Re: [ccp4bb] PHASER MR solution

haser I >>>> got the message which I have attached here. And only sum. file I got as an >>>> output. Does any one have suggestion what should I do ? I would highly >>>> appreciate your kind suggestions. Thank you in

Re: [ccp4bb] ligand bonds (AlF3) breaking up after refinement in refmac

but it was of no help. Kindly suggest how to carry out the refinement. regards, Ansuman -- Matthew Franklin, Ph. D. Senior Scientist New York Structural Biology Center 89 Convent Avenue, New York, NY 10027 (212) 939-0660 ext. 9374

Re: [ccp4bb] how to measure the angle between two aromatic ring plane in PYMOL?

the best fit planes? I tried svdplos.py and makeCGOplates.py which are downloaded on line. unfortunately both of these can't be loaded into pymol properly. Solutions? Thanks! Bing Wang -- Matthew Franklin, Ph. D. Senior Scientist New York Structural Biology Center 89 Convent Avenue, New

Re: [ccp4bb] rigaku micromax 007 cooling

cooled by chilled water supplied rather unreliably through the building infrastructure. I was wondering what alternatives exist. Could other MicroMax 007 users share their experiences with alternative cooling solutions with me? Thank you. Andreas -- Matthew Franklin, Ph. D. Senior

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

up crystals in capillaries). I have access to a passably stocked biochemistry teaching lab, and could at a pinch go rifle some more advanced research labs. (No, I'm not at home ;) Thanks! phx -- Matthew Franklin, Ph. D. Senior Scientist New York Structural Biology Center 89 Co

Re: [ccp4bb] Crystals Disappearing Overnight

ore setting the drop. The crystals appear right after the drop is set but unfortunately they dissolve overnight. The plate is kept at 16 degree. Could anyone elaborate on this. Is it possibly occurring because Adenosine has stability issues. Thanks for your suggestions. ~ Maria -- M

Re: [ccp4bb] AW: [ccp4bb] relation between redundancy and total reflection

ation to redundancy.. -- Regards Faisal School of Life Sciences JNU -- Regards Faisal School of Life Sciences JNU -- Matthew Franklin, Ph. D. Senior Scientist New York Structural Biology Center 89 Convent Avenue, New York, NY 10027 (212) 939-0660 ext. 9374

Re: [ccp4bb] small molecule crystallography

fraction on campus. I would very much appreciate advice on how to deal with this, anything in the range from "won't work" to "use software X to analyze data in space group P-43N" would be welcome. Thanks. Andreas -- Matthew Franklin, Ph. D. Senior Scientist Ne

Re: [ccp4bb] Table in NSMB

ligand belong to Protein or Ligand/Ion? Thanks, -- Matthew Franklin, Ph. D. Senior Scientist New York Structural Biology Center 89 Convent Avenue, New York, NY 10027 (212) 939-0660 ext. 9374

Re: [ccp4bb] no link_id

his link_id, and where can I find an example for the correct syntax? Is this done in mon_lib.cif or the drug.cif file?? The bond length, if I'm not mistaken should be ~1.82 A for distance between carbon and sulfur. Thanks for any help. -- Matthew Franklin, Ph. D. Senior Scientist New

Re: [ccp4bb] off-topic: bug busting

y repeat that advice? thank you, Phoebe Rice ++ Phoebe A. Rice Dept. of Biochemistry & Molecular Biology The University of Chicago 773 834 1723; pr...@uchicago.edu <mailto:pr...@uchicago.edu> http://bmb.bsd.uchicago.edu/Faculty_and_Research/ http://www.rsc.org/shop/books/2008

Re: [ccp4bb] making high res image in pymol

ree version of pymol) Thank you in advance, Alex -- Matthew Franklin, Ph. D. Senior Scientist New York Structural Biology Center 89 Convent Avenue, New York, NY 10027 (212) 939-0660 ext. 9374

Re: [ccp4bb] Two P1 xtals with same xtal contacts give 2 different asymmetric units

s of the same protein and condition (more or less). I hope I have been clear. Thanks! Gabriel -- Matthew Franklin, Ph. D. Senior Scientist New York Structural Biology Center 89 Convent Avenue, New York, NY 10027 (212) 939-0660 ext. 9374

