a Mosquito but it doesn't have to be a specific robot as long as it can dispense relatively tiny volumes of seed stock. Caveats: (1) if I am desperate enough to do this, then the situation is pretty bad indeed and I don

Re: [ccp4bb] To archive or not to archive, that's the question!

As the poster who mentioned the $1000 - $3000 per terabyte per year figure, I should point out that the figure originated not from "La La land" but from an NSF RDLM workshop in Princeton last summer. Certainly the actual costs may be higher or lower depending on economies/diseconomies of scale a

Re: [ccp4bb] To archive or not to archive, that's the question!

Dear Gerard, I think that a major achievement of this online debate will have been to actually get you to carry out a constructive analysis (an impressive one, I will be the first to say) of this question, instead of dismissing it right away. It is almost as great an achievement as getting th

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Re: [ccp4bb] To archive or not to archive, that's the question!

On Friday, October 28, 2011 02:02:46 pm Gerard DVD Kleywegt wrote: I'm a tad disappointed to be only in fourth place, Colin! What has the Pope ever done for crystallography? http://covers.openlibrary.org/b/id/5923051-L.jpg Fock'n'Pope! Great find, Ethan! So maybe he deserves fourth place

Re: [ccp4bb] To archive or not to archive, that's the question!

On Friday, October 28, 2011 02:02:46 pm Gerard DVD Kleywegt wrote: > I'm a tad disappointed to be only in fourth place, Colin! > What has the Pope ever done for crystallography? http://covers.openlibrary.org/b/id/5923051-L.jpg -- Ethan A Merritt Biomolecular Structure Center, K-428 Health

Re: [ccp4bb] To archive or not to archive, that's the question!

Gerard I said in INCREASING order of influence/power i.e. you are in first place. Ooo! *Now* it makes sense! :-) --Gerard The joke comes from " I used to think if there was reincarnation, I wanted to come back as the President or the Pope or a .400 baseball hitter. But now I want to com

Re: [ccp4bb] To archive or not to archive, that's the question!

Gerard I said in INCREASING order of influence/power i.e. you are in first place. The joke comes from " I used to think if there was reincarnation, I wanted to come back as the President or the Pope or a .400 baseball hitter. But now I want to come back as the bond market. You can intimidate ev

[ccp4bb] To archive or not to archive, that's the question!

Hi all, It appears that during my time here at Cold Spring Harbor, I have missed a small debate on CCP4BB (in which my name has been used in vain to boot). I have not yet had time to read all the contributions, but would like to make a few points that hopefully contribute to the discussion an

[ccp4bb] NCS 2-fold perpendicular to crystal 2-fold

Hello Everyone, I have data sets that scaled fairly welll in C2 2 21, but intensity statistics suggested twinning. I was able to solve the structure in P1 21 1 (Rwork0.19/Rfree0.24 at 2.3A) with OK looking maps. I notice that I have 2-fold NCS that is paralell to the crystallographic A axis, pe

[ccp4bb] shuttered vs continuous data collection

Changed the subject line to try and keep the original thread on-topic. George is right that the acceleration/decelleration introduces error, but only in what I like to call "standing start" mode. These days I think most facilities use "running starts" where the spindle is brought up to the de

Re: [ccp4bb] Seeded rescreening with robot?

I would be glad to share ours. Artem On Oct 28, 2011 1:29 PM, "Watson, Randy" wrote: > Hi all, > > I am trying to optimize crystals and have heard of a technique where one > can prepare a seedstock from existing crystals and use it to broadly > re-screen from scratch for hits in new conditions.

Re: [ccp4bb] raw data deposition

Hi Francis, Even though they are not published, there are enough models in the PDB for which reevaluation of the crystallographic data leads to new biological insight. Unfortunately, a lot of the insight is of the type "that ligand doesn't really bind, or at least not in that pose". Another nice o

[ccp4bb] Phaser: ensemble not set

Subject: Phaser: ensemble not set Hello: I try to use Phaser under MR. The program complain: ensemble not set. The ensemble box keeps blank and does not allow to click. I use: ccp4-6.2.0 Window Vista Business Thanks for advice ROS

[ccp4bb] Seeded rescreening with robot?

