Re: [ccp4bb] phased MR
Hi - I would not use mlphare for anything marginal (to be honest not at all). Both SHARP (use eternal pdb file in top page of the gui) and the new Phaser (look at the doc for scripts for this case) can do what you want. Tassos On Nov 4, 2008, at 11:55, Thomas Edwards wrote: Dear BB, I would like to ask for some advice on phased molecular replacement if possible. I have a MR model that has so far not proved successful with Phaser, Molrep, Amore, Beast etc. I have SeMet MAD data to 3.6A that gives decent looking anomalous difference peaks, looks stable in mlphare, and produces solvent flattened maps to 2.8A in DM that look like the density might be a sensible shape - wrt solvent gaps etc - but not interpretable so far (I will be trying phasing in SHARP, CNS etc). In the mean time, is there a good way to combine phases that may be slightly sensible with molecular replacement? Things may also be complicated by the possibility of NCS translations… Any advice gratefully received. Many thanks to all those who continue to provide excellent suggestions, Cheers Ed __ T.Edwards Ph.D. Garstang 8.53d Astbury Centre for Structural Molecular Biology University of Leeds, Leeds, LS2 9JT Telephone: 0113 343 3031 http://www.bmb.leeds.ac.uk/staff/tae/ If you're not part of the solution, you're part of the precipitate. ~Henry J. Tillman
[ccp4bb] ESRF School - 2nd - 5th February 2009
Dear all, We are pleased to announce the ESRF School titled *Getting the most from the ESRF MX beamlines* ESRF, Grenoble, France, 2nd - 5th February 2009 As part of its 2009 Users Meeting, the ESRF will host a short school *Getting the most from the ESRF MX beamlines* from 2nd to 5th February 2009. The School will be held on 3 days either side of the Users Meeting and is aimed at younger, relatively inexperienced users of the ESRF's MX beam-lines. The school is designed to (a) introduce the art of collecting good diffraction data at synchrotron-based MX facilities, (b) familiarize the participants with the tools available at the beam-line to allow correct pre- and post-data collection decisions to be taken and (c) present the various ancillary techniques and equipment accessible at the ESRF’s MX beam-lines. The number of participants will be limited to 20 with all _local costs_ (i.e. registration fees, accommodation, subsistence) being met by the ESRF. The deadline for applications is 15th December 2008. More detailed information, a preliminary programme and instructions as to how to apply to attend the school can be found at: http://www.esrf.fr/events/conferences/usersmeeting2009/mx-school The organising Committee
Re: [ccp4bb] tricoordinated ion?
Sebastiano, The density is possibly consistent with a trigonal planar anion such as bicarbonate or nitrate. Bicarbonate can enter the solution from CO2 in the atmosphere. Cheers, -- Roger S. Rowlett Professor Colgate University Presidential Scholar Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: [EMAIL PROTECTED] Sebastiano Pasqualato wrote: Hi all, I wanted to ask you what would you model in the density in which I have at the moment modelled 4 water molecules, which are however too close to be waters, I guess (see attached image). My crystallisation conditions contain NaCl, MgCl2, Peg400, TrisHCl, TCEP, glycerol. I can't think at a tricoordinated ion like that... thanks in advance for the hints, ciao S -- Sebastiano Pasqualato, PhD IFOM-IEO Campus Dipartimento di Oncologia Sperimentale Istituto Europeo di Oncologia via Adamello, 16 20139 - Milano Italy tel +39 02 9437 5094 fax +39 02 574 303 310
Re: [ccp4bb] tricoordinated ion?
