[ccp4bb] LN2 cryocooling system - manufacturers
Dear all, By looking for manufacturers of LN2 cryocooling systems for in-house single-crystal X-ray diffractometers, I seems that Oxford Cryosystems is the only company nowadays providing such systems in Europe. In the past, we used to have such systems of Bruker and Oxford Instruments, but these all seem to be discontinued. Does anyone have an idea of other manufacturers of such dedicated systems similar to the Oxford cryostreams 700, 800, 1000, Cobra,.. etc. please? Any input would be highly appreciated. Thank you very much! Regards Kristof To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] Off-topic - Cryojet5 - boiloff heater spare
Dear, My apologies for the off-topic post. Our (11-years old) Oxford Instruments Cryojet5 LN2 cryocooling has broken down and to repair this, we are looking to purchase a simple ‘boiloff heater’ element for the shield flow dewar leg. Oxford Instruments informed us that this product was discontinued in 2015 and they are no longer able to supply spares for it. Therefore, if anyone has spare parts for a Cryojet5, please get back to me? Thank you very much. Kristof Van Hecke Ghent University, Belgium To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] Lowering R factor from small molecule structure
Dear Jacob, An R-value of 17% is indeed suspiciously high for a small molecule structure. Some thoughts: Are you sure the space group is correct? There might be twinning involved,. Have you checked the ’signs of twinning’ for small molecules? There might be disordered solvent molecules, which could be modeled, although that’s not always trivial nor possible. How high are the residual peaks? This could give you info about what’s out there? If the residual peaks are located very close to heavy atoms, the data might suffer (severely) from absorption. Regards Kristof > On 3 Jun 2021, at 20:49, Jacob Summers > <60a137e4bf3a-dmarc-requ...@jiscmail.ac.uk> wrote: > > Greetings! > > I am currently trying to reduce the R factor of a cyclic small molecule > peptoid in ShelXle. The max resolution of the molecule is 0.8 angstroms. The > molecule itself fits the density very well, but there are a few unexplained > densities around the molecule which do not seem to be anything in the > crystallization conditions. The R1 factor of the refinement is 17.07% but I > am unsure how to lower this value. Any ideas on how to better refine this > molecule or fill densities to lower the R1 factor? I do not have much > experience working with small molecule refinement or with ShelX. > > Thanks so much, > Jacob Summers > > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing > list hosted by www.jiscmail.ac.uk, terms & conditions are available at > https://www.jiscmail.ac.uk/policyandsecurity/ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] SHELX - BIND instruction and connectivity list
Dear all, I’m sorry for the off-topic question. Using SHELX, I’m trying to get extra bonds between symmetry equivalents using the command ‘BIND’ and ‘EQIV’. However, although these bonds are visulised in e.g. Olex2, they do not show up in the connectivity list, hampering the addition of H-atoms on calculated positions. The same happens when using Shelxle. Could it be that this happens because the bonds are created between different PARTS (A and B in this case)? E.g. some commands I use: EQIV $1 1-X,1-Y,1-Z BIND C51A C52B_$1 BIND C51B C53A_$1 BIND C53B C52A_$1 Thank you very much for any suggestions?! Regards Kristof To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
[ccp4bb] PhD position - Ghent University, Belgium
Dear, I would like to draw your attention to this vacancy for a PhD position at the Department of Chemistry, Ghent University, Belgium. https://edit.ugent.be/en/work/vacancies/scientific/phd-student-l83o2/ <https://edit.ugent.be/en/work/vacancies/scientific/phd-student-l83o2/> https://www.ugent.be/en/ghentuniv <https://www.ugent.be/en/ghentuniv> We are looking for a highly motivated candidate to perform academic research to study the crystallization process of specific compounds using state-of- the-art nonlinear optical scattering techniques, combined with small angle X-ray scattering (SAXS) techniques. Prior experience with small angle X-ray scattering (SAXS) techniques is highly recommended. We can offer a funded PhD position for a period of four years in total, with expected starting date of 01/01/2020. Regards Kristof Van Hecke To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