Hi all, I am trying to optimize crystals and have heard of a technique where one can prepare a seedstock from existing crystals and use it to broadly re-screen from scratch for hits in new conditions. I have access to a mosquito robot and was wondering if anyone has a protocol or recommendatio

Re: [ccp4bb] raw data deposition

On Friday, October 28, 2011 08:29:46 am Boaz Shaanan wrote: > Besides, I thought that by now there are some standards on how data should > be processed > (this has been discussed on this BB once every few months, if I'm not > mistaken). If this is true, I must not have got the memo! I hear

Re: [ccp4bb] raw data deposition (off-list)

Dear Petr, I agree that we need tools to validate processing methods, but these tools will not come from pure thought alone: they will need vast amount of raw data with a full range of problematic features so that the ideas of new approaches and the algorithms to implement them can be develop

[ccp4bb] RE : [ccp4bb] RE : [ccp4bb] refmac 5.6 ccp4 6.2.0

Thanks all for your suggestions, Here's a little summary of my recent tests. I am currently using "WEIGHT AUTO" and BREF MIXED with a pdb file that contains ANISOU definition for all atoms except hydrogens. Final results for "BREF MIXED" refinement : InitialFinal

Re: [ccp4bb] raw data deposition

On Oct 27, 2011, at 11:56 PM, James Stroud wrote: > This is a poor criterion on which to base any conclusions or decisions. We > can blame the lack of examples on unavailability of the data. Agreed. Reprocessing the data resulting in a a different biological result is my personal reason and mo

Re: [ccp4bb] raw data deposition

I have said my piece of the issue of depositing but there is one comment I would like to address. Besides, I thought that by now there are some standards on how data should > be processed (this has been discussed on this BB once every few months, if > I'm not mistaken). Isn't that part of the vali

Re: [ccp4bb] RE : [ccp4bb] refmac 5.6 ccp4 6.2.0

Dear Pierre Resolution seems to be good enough for full anisotropic refinement. Why don't you try this and see if it stabilises refinement. regards Garib On 28 Oct 2011, at 16:22, LEGRAND Pierre wrote: > Dear Ed, > Not in my case. I still do *restrained* refinement. > I use: > refi type REST -

[ccp4bb] Fwd: Re: [ccp4bb] refmac 5.6 ccp4 6.2.0

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Sorry, "should NOT appear in the list of deviations", of course! - Original Message Subject: Re: [ccp4bb] refmac 5.6 ccp4 6.2.0 Date: Fri, 28 Oct 2011 17:39:06 +0200 From: Tim Gruene Reply-To: Tim Gruene To: CCP4BB@JISCMAIL.AC.UK

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Re: [ccp4bb] RE : [ccp4bb] refmac 5.6 ccp4 6.2.0

Hi my two cents ... At I would use full anisotropic refinement only with relaxed weights on B values. Weight "50" seems to me very very loose (but I haven't seen the log file). I would use weight auto and then look at the refmac log file. The Log file tells you what is the weight matrix being used

Re: [ccp4bb] refmac 5.6 ccp4 6.2.0

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear all, If those hydrogens are in riding position, their coordinates are calculated and should not be refined at all, isn't it? Hence they should appear in the list of deviations at all. Are the hydrogens present in the PDB file? Does it work to de

Re: [ccp4bb] raw data deposition

I don't think anyone is considering archiving all images *as a first step*! I think the obvious first step is to try to get depositors of new structures to the PDB to deposit images at the same time, which to me seems trivially easy and has a reasonably high benefit:cost ratio. Let's just do it, ma

Re: [ccp4bb] raw data deposition

Hi Jacob, There is (very) BIG difference between depositing images for deposited structures and depositing all images ever recorded by any crystallographer on the planet. In the case you presented, A and B can settle the issue by looking at each other's images whether through the database or by

[ccp4bb] RE : [ccp4bb] refmac 5.6 ccp4 6.2.0

Dear Ed, Not in my case. I still do *restrained* refinement. I use: refi type REST - resi MLKF - meth CGMAT - bref MIXED ncyc 10 blim 0.1 200.0 With both: weight MATRIX 50 or weight AUTO it gives the same problem. I have also tested the latest refmac5 version (Refmac_5.6.0119) and late

Re: [ccp4bb] raw data deposition

Dear Jacob, See the paper by J. Wang cited at the end of Francis Reyes's message under this thread yesterday: it is a case of exactly what you are talking about. With best wishes, Gerard. -- On Fri, Oct 28, 2011 at 10:05:44AM -0500, Jacob Keller wrote: > What about a c

Re: [ccp4bb] raw data deposition

Which trps protein check the MSGPP or SGPP website they might have what you are looking for. Jürgen .. Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry & Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street,

Re: [ccp4bb] raw data deposition

What about a case in which two investigators have differences about what cutoff to apply to the data, for example, A thinks that Rsym of 50 should be used regardless of I/sig, and B thinks that I/sig of 2 and Rpim should be used. Usually A would cut off the data at a lower resolution than B, especi

Re: [ccp4bb] raw data deposition

Hi Boaz, I see your point in regards to making a database of "all" diffraction images. The argument I clearly failed to make effectively was that improvement of structures can frequently yield useful biological information which is why I believe that, at the least, images of deposited structures s

Re: [ccp4bb] refmac 5.6 ccp4 6.2.0

Just to verify, is this by any chance *unrestrained* refinement? On Fri, 2011-10-28 at 09:37 +0200, Tim Gruene wrote: > -BEGIN PGP SIGNED MESSAGE- > Hash: SHA1 > > Dear Kenneth A. Satyshur, > > what is your weight set to? If it is set to 'auto', try setting it to a > specific value and l