May be something that tagged along from purification or one of the impurities in the chemicals... nitrate, carbonate, etc. Incidentally, a 3.9 M BMP file was a nasty surprise for my mail box. A JPEG or PNG file of similar quality would have taken less than 100K... Artem Hi all, I wanted to ask you what would you model in the density in which I have at the moment modelled 4 water molecules, which are however too close to be waters, I guess (see attached image). My crystallisation conditions contain NaCl, MgCl2, Peg400, TrisHCl, TCEP, glycerol. I can't think at a tricoordinated ion like that... thanks in advance for the hints, ciao S -- Sebastiano Pasqualato, PhD IFOM-IEO Campus Dipartimento di Oncologia Sperimentale Istituto Europeo di Oncologia via Adamello, 16 20139 - Milano Italy tel +39 02 9437 5094 fax +39 02 574 303 310
[ccp4bb] Crystals grown from high ammonium sulphate
Hi everyone, We got crystals that grew in ~3.2M ammonium sulphate and some tris-buffer at 18dgC. Unfortunately the crystals take a while to grow (~4-5 weeks) and so far we only have 4-5 xtals. I tried to freeze the crystals, but as soon as I broke though the skin of the drop the ammonium sulphate started to crystallise. I got the crystals out, froze them using sort of an artifical mother liquor with sodium malonate as cryo and tested the diffraction. The freezing seems to be OK and it is definitely a protein crystal. The crystal suffered when the ammonium sulphate in the drop started to crystallise, but didn't seem to deteriorate anymore in the cryo. Well the corners had already more or less disappeared by the time I got them out of the drop... Since we only have a few xtals at the moment and I can't try out a lot of things, I was wondering if anyone has experienced and solved a similar problem? My freezing attempt so far was in an airconditioned room with 18dgC. I thought about higher humidity and temperature in the room, and/or adding the cryo directly to the drop Any ideas are very much appreciated! Sabine -- Dr. Sabine Schneider Ludwig-Maximilians-University Department of Chemistry and Pharmacy Butenandtstrasse 5-13, Building F 81377 Munich Germany Phone: +49 (0)89 2180 77846 Fax: +49 (0)89 2180 77756 http://www.carellgroup.de/
Re: [ccp4bb] Crystals grown from high ammonium sulphate
Hi Sabine, I had a similar problem years ago. Have you tried oils ? (mineral oil, paraffin oil, 50:50 mixtures of either with N-paratone) You can either 1. add a small amount (1ul or less) to the drop containing the crystals and mount from there or 2. if you are quick enough, transfer the crystal to a small drop of oil and mount it in the cryostream straight from the oil. HTH, Iain Sabine Schneider wrote: Hi everyone, We got crystals that grew in ~3.2M ammonium sulphate and some tris-buffer at 18dgC. Unfortunately the crystals take a while to grow (~4-5 weeks) and so far we only have 4-5 xtals. I tried to freeze the crystals, but as soon as I broke though the skin of the drop the ammonium sulphate started to crystallise. I got the crystals out, froze them using sort of an artifical mother liquor with sodium malonate as cryo and tested the diffraction. The freezing seems to be OK and it is definitely a protein crystal. The crystal suffered when the ammonium sulphate in the drop started to crystallise, but didn't seem to deteriorate anymore in the cryo. Well the corners had already more or less disappeared by the time I got them out of the drop... Since we only have a few xtals at the moment and I can't try out a lot of things, I was wondering if anyone has experienced and solved a similar problem? My freezing attempt so far was in an airconditioned room with 18dgC. I thought about higher humidity and temperature in the room, and/or adding the cryo directly to the drop Any ideas are very much appreciated! Sabine -- Dr. Sabine Schneider Ludwig-Maximilians-University Department of Chemistry and Pharmacy Butenandtstrasse 5-13, Building F 81377 Munich Germany Phone: +49 (0)89 2180 77846 Fax: +49 (0)89 2180 77756 http://www.carellgroup.de/
Re: [ccp4bb] Crystals grown from high ammonium sulphate
Generally crystals require a much higher precipitant concentration for nucleation than for growth and maybe even less for maintenance of their crystalline state. Therefore I would a) try micro seeding into less Ammonium Sulpahte b) reduce the ammonium sulfate concentration in the drop by adding ammonium sulphate free mother liquor to the reservoir (not the drop itself!) This would re-equilibrate the drop to lower a AS concentration. You could remove one crytal and try to find the lowest possible AS concentration with it separately. Tim -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A On Tue, 4 Nov 2008, Sabine Schneider wrote: Hi everyone, We got crystals that grew in ~3.2M ammonium sulphate and some tris-buffer at 18dgC. Unfortunately the crystals take a while to grow (~4-5 weeks) and so far we only have 4-5 xtals. I tried to freeze the crystals, but as soon as I broke though the skin of the drop the ammonium sulphate started to crystallise. I got the crystals out, froze them using sort of an artifical mother liquor with sodium malonate as cryo and tested the diffraction. The freezing seems to be OK and it is definitely a protein crystal. The crystal suffered when the ammonium sulphate in the drop started to crystallise, but didn't seem to deteriorate anymore in the cryo. Well the corners had already more or less disappeared by the time I got them out of the drop... Since we only have a few xtals at the moment and I can't try out a lot of things, I was wondering if anyone has experienced and solved a similar problem? My freezing attempt so far was in an airconditioned room with 18dgC. I thought about higher humidity and temperature in the room, and/or adding the cryo directly to the drop Any ideas are very much appreciated! Sabine -- Dr. Sabine Schneider Ludwig-Maximilians-University Department of Chemistry and Pharmacy Butenandtstrasse 5-13, Building F 81377 Munich Germany Phone: +49 (0)89 2180 77846 Fax: +49 (0)89 2180 77756 http://www.carellgroup.de/
Re: [ccp4bb] tricoordinated ion?