[ccp4bb] Structure solution - hexapeptide
Dear all, I’m trying to solve a structure of a (modified) hexapeptide: - inhouse (very decent) data up to 0.8 Angstrom - average redundancy = 10 - according to the Matthews coefficient of 1.88 with 34.77 %solvent, there should be 3 Nmol/asym - ‘large’ unit cell of about a=54, b=54, c=12 - SG = P3(1)12 or P3(2)12 As there’s (presumably) only C, H, N and O in the structure, I’m not able to solve this via Direct Methods, Charge Flipping etc,. Trying MR (with Phaser) doesn’t give any results either, as there’s hardly any homologous models Has anyone encountered a similar problem please, and could provide any possible solutions? (building in heavy atoms isn’t my first option at the moment,. ) Thank you very much Regards Kristof To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
[ccp4bb] REMINDER: Invitation - School on X-ray and Neutron Diffraction Techniques - May 28-30 2018 - Ghent, Belgium
Dear colleagues, Under the auspices of the Belgian Biophysical Society, and supported by the Doctoral School of Natural Sciences – UGent, we would like to invite you to the School on X-ray and Neutron Diffraction Techniques, hosted by Ghent University, which will be held at the VIB-UGent Center for Inflammation Research in Zwijnaarde (Ghent), Belgium, on May 28-30, 2018. The aim of the school is to provide a survey of the broad range of X-ray and neutron scattering methods and their application to investigate biological structures and processes. Starting from an introduction to the basics of X-ray and neutron scattering we will move on to their application to study proteins and their complexes with other proteins or nucleic acids, to probe lipid/membrane structures and biological processes such as bacterial metabolism. Our program will also provide a survey of the state-of-the-art in terms of research facilities available worldwide to enable experimental work employing X-ray and neutron scattering. Our school is organized such that no prior knowledge of scattering techniques is required. For further information, venue and registration, and our list of TOP SPEAKERS!, please see the website: www.biophysics.be <http://www.biophysics.be/> Please do not hesitate to forward this to colleagues who might be interested. Looking forward seeing you on May 28-30, 2018! On behalf of the organizers: Kristof Van Hecke (UGent), Filip Meersman (UAntwerpen) and Savvas Savvides (UGent)
[ccp4bb] Invitation - School on X-ray and Neutron Diffraction Techniques - May 28-30 2018 - Ghent, Belgium
Dear colleagues, Under the auspices of the Belgian Biophysical Society, and supported by the Doctoral School of Natural Sciences – UGent, we would like to invite you to the School on X-ray and Neutron Diffraction Techniques, hosted by Ghent University, which will be held at the VIB-UGent Center for Inflammation Research in Zwijnaarde (Ghent), Belgium, on May 28-30, 2018. The aim of the school is to provide a survey of the broad range of X-ray and neutron scattering methods and their application to investigate biological structures and processes. Starting from an introduction to the basics of X-ray and neutron scattering we will move on to their application to study proteins and their complexes with other proteins or nucleic acids, to probe lipid/membrane structures and biological processes such as bacterial metabolism. Our program will also provide a survey of the state-of-the-art in terms of research facilities available worldwide to enable experimental work employing X-ray and neutron scattering. Our school is organized such that no prior knowledge of scattering techniques is required. For further information, venue and registration, please see the website: www.biophysics.be <http://www.biophysics.be/> Please do not hesitate to forward this to colleagues who might be interested. Looking forward seeing you on May 28-30, 2018! On behalf of the organizers: Kristof Van Hecke (UGent), Filip Meersman (UAntwerpen) and Savvas Savvides (UGent)
Re: [ccp4bb] [ccp4bb] Twinning in space group Pc