Re: [ccp4bb] Weird blob appears

On Thu, 2011-10-27 at 20:46 -0500, Jacob Keller wrote: > I went back to using > the original mtz from scala Curious. What were you using - the refmac output mtz? Just for the record - the refmac output mtz contains *modified* amplitudes, and Garib said many times it should not be used as the in

Re: [ccp4bb] [PyMOL] Putting a protein molecule into a grid and traversing through the grid

Hi Anasuya, at least, Gerard Kleywegt's program "moleman2" from the Uppsala Software Factory has a command "XYz ALign_inertia_axes" should do your first task. From the moleman2 manual: "This will move the currently selected atoms such that their centre-of-gravity i

Re: [ccp4bb] raw data deposition

I must "say" that there were some emails exchanged between me and Gerard later, in which I pointed out that I wasn't against deposition of images (data frames). In fact, if SR sources kept user's data there would be one more structure from here in the PDB: HDD failure here, the data on a mirror

Re: [ccp4bb] raw data deposition

Dear Remy, You are right, and I was about to send a message confessing that I had been rash in my response to Fred's. Another person e-mailed me off-list to point out that sometimes a structure can be quickly solved, but that doing all the rest of the work involved in wrapping that structure

Re: [ccp4bb] raw data deposition

Hi Katherine, It sounds as if you had all you needed to correct other people's (and your own) errors, as you described,  in the existing database (EDS, PDB) or your own data, right? That hardly justifies establishing a new database of which at least 80-90% is worthless. Furthermore, since much

Re: [ccp4bb] RE : [ccp4bb] refmac 5.6 ccp4 6.2.0

Hi All I think that is the reason. In version of refmac (with new dictio uses new pdb v3 hydrogen naming and there are a lot of differences. regards Garib On 28 Oct 2011, at 10:00, LEGRAND Pierre wrote: > Hi Kenneth, > > I am experiencing exactly the same problem, in similar conditions: refi

[ccp4bb] RE : [ccp4bb] refmac 5.6 ccp4 6.2.0

Hi Kenneth, I am experiencing exactly the same problem, in similar conditions: refinement with H at 0.84 A resolution. >From a bunch of tests made yesterday, I have found that it is linked to >incompatibilities between cif dictionaries definitions and H names in the >input PDB. For me, one si

Re: [ccp4bb] raw data deposition

Dear Fred, Frankly, with respect, this sounds to me like fanciful and rather non-sensical paranoia. The time frame for public disclosure of all SR data has been quoted at 5 years, or something of that order. If someone has been unable to solve a structure 5 years after having collected data o

[ccp4bb] scalepack2mtz for trigonal crystal

Dear colleagues We obtained the trigonal crystals (s.g. R3 or R32). We processed X-ray intensity data using HKL2000, which chose the hexagonal axes (a=b; alpha=beta=90, gamma=120). Then we tried converting the data to mtz using scalepack2mtz, but received an error message. LW: severe wa

Re: [ccp4bb] raw data deposition

D Bonsor wrote: and allow someone else to have ago at solving the structure. I'd be careful there if there was a motion to try to implement a policy at SR sources (for academic research projects) to make it compulsory to publically release all data frames after a period (1 year ? 2 years ?

Re: [ccp4bb] PDB header info wrong.

Dear Ian, Truncating the data to 10A and then filling in the missing hkl values and including them with Fo replaced by e.g. DFc is an established way of improving the maps (at the cost of a little model bias), but the novel twist in your example was the assignment of R-free flags to these missing

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Re: [ccp4bb] PDB header info wrong.

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Ian, "10.00A" sounds very much like somebody used shelxpro to create an ins-file from a PDB file and did not correct the SHEL card to include low resolution data. So the data may well contain data at 84A, but shelx does not use the data if the S

Re: [ccp4bb] refmac 5.6 ccp4 6.2.0

Hi Kenneth, This looks like an off-by-one bug in the restraint generation. Typical sources are weird LINKs, wrong atom names and bad luck. I suggest you make sure you have the very latest Refmac and dictionary and try setting up a new refinement instead of recycling an old job. If that doesn't

Re: [ccp4bb] Weird blob appears

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hello Jacob, On 10/28/2011 03:46 AM, Jacob Keller wrote: > Blob is gone--something funny happened, I guess. I went back to using > the original mtz from scala, removed and replaced a bunch of waters, ^^^ maybe that solves you

Re: [ccp4bb] refmac 5.6 ccp4 6.2.0

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Kenneth A. Satyshur, what is your weight set to? If it is set to 'auto', try setting it to a specific value and lower that value until the explosion stops. If this happens at low matrix values (at 1.24A it should be way above 5 or 10 for a well