Sebastiano, it might be a trigonal planar anion, as Roger and others suggest, but the density doesn't look very symmetrical to me; also, the bond lengths look too long (e.g., bicarbonate should be ~1.4 Angs., I believe). Try taking the waters out (zero occ.), and see what the maps tell you at that point after a bit of refinement (you also seem to have a fair amount of +ve -ve diff. density peaks around that region already). It could be a planar ion (maybe the bond lengths appear too long, due to water/water van der Waals repulsions of your refinement program), or several mutually-exclusive waters (will need alt. conf. flags), or maybe (hard to tell from a 2D picture) a hydrated Mg2+ ion (bond lengths look correct; you would expect hexacoordination, pretty close to octahedral geometry. Hope this helps, Dave David Borhani, Ph.D. D. E. Shaw Research, LLC 120 West Forty-Fifth Street, 39th Floor New York, NY 10036 [EMAIL PROTECTED] 212-478-0698 http://www.deshawresearch.com http://www.deshawresearch.com/ From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Roger Rowlett Sent: Tuesday, November 04, 2008 12:45 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] tricoordinated ion? Sebastiano, The density is possibly consistent with a trigonal planar anion such as bicarbonate or nitrate. Bicarbonate can enter the solution from CO2 in the atmosphere. Cheers, -- Roger S. Rowlett Professor Colgate University Presidential Scholar Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: [EMAIL PROTECTED] Sebastiano Pasqualato wrote: Hi all, I wanted to ask you what would you model in the density in which I have at the moment modelled 4 water molecules, which are however too close to be waters, I guess (see attached image). My crystallisation conditions contain NaCl, MgCl2, Peg400, TrisHCl, TCEP, glycerol. I can't think at a tricoordinated ion like that... thanks in advance for the hints, ciao S -- Sebastiano Pasqualato, PhD IFOM-IEO Campus Dipartimento di Oncologia Sperimentale Istituto Europeo di Oncologia via Adamello, 16 20139 - Milano Italy tel +39 02 9437 5094 fax +39 02 574 303 310
Re: [ccp4bb] Crystals grown from high ammonium sulphate
You can try microseeding. It is really suitable for crystallization in high ammonium sulphate. I got a similar problem as well, before. Microseeding can supply nucleus. You can get more crystals and spend less time. And for the salt crystallization, I think if you transfer quickly it can be fine. Or a high humidity might be useful. Liang On Tue, 4 Nov 2008 19:34:20 +0100, Sabine Schneider wrote Hi everyone, We got crystals that grew in ~3.2M ammonium sulphate and some tris-buffer at 18dgC. Unfortunately the crystals take a while to grow (~4-5 weeks) and so far we only have 4-5 xtals. I tried to freeze the crystals, but as soon as I broke though the skin of the drop the ammonium sulphate started to crystallise. I got the crystals out, froze them using sort of an artifical mother liquor with sodium malonate as cryo and tested the diffraction. The freezing seems to be OK and it is definitely a protein crystal. The crystal suffered when the ammonium sulphate in the drop started to crystallise, but didn't seem to deteriorate anymore in the cryo. Well the corners had already more or less disappeared by the time I got them out of the drop... Since we only have a few xtals at the moment and I can't try out a lot of things, I was wondering if anyone has experienced and solved a similar problem? My freezing attempt so far was in an airconditioned room with 18dgC. I thought about higher humidity and temperature in the room, and/or adding the cryo directly to the drop Any ideas are very much appreciated! Sabine -- Dr. Sabine Schneider Ludwig-Maximilians-University Department of Chemistry and Pharmacy Butenandtstrasse 5-13, Building F 81377 Munich Germany Phone: +49 (0)89 2180 77846 Fax: +49 (0)89 2180 77756 http://www.carellgroup.de/ -- Open WebMail Project (http://openwebmail.org)
[ccp4bb] Postdoc position