Dear, Indeed,. Pc is not compatible with chiral molecules,. my mistake. I’m trying to process/solve the structure in P1 now and see how far I get. Thank you very much for pointing things out. Regards Kristof On 13 Aug 2014, at 13:58, herman.schreu...@sanofi.com wrote: > Dear Kristof, > > Lijun is right, space group Pc is not compatible with chiral molecules. Maybe > diffraction of your non-chiral metal structure overwhelmed the chiral > contribution of your organic framework. Why not use a trick from protein > crystallography: process and solve your structure in P1? According to the > international tables there are two asymmetric units in Pc, so the > crystallographic problem should remain manageable. > > Best, > Herman > > Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Lijun > Liu > Gesendet: Mittwoch, 13. August 2014 11:59 > An: CCP4BB@JISCMAIL.AC.UK > Betreff: Re: [ccp4bb] Twinning in space group Pc > > Hi, Pc may not be the space group for your crystal, if the molecule is > chiral. Seems like the data were forced to be reduced to a mirror_related > SG. Lijun > > On Aug 13, 2014 2:00 AM, "Kristof Van Hecke" > wrote: > Dear, > > I’m struggling with the following (small molecule) problem: > > We are trying to solve the structure of a metal-organic framework containing > a chiral compound. > The space group is most probably Pc, but when refining, SHELX gives the error > “Possible racemic twin or wrong absolute structure - try TWIN refinement”. > As we know our compound is enantiopure, a racemic twin is very unlikely. In > this regard, also a centro-symmetric space group is not possible (although > CrysAlisPro always gives P2/c as the proper space group). As a matter of > fact, trying different space groups is not solving the problem. > > The second problem is that half of the structure is visible, but the other > half is completely not clear. Refinement is not possible at all (R-value of > 33%). > When running TwinRotMat (Platon), I get the following possible 2-fold twin > axes: > > 2-axis ( 0 1 -1 ) [ -2 5 -4 ], Angle () [] = 2.31 Deg, Freq =14 > * > (-0.992 -0.0190.015) (h1) (h2) Nr Overlap =84 > (-0.4300.075 -0.860) * (k1) = (k2) BASF = 0.96 > ( 0.459 -1.146 -0.083) (l1) (l2)DEL-R =-0.064 > > 2-axis ( 0 1 1 ) [ 2 5 4 ], Angle () [] = 2.31 Deg, Freq =15 > * > (-0.9920.0190.015) (h1) (h2) Nr Overlap = 229 > ( 0.4300.0750.860) * (k1) = (k2) BASF = 0.94 > ( 0.4591.146 -0.083) (l1) (l2)DEL-R =-0.050 > > 2-axis ( 1 0 -2 ) [ 3 0 -2 ], Angle () [] = 0.54 Deg, Freq =19 > * > (-0.1360.000 -0.576) (h1) (h2) Nr Overlap = 992 > ( 0.000 -1.0000.000) * (k1) = (k2) BASF = 0.86 > (-1.7030.0000.136) (l1) (l2)DEL-R =-0.030 > > 2-axis ( 1 2 -1 ) [ 5 5 -1 ], Angle () [] = 0.39 Deg, Freq =13 > * > (-0.3800.620 -0.124) (h1) (h2) Nr Overlap = 854 > ( 1.2560.256 -0.251) * (k1) = (k2) BASF = 0.88 > (-0.617 -0.617 -0.877) (l1) (l2)DEL-R =-0.019 > > However, none of these do actually improve the refinement. > > > Has anyone encountered possible twinning/twin laws in Pc please? > Or any other suggestions are most welcome? > > > Thank you very much > > Kristof
[ccp4bb] Twinning in space group Pc
Dear, I’m struggling with the following (small molecule) problem: We are trying to solve the structure of a metal-organic framework containing a chiral compound. The space group is most probably Pc, but when refining, SHELX gives the error “Possible racemic twin or wrong absolute structure - try TWIN refinement”. As we know our compound is enantiopure, a racemic twin is very unlikely. In this regard, also a centro-symmetric space group is not possible (although CrysAlisPro always gives P2/c as the proper space group). As a matter of fact, trying different space groups is not solving the problem. The second problem is that half of the structure is visible, but the other half is completely not clear. Refinement is not possible at all (R-value of 33%). When running TwinRotMat (Platon), I get the following possible 2-fold twin axes: 2-axis ( 0 1 -1 ) [ -2 5 -4 ], Angle () [] = 2.31 Deg, Freq =14 * (-0.992 -0.0190.015) (h1) (h2) Nr Overlap =84 (-0.4300.075 -0.860) * (k1) = (k2) BASF = 0.96 ( 0.459 -1.146 -0.083) (l1) (l2)DEL-R =-0.064 2-axis ( 0 1 1 ) [ 2 5 4 ], Angle () [] = 2.31 Deg, Freq =15 * (-0.9920.0190.015) (h1) (h2) Nr Overlap = 229 ( 0.4300.0750.860) * (k1) = (k2) BASF = 0.94 ( 0.4591.146 -0.083) (l1) (l2)DEL-R =-0.050 2-axis ( 1 0 -2 ) [ 3 0 -2 ], Angle () [] = 0.54 Deg, Freq =19 * (-0.1360.000 -0.576) (h1) (h2) Nr Overlap = 992 ( 0.000 -1.0000.000) * (k1) = (k2) BASF = 0.86 (-1.7030.0000.136) (l1) (l2)DEL-R =-0.030 2-axis ( 1 2 -1 ) [ 5 5 -1 ], Angle () [] = 0.39 Deg, Freq =13 * (-0.3800.620 -0.124) (h1) (h2) Nr Overlap = 854 ( 1.2560.256 -0.251) * (k1) = (k2) BASF = 0.88 (-0.617 -0.617 -0.877) (l1) (l2)DEL-R =-0.019 However, none of these do actually improve the refinement. Has anyone encountered possible twinning/twin laws in Pc please? Or any other suggestions are most welcome? Thank you very much Kristof
Re: [ccp4bb] DNA geometry
Dear Sheng, On the website of the NDB (Nucleic Acid Database), there's plenty of links to software tools like 3DNA, Freehelix,.., which will do the trick. (I would recommend 3DNA) http://ndbserver.rutgers.edu/services/index.html Regards Kristof On 28 Aug 2012, at 09:57, cuisheng2007 wrote: Dear all: Is there software or web-server that can measure DNA geometry (PDB coordinates) precisely, such as groove width, helix diameter, helix axis, base tilt angle, helix rise per base pair… It is surely doable to measure and estimate them manually, but I am just wondering if there are better ways or automatic ways. Many thanks sheng
[ccp4bb] Melting point and heat of fusion
Dear, We're wondering what tools there are available in order to estimate the 'melting point' and 'heat of fusion' from a known crystal structure (e.g. coordinate file)..? It concerns mostly small molecules (> 100 atoms). Many thanks Kristof ----------- Kristof Van Hecke, PhD Biomolecular Architecture Celestijnenlaan 200F 3001 Heverlee (Leuven) Belgium ---
[ccp4bb] Measuring dimensions of channels
Dear, Does anybody know a conventional method/program for measuring the dimensions (e.g. in Å), not the volume, of solvent channels in metal organic frameworks (MOF's)..? Thank you very much Kristof --- Kristof Van Hecke, PhD Biomolecular Architecture Celestijnenlaan 200F 3001 Heverlee (Leuven) Belgium ---
Re: [ccp4bb] recommendation for ammonium dihydrogen phosphate cryo
Dear Chris, Indeed,. according to McFerrin and Snell, 2002, Appl. Crystallogr., they recommend 30%(v/v) PEG400, or 35% EG (ethlylene glycol) or 30% PG (propylene glycol) However, they also mention the use of 35% (v/v) glycerol. regards Kristof On 26 May 2011, at 13:01, herman.schreu...@sanofi-aventis.com wrote: Dear Chris, I have not used this particular condition, but as a rule of thumb I use "like with like", e.g. glycerol, ethylene glycol, PEG400 etc. with PEG conditions, and saltlike compounds (sucrose, xylitol, salts) for salt conditions. In your case I would try glucose or xylitol or just look what happens if you increase the ammonium phosphate concentration to say 2M without adding glycerol. Good luck! Herman -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Chris Ulens Sent: Thursday, May 26, 2011 12:27 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] recommendation for ammonium dihydrogen phosphate cryo Hi, I would like to get recommendations for a proper cryo solution for a crystallization hit from the Hampton crystal screen Ammonium di- hydrogen phosphate 0.4M. I tried increasing glycerol up to 30% with the same ammonium phosphate concentration or increasing glycerol up to 30% in the presence of 1.3M ammonium phosphate. Both gave iced up drops (I only tried quick and dirty tests by dipping a cover glass in liquid nitrogen). Thank you. -Chris ------ Kristof Van Hecke, PhD Biomoleculaire Architectuur Celestijnenlaan 200 F B-3001 Heverlee (Leuven) Tel: +32(0)16327477 --
[ccp4bb] Structure containing nickel ions from Ni-NTA column
Dear, I was wondering if anybody has experienced before the leakage of Ni- ions (from a Ni-NTA column) and additionally binding to specific sites in the protein structure..? Many thanks Regards Kristof -- Kristof Van Hecke, PhD Biomoleculaire Architectuur Celestijnenlaan 200 F B-3001 Heverlee (Leuven) Tel: +32(0)16327477 --
[ccp4bb] ARCIMBOLDO - successful solution