Re: [ccp4bb] Best compounds for heavy atom soaks

asing and maybe concentrations to use and soaking time. Cheers, Rhys -- Matthew Franklin, Ph. D. Senior Scientist New York Structural Biology Center 89 Convent Avenue, New York, NY 10027 (212) 939-0660 ext. 9374

Re: [ccp4bb] Protein concentration form chromatograms

if I really tried, but why bother when I have access to so many brilliant minds Thanks to all, K -- Matthew Franklin, Ph. D. Senior Scientist New York Structural Biology Center 89 Convent Avenue, New York, NY 10027 (212) 939-0660 ext. 9374

Re: [ccp4bb] Fix cell dimensions

arameters, but sometimes the program would not follow the input values > and switch back to the one it thinks best. Any suggestions will be appreciated. Thanks! > > Best, > Niu -- Matthew Franklin, Ph. D. Senior Scientist New York Structural Biology Center 89 Convent Avenue, New York, NY 10027 (212) 939-0660 ext. 9374

Re: [ccp4bb] observed criterion sigma

ods of data integration and scaling ? if yes then what are the values for the data processed through scalepack2mtz (HKL2000) and scala (mosflm).. -- Matthew Franklin, Ph. D. Senior Scientist New York Structural Biology Center 89 Convent Avenue, New York, NY 10027 (212) 939-0660 ext. 9374

Re: [ccp4bb] SA-omit map

11-04 dengzq1987 -- Matthew Franklin, Ph. D. Senior Scientist New York Structural Biology Center 89 Convent Avenue, New York, NY 10027 (212) 939-0660 ext. 9374

Re: [ccp4bb] A photograph of the Arndt-Wonacott rotation camera?

e the source of it. Thank you in advance! With fingers crossed ... . Gerard. -- Matthew Franklin, Ph. D. Senior Scientist New York Structural Biology Center 89 Convent Avenue, New York, NY 10027 (212) 939-0660 ext. 9374

Re: [ccp4bb] changes in small sections of secondary structure

g how real such small changes are and if they are real could they be enough to perturb the energy potential of the protein significantly. I apologize if this is a naive question as this is clearly not my area of expertise. Thanks for your input Mahesh -- Matthew Franklin, Ph. D. Senio

Re: [ccp4bb] Supplier for X-ray sensitive paper

at you must not copy, distribute or take any action in reliance on it. Any unauthorized use or disclosure of the contents of this message is not permitted and may be unlawful. -- Matthew Franklin, Ph. D. Senior Scientist New York Structural Biology Center 89 Convent Avenue, New York, NY 1002

Re: [ccp4bb] Puzzling observation about size exclusion chromatography

er and properly dispose of the e-mail. -- Matthew Franklin, Ph. D. Senior Scientist New York Structural Biology Center 89 Convent Avenue, New York, NY 10027 (212) 939-0660 ext. 9374

Re: [ccp4bb] Crystallisation below 0°C

°C) and 4H0W (-2°C), but I was wondering if anyone has a more systematic knowledge, some more examples, and what the parameters and best practice of this technique are. Many thanks, Glenn Masson MRC-Laboratory of Molecular Biology -- Matthew Franklin, Ph. D. Senior Scientist New York St

Re: [ccp4bb] side chain density

or leave them as such..The density fit analysis in COOT ( traffic light) showing those regions with side chain as red.. thanx in advance Regards Faisal School of Life Sciences JNU -- Matthew Franklin, Ph. D. Senior Scientist New York Structural Biology Center 89 Convent Avenue, New York, NY 10027 (212) 939-0660 ext. 9374

Re: [ccp4bb] OFF TOPIC

emeritus-staff http://rexpalmer2010.homestead.com -- Matthew Franklin, Ph. D. Senior Scientist New York Structural Biology Center 89 Convent Avenue, New York, NY 10027 (212) 939-0660 ext. 9374

Re: [ccp4bb] ideal rms bond length

998 0.150 14 0.2120 0.2590 0.805228461. 12455.0 0.0188 0.941 2.194 0.996 0.150 15 0.2121 0.2593 0.804228480. 12456.9 0.0188 0.939 2.190 0.995 0.150 -- Regards Faisal School of Life Sciences JNU -- Matthew Franklin, Ph. D. Senior Scientist