*Postdoctoral Positions in Macromolecular Crystallography* are immediately available in the Lucy Malinina laboratory at the Structural Biology Department of CICbioGUNE (Bilbao, Spain). We use the X-ray crystallographic approaches to elucidate structural principles of a biological intermolecular recognition for developing the means to effectively use and pharmacologically modulate protein specificity of a diverse nature. We focus our efforts on human neurodegenerative diseases, and currently study complexes with RNA in Project_1 Structural Basis for Suppression of Human Trinucleotide Repeat Expansion Diseases (TREDs) and glycolipids in Project_2 Molecular Basis for Manipulating the Selectivity of Glycolipid Transfer. Other projects are under development. *The crystallographic platform* includes a Bruker Microstar-H rotating anode generator, MAR345-DTB image plate, Bruker-135 mm CCD detector system, Helios confocal optics, two Oxford Cryosystem Series 700, TECAN-EVO100 liquid handling robot, Mosquito nanodispenser, a Bruker Crystal Farm, and supporting computers/software. *The biochemical laboratory *is supported by all necessary equipment for protein expression/isolation/purification, and oligonucleotide synthesis/purification as well. *Key Qualifications:* - PhD in physics, chemistry, biochemistry, biophysics or related field - Experience working in the area of macromolecular crystallography, including o the X-ray data collection for biological crystallography, o the use of computer programs required for biological crystallography, o crystallization with use of robotics hardware and control systems. To apply please submit before December 20, 2008 a cover letter, CV, and three references addressed to [EMAIL PROTECTED] with ref. postdoc application in the subject line.
Re: [ccp4bb] Crystals grown from high ammonium sulphate
Dear Sabine, I recently dealt with a very similar situation as follows: -I ended up growing the crystals in 4+4 uL drops. Skin formation tends to be less of a problem in larger drops. This kind of experimentation is of course only possible if protein production is not a limiting factor. -For crystal manipulation, I used to add 10-20 uL of the reservoir solution directly to the drop. In this way I could easily manipulate the 5-6 crystals that grew per drop within 5 minutes without any noticeable effects on the crystals. -I found out that cryo-cooling the crystals by plunging them into liquid nitrogen straight out the drop was the only way to effectively cryo-cool such crystals. In fact the crystal condition was very similar to yours (3.2 M AS, 20 mM potassium phosphate pH 6.0). I cite the most relevant paragraph from our paper (Kyndt et al. Biochemistry. 2007 46(1):95-105.): To prepare crystals for data collection under cryogenic conditions (100 K), crystals were flash-cooled by plunging them directly from their native drops into liquid nitrogen. A series of cryocooling conditions using a variety of cryoprotecting reagents such as glycerol, sucrose, PEG 400, and paratone indicated that only crystals flash-cooled by plunging them directly from their native drops into liquid nitrogen produced diffraction of acceptable quality. Best wishes Savvas Savvas Savvides L-ProBE, Unit for Structural Biology Ghent University K.L. Ledeganckstraat 35 9000 Ghent, BELGIUM office: +32-(0)9-264.51.24 ; mobile: +32-(0)472-92.85.19 Email: [EMAIL PROTECTED] http://www.eiwitbiochemie.ugent.be/units_en/structbio_en.html -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Sabine Schneider Sent: Tuesday, November 04, 2008 7:34 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Crystals grown from high ammonium sulphate Hi everyone, We got crystals that grew in ~3.2M ammonium sulphate and some tris-buffer at 18dgC. Unfortunately the crystals take a while to grow (~4-5 weeks) and so far we only have 4-5 xtals. I tried to freeze the crystals, but as soon as I broke though the skin of the drop the ammonium sulphate started to crystallise. I got the crystals out, froze them using sort of an artifical mother liquor with sodium malonate as cryo and tested the diffraction. The freezing seems to be OK and it is definitely a protein crystal. The crystal suffered when the ammonium sulphate in the drop started