Dear, Because this can certainly be of interest to other crystallographers, I would like to post the following positive comment: The recently developed software ARCIMBOLDO: Crystallographic Ab Initio protein solution far below atomic resolution, (Rodriguez et al., Nature Methods, 6, 651, 2009) http://chango.ibmb.csic.es/ARCIMBOLDO/ was able to find a successful solution for one of our protein structures. The protein showed only 30% sequence identity and ,although we've built several homology models, failed all MR attempts. Furthermore, crystal data were complete (1.6 angstrom), showed high redundancy (cubic space group) and lot's of alpha helices. In the future, a public web server will be provided to run the software on, but in the meantime very kind help was provided by the authors Dayté Rodriguez and Isabel Uson. I hope this comment will stimulate the use and the further development/implementation of the program. Regards Kristof ------ Kristof Van Hecke, PhD Biomoleculaire Architectuur Celestijnenlaan 200 F B-3001 Heverlee (Leuven) Tel: +32(0)16327477 --
[ccp4bb] iMosflm 1.0.4 - font size
Dear, I've just installed the latest iMosflm 1.0.4, as well as the CCP4 6.1.13 suite (under Mac OS 10.5.8). However, where does iMosflm get its font sizes..? (these are quite big actually, and I'd like to reduce them) Thank you very much Sincerely Kristof Van Hecke ------- Kristof Van Hecke, PhD Biomolecular Architecture Celestijnenlaan 200F 3001 Heverlee (Leuven) Belgium ---
[ccp4bb] Restraint hydrogen bond Refmac
Dear, When (trying) to refine a DNA-structure (resolution 2.5) using Refmac_5.5.0072 (CCP4 6.1.1), some of the H-bonds between Watson- Crick bases are becoming too large. Reducing the Matrix weighting term to tighten the geometry, doesn't effect these H-bond distances much. Reducing the "VDW SIGMA HBOND" also doesn't solve the problem. Adding "external distance restraints" does the trick, but some B- factors (not the ones involved in H-bonding!) blow up completely. Hence, what's actually the best way of tighten H-bond restraints in Refmac, or am I overlooking some other issues here..? Thank you very much. Regards Kristof Van Hecke ---------- Kristof Van Hecke, PhD Biomoleculaire Architectuur Celestijnenlaan 200 F B-3001 Heverlee (Leuven) Tel: +32(0)16327477 --
[ccp4bb] Modeling DNA triple helices - MORCAD
Dear, I apologize for the non-ccp4 question. I'm looking for an (alternative) modeling tool for DNA triple helices, such as the earlier Morcad program: MORCAD, and object-oriented molecular modelling package running on IBM RS/6000 and SGI 4Dxxx workstations M. Le Bret, J. Gabarro-Arpa, J.C. Gilbert, C. Lemaréchal J. Chim. Phys. Phys. Chim. Biol. 88, 2489 (1991). Many thanks Kristof -- Kristof Van Hecke, PhD Biomoleculaire Architectuur Celestijnenlaan 200 F B-3001 Heverlee (Leuven) Tel: +32(0)16327477 --
Re: [ccp4bb] Software for RNA model building
Dear Rafal, The program 'Coot' or (X)3DNA can easily do this for you. Regards Kristof On 12 May 2009, at 10:05, Rafal Dolot wrote: Sorry, for mistake in the title of my last post. Please ingnore it. Dear CCP4BB users, Sorry, for non-CCP4 question. I'm looking for any freeware program for molecule model building, especially for perfect matching RNA duplex. Could you help me? I found some programs with options of "de novo" protein chain building, but without options of DNA/RNA chain building. With best wishes Rafal |--| |Rafal Dolot, Ph.D.| | | |Polish Academy of Sciences| |Centre of Molecular and Macromolecular Studies| |Department of Bioorganic Chemistry| |Sienkiewicza 112 | |90-363 Lodz, Poland | |Phone: +48(42)6803215 | |Cell: +48 502897781 | |--| --------------- Kristof Van Hecke, PhD Biomolecular Architecture Celestijnenlaan 200F 3001 Heverlee (Leuven) Belgium ---
[ccp4bb] Structure idealisation Refmac_5.5.0072
Dear, I want to optimize a DNA-helix with the function "Structure idealisation" in Refmac_5.5.00782 (CCP4_6.1.1). My question, is this performing just a geometry optimization (against a library), or is there also an energy-optimization of some kind involved,..? And according to the number of cycles (default 10) used, different structural results are obtained, hence is there a means of estimating the ideal number of cycles to use..? Many thanks Kristof Van Hecke ------ Kristof Van Hecke, PhD Biomoleculaire Architectuur Celestijnenlaan 200 F B-3001 Heverlee (Leuven) Tel: +32(0)16327477 -- Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm
[ccp4bb] Error ARP/wARP MODE_WILSON
Dear all, When refining a DNA-structure (poor data, resolution 2.5) and using ARP/wARP Solvent 7.0.1. for water divining with CCP4 6.1.1 and GUI 2.0.4, I get the following error: QUITTING ... ARP/wARP module stopped with an error message: ARP_WARP_MODE_WILSON When checking the "warp_wilson_log" file, I get: Comments: Overall fit of the data to the Wilson curve: Comments: Problems Resolution range 5.15 to 4.89 Comments: Problems Resolution range 4.89 to 4.67 Comments: Problems Resolution range 2.89 to 2.84 Comments: Possible reasons - missing overloads Solvent content1.00 Computed solvent content is too high - check your input * ERROR * I was kind of surprised, because with the same data! and an older version of ARP/wARP, which was integrated in the Refmac5 program, I did not get any errors of this kind..!? Is there a way to circumvent this please..? Many thanks Kristof Van Hecke Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm
[ccp4bb] differentiating cation and anions in high resolution structures
Dear all, I'm looking for some means (literature references,.. possible programs) to differentiate between cations (Na+), anions (e.g. Cl-) and water molecules in high resolution protein/DNA structures, based on B-factors, distances, coordination, etc.. Does anyone has got an idea of what's the best strategy to follow in these cases..? many thanks Kristof ------ Kristof Van Hecke, PhD Biomoleculaire Architectuur Celestijnenlaan 200 F B-3001 Heverlee (Leuven) Tel: +32(0)16327477 -- Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm
[ccp4bb] HKL2MAP
Dear, I'm looking to obtain a copy from HKL2MAP..? Does anyone know who to contact and the correct email address please..? The email of Thomas Schneider ([EMAIL PROTECTED]) is apparently not working anymore. Many thanks Kristof -- Kristof Van Hecke, PhD Biomoleculaire Architectuur Celestijnenlaan 200 F B-3001 Heverlee (Leuven) Tel: +32(0)16327477 -- Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm
[ccp4bb] merohedral twinning problem
Dear, Sorry for the off-topic question. I'm facing a (probably) merohedral twinning problem, regarding a small molecule. Using Xprep, I get a Hexagonal P-lattice with cell: 18.014 18.014 22.048 90.00 90.00 120.00 Mean |E*E-1| = 0.902 [expected .968 centrosym and .736 non-centrosym] However, based on the systematic absence exceptions, the probable (apparent) SG's are: P6(3)/m (Laue '6/m') P6(3) (Laue '6') P6(3)22 (Laue '622') 61/65 62=31 63-c- --c N60 50 36 2471 1420 N I>3s 19 19 0 420 161 186.6 223.1 4.6 30.015.5 2.3 2.6 0.3 1.6 1.2 I know there is a twin law to transform the (apparent) Laue group '6/ m' to the (true) Laue group '-3' (TWIN law -1 0 0 0 -1 0 0 0 1) and merging the data in a trigonal SG, but this is not solving the structure at all... Has anyone noticed a similar case that could be of any help please..? Many thanks Kristof Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm
Re: [ccp4bb] helix generator
3DNA..?! http://rutchem.rutgers.edu/~xiangjun/3DNA/ Kristof On 31 Jul 2008, at 16:55, Jacob Keller wrote: Dear crystallographers, is there a program around, ccp4 or otherwise, into which one can input a sequence and get a .pdb of an ideal helix of the input sequence? Thanks, Jacob Keller *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program Dallos Laboratory F. Searle 1-240 2240 Campus Drive Evanston IL 60208 lab: 847.491.2438 cel: 773.608.9185 email: [EMAIL PROTECTED] *** -- Kristof Van Hecke, PhD Biomoleculaire Architectuur Celestijnenlaan 200 F B-3001 Heverlee (Leuven) Tel: +32(0)16327477 -- Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm
[ccp4bb] convert and direction cosines
Dear, I was wondering if it is possible to preserve the direction cosines when converting an .mtz file (without scaling) to an .hkl file using the CCP4 program 'convert'..? (or perhaps another program..?) Many thanks Kristof ------ Kristof Van Hecke, PhD Biomoleculaire Architectuur Celestijnenlaan 200 F B-3001 Heverlee (Leuven) Tel: +32(0)16327477 -- Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm
[ccp4bb] program for distribution of distances