Re: [ccp4bb] poorly diffracting and twinned trigonal crystal

Wilson plot around 4. Perhaps this data does extend to 4.1. - Matt On 9/7/12 11:39 AM, Edwin Pozharski wrote: Matt, On 09/07/2012 09:56 AM, Matthew Franklin wrote: I'm also a bit dubious about the 4.3 A limit; your useful data may be ending around 4.6 instead, despite the high I/sigma numbers

Re: [ccp4bb] poorly diffracting and twinned trigonal crystal

ent? Why does including the partial twinning in our refinement cause Rfree and Rwork to diverge so dramatically? Given the trouble I’ve had so far and the poor quality of the data, I’m about ready to give up on this structure, but if anyone has any ideas please let me know. -- Matthew

Re: [ccp4bb] Question about weird diffraction map

Very indicative also the few strong and isolated high resolution reflections Cheers, BR -- Matthew Franklin, Ph. D. Senior Scientist New York Structural Biology Center 89 Convent Avenue, New York, NY 10027 (212) 939-0660 ext. 9374

Re: [ccp4bb] Question about weird diffraction map

rom this diffraction, even in the low diffract angle, no diffraction spots theremeaning-this is not a protein crystal? Any experienced idea/questions welcomed to discuss here. Zhao, -- Matthew Franklin, Ph. D. Senior Scientist New York Structural Biology Center 89 Convent Avenue, New York,

Re: [ccp4bb] help regarding structure solution

ively in Refmac with all the solutions. I will highly appreciate all the suggestions for this kind of problem. Thanks and regards -- Sonali -- Matthew Franklin, Ph. D. Senior Scientist New York Structural Biology Center 89 Convent Avenue, New York, NY 10027 (212) 939-0660 ext. 9374

Re: [ccp4bb] P21221 to P21212 conversion

is "sticky" - you don't need to select it again for subsequent rounds of scaling. Hope that helps - feel free to contact me if you want more explanation. - Matt -- Matthew Franklin, Ph. D. Senior Scientist New York Structural Biology Center 89 Convent Avenue, New York, NY 10027 (212) 939-0660 ext. 9374

Re: [ccp4bb] problem in scaling the Zn-MAD data

- * BUSTER Development Group (http://www.globalphasing.com) ******* -- Deepthi -- Matthew Franklin, Ph. D. Senior Research Scientist New York Structural Biology Center 89 Convent Avenue, New York, NY 10027 (646) 275-7165

Re: [ccp4bb] REFMAC Riding Hydrogens

ardless of they are explicitly defined? Can the hydrogen behavior in REFMAC be more explicitly controlled. Thanks, --Paul -- Matthew Franklin, Ph. D. Senior Research Scientist New York Structural Biology Center 89 Convent Avenue, New York, NY 10027 (646) 275-7165

Re: [ccp4bb] Invisible Reference on Pubmed?

Either that, or it's THE MAN suppressing the research needed to cure cancer and the common cold, and build a car that runs on water... :) - Matt -- Matthew Franklin, Ph. D. Senior Research Scientist New York Structural Biology Center 89 Convent Avenue, New York, NY 10027 (646) 275-7165

Re: [ccp4bb] synchrotron X-ray picture

On 2/1/12 2:34 PM, Matthew Franklin wrote: Hi Pat - I, too, have a memory of such a picture. This isn't quite the one I was thinking of, but it should hopefully serve the purpose: http://www.nsls.bnl.gov/about/imagelibrary/images/hr/Synchrotron_Light2_hires.tif (there are a couple

Re: [ccp4bb] synchrotron X-ray picture

lege Building 245 N. 15th St., Mailstop 497 Philadelphia, PA 19102-1192 USA (215) 762-7706 pat.l...@drexelmed.edu -- Matthew Franklin, Ph. D. Senior Research Scientist New York Structural Biology Center 89 Convent Avenue, New York, NY 10027 (646) 275-7165

Re: [ccp4bb] Lithium versus Sodium

at 10:23 -0500, Matthew Franklin wrote: On 1/12/12 9:42 AM, Ed Pozharski wrote: On Thu, 2012-01-12 at 09:52 +, Patel, Joe wrote: Do you have ultra-high resolution? Something I did not…. Are there many examples in the pdb of proteins with Li+ refined? http://www.ebi.ac.uk/thornton-srv/da