to crystallise, but didn't seem to deteriorate anymore in the cryo. Well the corners had already more or less disappeared by the time I got them out of the drop... Since we only have a few xtals at the moment and I can't try out a lot of things, I was wondering if anyone has experienced and solved a similar problem? My freezing attempt so far was in an airconditioned room with 18dgC. I thought about higher humidity and temperature in the room, and/or adding the cryo directly to the drop Any ideas are very much appreciated! Sabine -- Dr. Sabine Schneider Ludwig-Maximilians-University Department of Chemistry and Pharmacy Butenandtstrasse 5-13, Building F 81377 Munich Germany Phone: +49 (0)89 2180 77846 Fax: +49 (0)89 2180 77756 http://www.carellgroup.de/ E-mail message checked by Spyware Doctor (6.0.0.386) Database version: 5.11050 http://www.pctools.com/en/spyware-doctor-antivirus/
Re: [ccp4bb] tricoordinated ion?
Hi Sebastiano, I had similar experiences with various crystal structures. After a lot of modeling (albeit at about 1 A resolution) I came to the conclusion that these atoms correspond to disordered solvent molecules, e.g. water and/or Zn. In other words the atoms have occupancies of 1, but in the sum it should be 1. For CO2 or similar molecules the bond length are far too long (C-O is about 1.4 A or so). Good luck. Klaus Piontek Sebastiano Pasqualato wrote: Hi all, I wanted to ask you what would you model in the density in which I have at the moment modelled 4 water molecules, which are however too close to be waters, I guess (see attached image). My crystallisation conditions contain NaCl, MgCl2, Peg400, TrisHCl, TCEP, glycerol. I can't think at a tricoordinated ion like that... thanks in advance for the hints, ciao S -- Dr. Klaus Piontek Albert-Ludwigs-University Freiburg Institute of Organic Chemistry and Biochemistry, Room 401 H Albertstrasse 21 D-79104 Freiburg Germany Phone: ++49-761-203-6036 Fax: ++49-761-203-8714 Email: [EMAIL PROTECTED] Web: http://www.chemie.uni-freiburg.de/orgbio/w3platt/
Re: [ccp4bb] tricoordinated ion?
Before jumping to any conclusions, you should definitely see what this density looks like without the water molecules in this portion of the model. I think it would be difficult to decide on what the actual "bond lengths" are without removing model bias. If you model with waters, of course the electron density will conform to some degree to what is modeled there. You may find that without the waters, the electron density shrinks up a bit, or can be adequately modeled with a trigonal planar anion. On the other hand, maybe it is just a cluster of water molecules, or an anion at less than 100% occupancy. From your water model, however, it looks like you may have enough density for a full occupancy anion. FYI, the surrounding ligands, Arg + Glu + another H-bonding donor are certainly compatible with the few known bicarbonate binding sites in proteins. Roger Rowlett Klaus Piontek wrote: Hi Sebastiano, I had similar experiences with various crystal structures. After a lot of modeling (albeit at about 1 A resolution) I came to the conclusion that these atoms correspond to disordered solvent molecules, e.g. water and/or Zn. In other words the atoms have occupancies of 1, but in the sum it should be 1. For CO2 or similar molecules the bond length are far too long (C-O is about 1.4 A or so). Good luck. Klaus Piontek Sebastiano Pasqualato wrote: Hi all, I wanted to ask you what would you model in the density in which I have at the moment modelled 4 water molecules, which are however too close to be waters, I guess (see attached image). My crystallisation conditions contain NaCl, MgCl2, Peg400, TrisHCl, TCEP, glycerol. I can't think at a tricoordinated ion like that... thanks in advance for the hints, ciao S -- Dr. Klaus Piontek Albert-Ludwigs-University Freiburg Institute of Organic Chemistry and Biochemistry, Room 401 H Albertstrasse 21 D-79104 Freiburg Germany Phone: ++49-761-203-6036 Fax: ++49-761-203-8714 Email: [EMAIL PROTECTED] Web: http://www.chemie.uni-freiburg.de/orgbio/w3platt/
[ccp4bb] is it possible or is it existing ?