Dear all, I apologize for the off-topic question. I'm looking for some software that is able to read in (small molecule) structure files (e.g. .pdb, .cif,..) and subsequently outputs a listing of bond lengths AND 'environment' distances for each atom within a certain radius. Additionally, the listing should allow to construct a distribution diagram for each atom-atom distance. I already played a bit with Vista en Mercury (CCDC), but to my knowledge it's not possible to include such 'environment' distances... Thanks a lot Kristof ---------- Kristof Van Hecke, PhD Biomoleculaire Architectuur Celestijnenlaan 200 F B-3001 Heverlee (Leuven) Tel: +32(0)16327477 -- Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm
[ccp4bb] Phaser - NCS and Z-score
Dear all, I'm facing a particular MR problem: I'm trying to solve the structure of a 20kDa protein (1 mol/AU) in a cubic SG P432 (according to systematic absences and pointless) Sequence homology is about 30%. As I only get 'flat' scores with Phaser in P432, I lowered to SG P4 (with 6 mol/AU) and get following Z-scores: RFZ= 7.9 TFZ= 9.9 (LLG=111) However, when refining this result (Refmac), things do not look allright at all...? I'm aware of the fact that in the presence of translational NCS, Phaser can give large Z-scores. But when using 6 molecules/AU as a one model in Phaser, I'm in the feeling that this should be ruled out..?? Has anyone noticed such a case before please..? Regards Kristof ---------- Kristof Van Hecke, PhD Biomoleculaire Architectuur Celestijnenlaan 200 F B-3001 Heverlee (Leuven) Tel: +32(0)16327477 -- Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm
[ccp4bb] font size CCP4i
Dear all, I recently installed the CCP4 Program Suite 6.0.2., together with the CCP4Interface 1.4.4.2 under an Intel Mac Book Pro (running Leopard 10.5.2). All works fine, except for a minor issue: The font size in the GUI seems quit 'big' on both sides of the 'List of jobs', e.g. on the 'Data Reduction', 'Experimental Phasing',...buttons. The 'List of jobs' itself shows a 'normal' font size. This is probably due to some minor settings, which are not properly adjusted. But somehow I don't find where to adjust these...?? When installing under my (old) PPC running Tiger, this problem does not occur. Does anyone knows how to solve this please..? Many thanks Regards Kristof -- Kristof Van Hecke, PhD Biomoleculaire Architectuur Celestijnenlaan 200 F B-3001 Heverlee (Leuven) Tel: +32(0)16327477 -- Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm
[ccp4bb] OMIT map from Sfcheck
Dear, I'm intending to make an OMIT map using Sfcheck (ccp4i 6.0.2, Mac OS X Tiger, PPC). However, the program terminates with: "has failed with error message 1525-005 1525-005 1525-005 1525-005 1525-005 1525-005 " When using 'command line' from a script (with '-nomit 2 -map -origin - out y') I got: "Last system error message: No such file or directory CCP4: Open failed: File: /Users/kristof/data/11mer/data2/ sfcheck_scr.dat " Does anyone know this problem please..? Many thanks Kristof ---------- Kristof Van Hecke, PhD Biomoleculaire Architectuur Celestijnenlaan 200 F B-3001 Heverlee (Leuven) Tel: +32(0)16327477 -- Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm
[ccp4bb] convert .cif to .mtz
Dear all, I'm looking for a convenient way of converting a .cif structure factor file (from PDB) to a map-file (e.g. .mtz) to open with COOT for example..? Already tried ccp4i with 'Convert to/modify/extend MTZ', but got a bunch of errors when opening with coot.. Many thanks Kristof ---------- Kristof Van Hecke, PhD Biomoleculaire Architectuur Celestijnenlaan 200 F B-3001 Heverlee (Leuven) Tel: +32(0)16327477 -- Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm
[ccp4bb] Refmac extra restraint
Dear all, I'm wondering what's the best way to add an extra (tighter) distance restraint on the linkage between the P-atom of a guanidine (Gd)-residue and the O3'-atom of a thymidine (Td)-residue in an oligonucleotide structure, with use of the program Refmac_5.2.0019 (ccp4-6.0.2)...? And is it possible to specify this restraint for only two particular residues (e.g. T1 and G2)..? Many thanks Regards Kristof ---------- Kristof Van Hecke, PhD Biomoleculaire Architectuur Celestijnenlaan 200 F B-3001 Heverlee (Leuven) Tel: +32(0)16327477 -- Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm
Re: [ccp4bb] Protein interface prediction tool?
