Re: [ccp4bb] PHASER MR solution

kind suggestions. Thank you in advance. -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -- Matthew Franklin, Ph. D

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

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?

? 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 York, NY 10027 (212) 939

Re: [ccp4bb] rigaku micromax 007 cooling

that is 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 Convent

Re: [ccp4bb] Crystals Disappearing Overnight

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 -- Matthew Franklin

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

.. -- 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

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 New York Structural Biology Center 89 Convent Avenue, New York, NY 10027 (212) 939

Re: [ccp4bb] Table in NSMB

, -- 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

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 York Structural Biology Center 89 Convent Avenue

Re: [ccp4bb] off-topic: bug busting

++ 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/2008/9780854042722.asp -- Matthew Franklin, Ph. D. Senior Scientist

Re: [ccp4bb] making high res image in pymol

-- 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

(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] Protein concentration form chromatograms

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] Best compounds for heavy atom soaks

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] Fix cell dimensions

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

Re: [ccp4bb] observed criterion sigma

? 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

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?

! 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

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. Senior Scientist New

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

, 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 10027 (212) 939-0660 ext. 9374

Re: [ccp4bb] Puzzling observation about size exclusion chromatography

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

), 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 Structural Biology

Re: [ccp4bb] OFF TOPIC

.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

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 New York Structural

Re: [ccp4bb] poorly diffracting and twinned trigonal crystal

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 Franklin, Ph. D. Senior

Re: [ccp4bb] poorly diffracting and twinned trigonal crystal

. 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. Why? I would rather

Re: [ccp4bb] Question about weird diffraction map

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

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, NY 10027 (212

Re: [ccp4bb] help regarding structure solution

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

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

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

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?

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

. 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

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 Franklin, Ph. D. Senior Research

Re: [ccp4bb] Lithium versus Sodium

, 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/databases/cgi-bin

Re: [ccp4bb] refmac problem with anisotropic Us

/ 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 -- Matthew Franklin, Ph

[ccp4bb] refmac problem with anisotropic Us

, 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

? 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 Research Scientist New York Structural Biology Center 89

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

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 -- Matthew Franklin, Ph. D

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

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 want. Hope that helps, Matt -- Matthew Franklin

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

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 Scientist New York

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

(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 -- Matthew Franklin, Ph. D. Senior Research Scientist New York Structural Biology Center

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

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 with FFT at all. Hope that helps (and I hope I didn't make any egregious mistakes there!), Matt -- Matthew Franklin, Ph. D. Senior

[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?

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 done! - Matt -- Matthew Franklin

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

: 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 wholly owned subsidiary of Eli Lilly Company 180 Varick Street, 6th floor New York

Re: [ccp4bb] Cold Cabinet Vs Fridge, FPLC

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:ccp...@jiscmail.ac.uk] On Behalf

[ccp4bb] open research assistant position at ImClone Systems

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-mail, and any attachment

Re: [ccp4bb] Crystallizing Fluorescent Molecules

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 Systems, a wholly owned subsidiary of Eli Lilly Company 180

Re: [ccp4bb] Building PEG-400 in Coot

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 180 Varick Street, 6th floor New York, NY 10014 phone:(917)606-4116 fax

Re: [ccp4bb] missing carboxyl oxygen

- 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 makes sense chemically, of course. - Matt -- Matthew Franklin , Ph.D. Senior Scientist

Re: [ccp4bb] protein folds

-- 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 confidential information intended only for the use

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

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 privileged and confidential information

Re: [ccp4bb] pink/green paper?

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 -- Matthew Franklin , Ph.D. Senior Scientist, ImClone

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

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 York, NY 10014 phone:(917)606-4116 fax:(212)645-2054 Confidentiality Note: This e-mail, and any attachment

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

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 confidential information intended only

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

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 Confidentiality Note: This e-mail, and any attachment to it, contains privileged

Re: [ccp4bb] Good NMR Board

... - 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 confidential information intended only for the use