Dear ccp4bb caretakers, I am very young for the ccp4bb thread(2007 jan-my thread date of birth). Is is possible to compile very important issues in a hyperlinked style of the important problems,discussions and queries with in ccp4 threads. for example when am reading a query of 2006 regarding software compatability, i may have very apt answer which is posted on 2005 or any other time. Or regarding MAD phasing in 2008, might have answer in 2007..like that. or, is there something already like this. S.Jayashankar Research Student Institute for Biophysical Chemistry Hannover Medical School Germany.
Re: [ccp4bb] Crystals grown from high ammonium sulphate
also, don't forget to measure at least one crystal at RT, probably most easily done in a Mitegen loop-and-sleeve - to have an idea of the intrinsic diffraction quality of the crystals without freezing. Mark Quoting Savvas Savvides [EMAIL PROTECTED]: Dear Sabine, I recently dealt with a very similar situation as follows: -I ended up growing the crystals in 4+4 uL drops. Skin formation tends to be less of a problem in larger drops. This kind of experimentation is of course only possible if protein production is not a limiting factor. -For crystal manipulation, I used to add 10-20 uL of the reservoir solution directly to the drop. In this way I could easily manipulate the 5-6 crystals that grew per drop within 5 minutes without any noticeable effects on the crystals. -I found out that cryo-cooling the crystals by plunging them into liquid nitrogen straight out the drop was the only way to effectively cryo-cool such crystals. In fact the crystal condition was very similar to yours (3.2 M AS, 20 mM potassium phosphate pH 6.0). I cite the most relevant paragraph from our paper (Kyndt et al. Biochemistry. 2007 46(1):95-105.): To prepare crystals for data collection under cryogenic conditions (100 K), crystals were flash-cooled by plunging them directly from their native drops into liquid nitrogen. A series of cryocooling conditions using a variety of cryoprotecting reagents such as glycerol, sucrose, PEG 400, and paratone indicated that only crystals flash-cooled by plunging them directly from their native drops into liquid nitrogen produced diffraction of acceptable quality. Best wishes Savvas Savvas Savvides L-ProBE, Unit for Structural Biology Ghent University K.L. Ledeganckstraat 35 9000 Ghent, BELGIUM office: +32-(0)9-264.51.24 ; mobile: +32-(0)472-92.85.19 Email: [EMAIL PROTECTED] http://www.eiwitbiochemie.ugent.be/units_en/structbio_en.html -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Sabine Schneider Sent: Tuesday, November 04, 2008 7:34 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Crystals grown from high ammonium sulphate Hi everyone, We got crystals that grew in ~3.2M ammonium sulphate and some tris-buffer at 18dgC. Unfortunately the crystals take a while to grow (~4-5 weeks) and so far we only have 4-5 xtals. I tried to freeze the crystals, but as soon as I broke though the skin of the drop the ammonium sulphate started to crystallise. I got the crystals out, froze them using sort of an artifical mother liquor with sodium malonate as cryo and tested the diffraction. The freezing seems to be OK and it is definitely a protein crystal. The crystal suffered when the ammonium sulphate in the drop started to crystallise, but didn't seem to deteriorate anymore in the cryo. Well the corners had already more or less disappeared by the time I got them out of the drop... Since we only have a few xtals at the moment and I can't try out a lot of things, I was wondering if anyone has experienced and solved a similar problem? My freezing attempt so far was in an airconditioned room with 18dgC. I thought about higher humidity and temperature in the room, and/or adding the cryo directly to the drop Any ideas are very much appreciated! Sabine -- Dr. Sabine Schneider Ludwig-Maximilians-University Department of Chemistry and Pharmacy Butenandtstrasse 5-13, Building F 81377 Munich Germany Phone: +49 (0)89 2180 77846 Fax: +49 (0)89 2180 77756 http://www.carellgroup.de/ E-mail message checked by Spyware Doctor (6.0.0.386) Database version: 5.11050 http://www.pctools.com/en/spyware-doctor-antivirus/
[ccp4bb] phased MR
Dear BB, I would like to ask for some advice on phased molecular replacement if possible. I have a MR model that has so far not proved successful with Phaser, Molrep, Amore, Beast etc. I have SeMet MAD data to 3.6A that gives decent looking anomalous difference peaks, looks stable in mlphare, and produces solvent flattened maps to 2.8A in DM that look like the density might be a sensible shape - wrt solvent gaps etc - but not interpretable so far (I will be trying phasing in SHARP, CNS etc). In the mean time, is there a good way to combine phases that may be slightly sensible with molecular replacement? Things may also be complicated by the possibility of NCS translations... Any advice gratefully received. Many thanks to all those who continue to provide excellent suggestions, Cheers Ed __ T.Edwards Ph.D. Garstang 8.53d Astbury Centre for Structural Molecular Biology University of Leeds, Leeds, LS2 9JT Telephone: 0113 343 3031 http://www.bmb.leeds.ac.uk/staff/tae/ http://www.bmb.leeds.ac.uk/staff/tae/Research http://www.bmb.leeds.ac.uk/staff/tae/ If you're not part of the solution, you're part of the precipitate. ~Henry J. Tillman
Re: [ccp4bb] ccp4 6.0.99e test release
Hello ccp4-ers I have been happily running ccp4-6.0.99e, which I self compiled on an Ubuntu 64bit ( Version 8.04) box Things have been going smoothly till I noticed a segmentation fault when I tried to get a postscript file using xplot84driver . The binary run from a shell and the ccp4i gui give the following error FROM SHELL [EMAIL PROTECTED]:~/ccp4-6.0.99e/x-windows/XCCPJIFFY$ ./xplot84driver ~/yjchotmp/yjchotmp_2_1.plt Warning: Representation size 1 must match superclass's to override useStringInPlace Segmentation fault FROM CCP4 GUI [EMAIL PROTECTED]:~$ Warning: Representation size 1 must match superclass's to override useStringInPlace Any ideas on how to overcome this I am attaching the Makefile I used to compile this xplot84driver binary on my system Thank you for your help Hari On Fri, Jul 25, 2008 at 11:54 AM, Martyn Winn [EMAIL PROTECTED] wrote: Dear All the latest test version is on the ccp4 ftp server. ftp://ftp.ccp4.ac.uk/ccp4/6.1/ccp4-6.0.99e-core-src.tar.gz- core ccp4, rapper, clipper ftp://ftp.ccp4.ac.uk/ccp4/6.1/ccp4-6.0.99e-phaser-src.tar.gz - cctbx and phaser ftp://ftp.ccp4.ac.uk/ccp4/6.1/ccp4-6.0.99e-balbes_db.tar.gz - balbes database only There is also the dependency of PyXML if you want to run balbes ftp://ftp.ccp4.ac.uk/ccp4/6.1/ccp4-6.0.99e-PyXML.tar.gz for the first 3 tarballs unpack into the same directory, then configure...make...make install. For the PyXML, follow the instructions in the PyXML-0.8.4 directory. Major changes: refmac5.5 built by default. This gives twinning and sad refinement. dbhandler. Many optimisations, so this should be much more responsive. For other updates see the CHANGES file. Still to come: downloads pages (under internal testing). documentation updates (lots of) Feedback to the usual locale ([EMAIL PROTECTED]) Thanks Charles and the rest of us here at DL. -- *** * * * Dr. Martyn Winn * * * * STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K. * * Tel: +44 1925 603455E-mail: [EMAIL PROTECTED] * * Fax: +44 1925 603825Skype name: martyn.winn * * URL: http://www.ccp4.ac.uk/martyn/ * *** Makefile Description: Binary data