Re: [ccp4bb] Lithium versus Sodium

istances were consistent with lithium coordination, for what that's worth at this resolution That was the first structure (1TW7), and all of the others were treated the same since it was the same crystals soaked with different compounds in the same conditions. - Matt -- Matthew Fra

Re: [ccp4bb] refmac problem with anisotropic Us

so alone: 0.182 / 0.238 TLS + Biso: 0.188 / 0.228 TLS + Baniso: 0.177 / 0.230 The TLS + Biso job gives the lowest free R and the smallest difference between R and Rfree, so it's the winner. Thanks to all for your input. And thanks to Mischa for answering my original question! - Matt

[ccp4bb] refmac problem with anisotropic Us

so B refinement, so I haven't encountered this before. Thanks for any advice, Matt -- Matthew Franklin, Ph. D. Senior Research Scientist New York Structural Biology Center 89 Convent Avenue, New York, NY 10027 (646) 275-7165

[ccp4bb] flex-wARP error

bs can be run in parallel? I'm running "Arp/Warp Expert System" (i.e. flex-wARP) from ccp4i, and I don't think this is happening with other Arp/Warp modes. (I'll be happy to provide more logfiles, input files, etc.) Thanks, Matt -- Matthew Franklin, Ph. D. Senior Res

Re: [ccp4bb] (off-topic) Measurement of channel pore dimensions

that this would give you a number for the radius accurate to 0.5 A, maybe better. It's not a true cross-sectional area, but that doesn't seem as biologically relevant to me as whether a certain sphere (e.g. calcium or magnesium ions) can fit through the pore. Hope that helps, Matt -

Re: [ccp4bb] Model Building: continuous update of distances as fragment moved

I think not. I'm fairly sure that this still works - the last time I used O was about six months ago, and the O package I was using was from c. 2005. More on-topic, Coot seems to have a "dynamic distance" command (look under the "Measure" menu) which will do what you wa

Re: [ccp4bb] Crystals that "fly" around a drop until they land and grow.

ome random position in the drop, then dropping to the bottom (or sliding down the curved lower face of a hanging drop). I haven't seen this movie myself, so I don't know if this is a reasonable explanation of the motion. - Matt -- Matthew Franklin, Ph. D. Senior Research

Re: [ccp4bb] Looking for the following values...

completeness - for example, a dataset with 31984 unique observed reflections (you can get these numbers from the scaling log files of Scalepack or scala) with 99.8% completeness would give you (31984/0.998)=32048 as the number of "all" reflections. Hope that helps, Matt --

Re: [ccp4bb] The density shown in Pymol and Coot is different.

2Fo-Fc and Fo-Fc maps automatically at the end of a refinement run. If you're using the ccp4i GUI, expand the "Monitoring and output options" section of the Refmac window, and check the box marked "Generate weighted difference maps..." Then you don't need to mess around

[ccp4bb] crystallographer position available

be helpful. Salary level is commensurate with qualifications and experience. Thank you for your attention to this. - Matt Franklin -- Matthew Franklin, Ph. D. Senior Research Scientist New York Structural Biology Center 89 Convent Avenue, New York, NY 10027 (646) 275

Re: [ccp4bb] Extremely long c-axis...reasonable?

om the dropdown list of query types. Performing this search finds 12 structures in the PDB with c axis > 600 A and a and b axes < 100 A. Two of these are fiber diffraction molecular envelopes, but the other 10 are well-refined crystal structures at reasonable resolutions. So it can be

Re: [ccp4bb] pdb-l: Retraction of 12 Structures

ture 2HR0. Once again, I'd like to get the community's thoughts: should we ask the PDB to stop using 0 and 1 in its IDs? I'll get off the soapbox now. - Matt (who has nothing to do with any of these structures...) -- Matthew Franklin , Ph.D. Senior Scientist, ImClone Systems, a

Re: [ccp4bb] mammalian cell culture on IMAC

you can spin out the precipitate then load the supernatant on to your nickel column with no further processing. Hope that helps, Matt -- Matthew Franklin , Ph.D. Senior Scientist, ImClone Systems, a wholly owned subsidiary of Eli Lilly & Company 180 Varick Street, 6th floor New York, NY 10014

Re: [ccp4bb] Cold Cabinet Vs Fridge, FPLC

ates around an FPLC. This may not be a bad thing! - Matt -- Matthew Franklin , Ph.D. Senior Scientist, ImClone Systems, a wholly owned subsidiary of Eli Lilly & Company 180 Varick Street, 6th floor New York, NY 10014 phone:(917)606-4116 fax:(212)645-2054 From: CCP4 bulletin board [mailto:c

Re: [ccp4bb] Twinning

to me earlier, so I've got no suggestions on that front. But if your initial intensities are bad due to indexing or crystal problems, you'll never get a well-refined structure. Hope that helps, Matt -- Matthew Franklin , Ph.D. Senior Scientist, ImClone Systems, a wholly owned subsidi

[ccp4bb] is my crystal twinned or not?

t the intensity statistics could be misleading me? On the other side, am I doing something wrong with the structure determination if the crystal is twinned? How should I proceed? Thanks for any help anyone can provide. - Matt -- Matthew Franklin , Ph.D. Senior Scientist, ImClone Systems, a

[ccp4bb] open research assistant position at ImClone Systems

crystallization and related skills will be taught on the job -- Matthew Franklin , Ph.D. Senior Scientist, ImClone Systems, a wholly owned subsidiary of Eli Lilly & Company 180 Varick Street, 6th floor New York, NY 10014 phone:(917)606-4116 fax:(212)645-2054 Confidentiality Note: This e-mai

Re: [ccp4bb] Crystallizing Fluorescent Molecules

ll over the outside of the crystal, painting it and making it look green! Are you certain that your peptide doesn't precipitate under your crystallization conditions? I hope for your sake that my problem is not yours... - Matt -- Matthew Franklin , Ph.D. Senior Scientist, ImClone Syste

Re: [ccp4bb] Building PEG-400 in Coot

y tube of density was PEG when I saw the regular pattern of hydrogen bonds alternating with hydrophobic patches that the modeled PEG presented to the protein. Hope that helps, Matt -- Matthew Franklin , Ph.D. Senior Scientist, ImClone Systems, a wholly owned subsidiary of Eli Lilly & Company

Re: [ccp4bb] friction or releasing pdb's

courage the PDB to STOP using both the number 0 and the letter O in PDB codes? This isn't the first time I've been confused about which structure is which; most fonts don't make a clear distinction between the two characters. - Matt -- Matthew Franklin , Ph.D. Senior Scientist, I

Re: [ccp4bb] missing carboxyl oxygen

there should be some sort of "flip peptide" command - if not, you'll need to move things manually. Just so we're clear, I'm talking about turning this: H Ca-N-C-Ca O into: O Ca-N-C-Ca H Check hydrogen bonding patterns to see if the flipped peptide group mak

Re: [ccp4bb] protein folds

1392 We're not done finding new folds yet, folks... - Matt -- Matthew Franklin , Ph.D. Senior Scientist, ImClone Systems 180 Varick Street, 6th floor New York, NY 10014 phone:(917)606-4116 fax:(212)645-2054 Confidentiality Note: This e-mail, and any attachment to it, contains privileged and conf

Re: [ccp4bb] temperature after 30 minutes using microscopes ?

re my fiber optic setup can be retrofitted to most microscopes... - Matt -- Matthew Franklin , Ph.D. Senior Scientist, ImClone Systems 180 Varick Street, 6th floor New York, NY 10014 phone:(917)606-4116 fax:(212)645-2054 Confidentiality Note: This e-mail, and any attachment to it, contains pri

Re: [ccp4bb] tortion angle restraints in REFMAC

oms. I needed to trim the plane definitions and delete a lot of inappropriate torsion angle restraints before my ligands would refine correctly. - Matt -- Matthew Franklin , Ph.D. Senior Scientist, ImClone Systems 180 Varick Street, 6th floor New York, NY 10014 phone:(917)606-4116 fax:(212)645-2

Re: [ccp4bb] suggestions for UV spectrometer

o do more sophisticated analysis, such as analyzing dye labeling efficiency by deconvoluting the dye absorbance spectrum from the protein absorbance spectrum. If you get one, you'll never want to go back to the old way. (And no, they didn't pay me to say this!) - Matt -- Matthew Franklin ,

Re: [ccp4bb] ccp4 database error

-- Matthew Franklin , Ph.D. Senior Scientist, ImClone Systems 180 Varick Street, 6th floor New York, NY 10014 phone:(917)606-4116 fax:(212)645-2054 CCP4 bulletin board wrote on 10/17/2008 02:09:38 PM: > Dear CCP4 community, > > Due to power failure during ccp4i session the database

Re: [ccp4bb] pink/green paper?

nlight) and there's no development needed. Gafchromic sells a whole bunch of films; I'm afraid I don't remember which one you should get. They're rated by radiation dose, but I don't remember how many Grays per second an X-ray generator will deposit in the film... - Matt

Re: [ccp4bb] Mosflm : data process of crystal with huge unit cell

s of data, but a 0.1 degree oscillation is still 0.7 deg of data, and five times the number of images! I wouldn't go below 50% of the crystal mosaicity for my oscillation angle. Hope that's useful to you. - Matt -- Matthew Franklin , Ph.D. Senior Scientist, ImClone Systems 180 Varick S

Re: [ccp4bb] CNS 1.2.2 binary running out of memory

emory to run this job. It is possible to allocate more swap space (virtual memory) on your hard disk, but a compute job that's running mostly in virtual memory will be so slow that you'll collect Social Security before it's done... Let me know if you need more detailed help. - Matt

Re: [ccp4bb] def file for restraining dna and long helices

stick with energy minimization and manual rebuilding. If you got your initial model from molecular replacement, you need to be certain that your solution is correct. Sorry for the bad news, Matt -- Matthew Franklin , Ph.D. Senior Scientist, ImClone Systems 180 Varick Street, 6th floor New Yo

Re: [ccp4bb] source for forceps/clamps that fit around cryovials

u want are almost at the bottom of the page. HTH, Matt -- Matthew Franklin , Ph.D. Senior Scientist, ImClone Systems 180 Varick Street, 6th floor New York, NY 10014 phone:(917)606-4116 fax:(212)645-2054 Confidentiality Note: This e-mail, and any attachment to it, contains privileged and conf

Re: [ccp4bb] The importance of USING our validation tools

r limit of the F/sigF distribution. - Matt PS. The above are my views, not those of ImClone Systems, CCP4, the companies which send this email, the Boy Scouts, or any other organization which I may be associated with now, in the past, or in the future :P -- Matthew Franklin , Ph.D. Senior Scien

Re: [ccp4bb] Help with reducing crystal mosaicity

o only the bit with the crystal is in the free stream. It's not a cheap solution, but you've almost certainly got a cryosystem already... - Matt -- Matthew Franklin , Ph.D. Senior Scientist, ImClone Systems 180 Varick Street, 6th floor New York, NY 10014 phone:(917)606-4116 fax:(212

Re: [ccp4bb] Molecular Replacement issues with a WD-40 7-bladed beta propeller

nd out) and try Refmac refinement. Again, one will hopefully look better than the others. Hope this works for you - it's certainly something to try while you're trying to get derivatives... And feel free to contact me if this wasn't clear enough for you to try it. - Matt -- Matthew Fra

Re: [ccp4bb] X-ray generator uninterruptible power supply

of the night, I can come in and rescue the crystal the next day. Email me if you want more info on my choice of UPS for my cryo. - Matt -- Matthew Franklin , Ph.D. Senior Scientist, ImClone Systems 180 Varick Street, 6th floor New York, NY 10014 phone:(917)606-4116 fax:(212)645-2054 Confide

Re: [ccp4bb] previous message monomer library

ot with linked aromatic ring systems. Then take your new library file and feed it to Refmac (using the LIBIN keyword for a script file or the "Library" line in ccp4i. Your new definitions will supplement the default library. Hope that helps, Matt -- Matthew Franklin , Ph.D. Senior Sci

Re: [ccp4bb] Good NMR Board

. You might want to try it on a dry tube first... - Matt -- Matthew Franklin , Ph.D. Senior Scientist, ImClone Systems 180 Varick Street, 6th floor New York, NY 10014 phone:(917)606-4116 fax:(212)645-2054 Confidentiality Note: This e-mail, and any attachment to it, contains privileged and