HADDOCK..? protein-protein docking.. Dominguez et al., 2003, JACS, 125, 1731-1737 Kristof On 29 Nov 2007, at 13:22, karen yates wrote: Hi, I would like to find a bioinformatic tool that will allow me to predict the dimerisation interface of a protein. A structural model has been generated, and it is known to exist as a homo-dimer. Does anyone know of a suitable program? Thank you for your help. Karen This message was sent using IMP, the Internet Messaging Program. -- Kristof Van Hecke, PhD Biomoleculaire Architectuur Celestijnenlaan 200 F B-3001 Heverlee (Leuven) Tel: +32(0)16327477 -- Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm
[ccp4bb] Pointless and space group P 4 3 2
Dear all, When running Pointless 1.2.0 (see summary below), I get the cubic space group P 4 3 2 (mosflm gave P 2 3 or P 4 3 2) Best Solution space group P 4 3 2 Reindex operator: [h,k,l] Laue group probability: 1.000 Systematic absence probability: 0.975 Total probability: 0.975 Space group confidence: 0.964 Laue group confidence 1.000 However, although I have multiple models (ensemble) with approximately 30% sequence identity (44% homology), I'm not able to get any reasonable solution with Phaser. As we know the protein can form dimers and even trimers, is it possible that Poinless is giving a higher space group because of pseudo-symmetry in this case..? Does anyone has got experience with Pointless and this kind of space group please..? Many thanks Kristof -- Kristof Van Hecke, PhD Biomoleculaire Architectuur Celestijnenlaan 200 F B-3001 Heverlee (Leuven) Tel: +32(0)16327477 -- Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm
[ccp4bb] Poinless and space group P 4 3 2
Dear all, When running Pointless 1.2.0 (see summary below), I get the cubic space group P 4 3 2 (mosflm gave P 2 3 or P 4 3 2) Best Solution space group P 4 3 2 Reindex operator: [h,k,l] Laue group probability: 1.000 Systematic absence probability: 0.975 Total probability: 0.975 Space group confidence: 0.964 Laue group confidence 1.000 However, although I have multiple models (ensemble) with approximately 30% sequence identity (44% homology), I'm not able to get any reasonable solution with Phaser. As we know the protein can form dimers and even trimers, is it possible that Poinless is giving a higher space group because of pseudo-symmetry in this case..? Does anyone has got experience with Pointless and this kind of space group please..? Many thanks Kristof -- Kristof Van Hecke, PhD Biomoleculaire Architectuur Celestijnenlaan 200 F B-3001 Heverlee (Leuven) Tel: +32(0)16327477 -- Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm
[ccp4bb] small molecule refinement GUI for Mac
Dear all, I'm looking for a small molecule refinement GUI for shelxl under Mac OSX (commercially or non-commercially available). Any suggestions are very welcome! Many thanks Sincerely Kristof -- Kristof Van Hecke, PhD Biomoleculaire Architectuur Celestijnenlaan 200 F B-3001 Heverlee (Leuven) Tel: +32(0)16327468 -- Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm
[ccp4bb] antibumping restraint in Refmac
Dear, I was wondering what is the best method for applying 'anti-bumping' restraints in Refmac? (e.g. for preventing some specific water molecules coming too close to each other) Many thanks Greetings Kristof ------ Kristof Van Hecke, PhD Biomoleculaire Architectuur Celestijnenlaan 200 F B-3001 Heverlee (Leuven) Tel: +32(0)16327468 -- Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm
[ccp4bb] DTT in crystallization conditions
Dear all, I apologize for the non-ccp4 related question. However, I am trying to crystallize a (very pure) protein, but according to the mass-spectrometry data, it's able to form dimers and even trimers.. I was told that adding DTT (dithiothreitol) to the crystallization conditions could prevent dimerization..? Does anyone has got experience with this please..? Regards Kristof Van Hecke -- Kristof Van Hecke, PhD Biomoleculaire Architectuur Celestijnenlaan 200 F B-3001 Heverlee (Leuven) Tel: +32(0)16327468 -- Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm
Re: [ccp4bb] MarView on OSX
Hi Michael, I can run the program under MacOSX (Tiger) PPC from a terminal (had to change permissions): Just type './marView' However, some 'buttons' are not working...like 'File' and 'Options'... but you can browse to an image and view it... Greetings Kristof On 25 Jan 2007, at 23:15, Michael McCormick wrote: Hi Everyone, Has anyone ever run the .mccd diffraction image viewing/editing program "MarView" on Mac OSX? You can download it free form MarResearch (http://www.marresearch.com/), and I can get it to execute fine in Linux, but not on my Mac. The main problem is I can't get the "marView" file to execute from a terminal, from X11, or simply by double-clicking on it in the Finder. MarResearch claims that it runs in OSX X11, but thier tech support had no suggestions as how to get it running exactly. I have the same problem with "EMPR" in OSX. Maybe this is a unix "path" issue (?)... Any help anyone can provide will be greatly appreciated. MSM _ Get Hilary Duff’s homepage with her photos, music, and more. http:// celebrities.live.com -- Kristof Van Hecke, PhD Biomoleculaire Architectuur Celestijnenlaan 200 F B-3001 Heverlee (Leuven) Tel: +32(0)16327468 -- Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm
