[ccp4bb] Notebook and stereo
Hi All, I am looking for a laptop computer that works well with stereo viewing on Coot, Pymol, and Discovery Studio. Nvidia 3Dvision webpage offers quite a few models but almost all of them in market is 17 and thus too heavy to carry around. Please, if any of you could suggest any model of laptop that is lighter than 3 kg + a pair of stereo glasses (brand?), I would be very grateful. Cheers, Duangrudee
Re: [ccp4bb] Error in scalepack(Denzo)
Can you send a bit of the input file and the command script generated by the GUI Eleanor On 07/02/2011 07:48 AM, Sudhir Kumar wrote: Dear all I am trying to convert a scaled file (scaled using Automar) to mtz butit is showing follwoing error : #CCP4I TERMINATION STATUS 0 Error from script /opt/ccp4i/ccp4-6.1.1/ccp4i/scripts/import_scaled.script: can't read dataset_name: no such variable #CCP4I TERMINATION TIME 02 Jul 2011 12:14:22 #CCP4I MESSAGE Task failed I am trying to give data set names but it not rectified. Kindly advise
[ccp4bb] Twinning and Free R set generation
Hi all, I am worried about mixing working and free reflexions during TWIN refinement. Is there any keyword in UNIQUEIFY to generate a R-free flag in the case of twinning? I mean in that way that the possible twinning operators are taken into account for a following refmac job using the TWIN keyword. I couldn't find any information in the UNIQUEIFY, REFMAC or TWINNING manual. Thank you Peter Vidani
[ccp4bb] Twinning and Free R set generation
Hi all, I am worried about mixing working and free reflexions during TWIN refinement. Is there any keyword in UNIQUEIFY to generate a R-free flag in the case of twinning? I mean in that way that the possible twinning operators are taken into account for a following refmac job using the TWIN keyword. I couldn't find any information in the UNIQUEIFY, REFMAC or TWINNING manual. Thank you Peter Vidani
Re: [ccp4bb] Twinning and Free R set generation
This is a problem not properly addressed - if you generate your FreeRflags in the highest possible Laue group for a system - eg P6/mmm if you SG is trigonal, then add these to the lower symmetry reflection list you are safe. It really should be done at the pointless stage but it isnt.. Here is a script I used - rather messy but it works Eleanor On 07/04/2011 03:02 PM, Peter Vidani wrote: Hi all, I am worried about mixing working and free reflexions during TWIN refinement. Is there any keyword in UNIQUEIFY to generate a R-free flag in the case of twinning? I mean in that way that the possible twinning operators are taken into account for a following refmac job using the TWIN keyword. I couldn't find any information in the UNIQUEIFY, REFMAC or TWINNING manual. Thank you Peter Vidani Here is an exaple How to generate suitable FreeRflags for twinned data 1) change spacegroup to highest possible Laue group and only keep FreeRflag mtzutils hklin1 /y/people/ccp4/projects/mariaH/JGdUTPase1_9_reindex1.mtz symm P213 include FreeRflag Symm goes from P212121 to P213 2) cad all data in the new spacegroup - the asymm unit limits will now be cubic and FreeRflags restricted to cubic ones cad hklin1 /y/people/ccp4/projects/mariaH/JGdUTPase1_9_reindex1-P213.mtz hklout JGdUTPase1_9_reindex1-P213limited.mtz LABIN FILE 1 ALLIN end 3) Use cad to extend this file to have data with the pointgroup P222 limits (ie h0,k=0,l=0 cad HKLIN1 /y/people/ccp4/projects/mariaH/JGdUTPase1_9_reindex1-P213limited.mtz HKLOUT /y/people/ccp4/projects/mariaH/JGdUTPase1_9_reindex1-P213extended.mtz outlim spacegroup P222 labin file 1 ALL end 4) change spacegroup in output mtz to true space group mtzutils hklin1 /y/people/ccp4/projects/mariaH/JGdUTPase1_9_reindex1-P213extended.mtz HKLOUT /y/people/ccp4/projects/mariaH/JGdUTPase1_9_reindex1-P212121FreeR.mtz symm P212121 end Get rid of Free R flag from the original data set mtzutils hklin1 /y/people/ccp4/projects/mariaH/JGdUTPase1_9_reindex1.mtz hklout /y/people/ccp4/projects/mariaH/JGdUTPase1_9_reindex1-noFree.mtz exclude FreeRflag end cad together the P212121 data without FreeRflag, and add the new FreeRflag where all cubic equivalences will have the same setting cad HKLIN1 /y/people/ccp4/projects/mariaH/JGdUTPase1_9_reindex1noFree.mtz HKLIN2 /y/people/ccp4/projects/mariaH/JGdUTPase1_9_reindex1-P212121FreeR.mtz HKLOUT /y/people/ccp4/projects/mariaH/JGdUTPase1_9_reindex1-P212121-FreeP213.mtz labi file 1 allin labi file 2 allin end
[ccp4bb] 2 Postdoctoral Positions - Research Complex at Harwell
*** Research Officers in Dynamic Structural Science at the Research Complex at Harwell and the University of Bath (2 posts, fixed term for 4 years) *** Applications are invited from suitably qualified candidates for two EPSRC funded four-year post doctoral Research Officer posts in Dynamic Structural Science. The successful applicants will have proven track records in either molecular/macromolecular crystallography (post 1) or in XAFS techniques (post 2). They will be housed in the Research Complex at Harwell, at the Rutherford Appleton Laboratory (RAL), Didcot, Oxfordshire, and will also be associated with the Department of Chemistry, at the University of Bath. The posts are associated with an EPSRC supported four-year project, centered at the new Research Complex at Harwell, to work on Dynamic Structural Science, using synchrotron and neutron diffraction techniques and/or XAFS methodologies. The successful applicants will join a team of chemists and biologists from six UK Universities and from the Central Facilities at RAL, led by Professor Paul Raithby from the University of Bath. The main duties of the successful applicants will be to develop new methodologies for carrying out time resolved crystallographic and XAFS experiments on a range of molecular and macromolecular species. The work will also include some synthesis, spectroscopic characterisation, computational studies and instrument development. The posts are available from 1st August, 2011. Salary: £29,972 to £35,788 Closing Date: Thursday 21 July 2011 Reference: JK589 http://www.bath.ac.uk/jobs/Vacancy.aspx?ref=JK589 Informal enquiries may be addressed to Professor Paul Raithby (p.r.rait...@bath.ac.uk, tel. 01225 383183), however please ensure that applications are submitted through the University of Bath website. -- Dr Arwen R Pearson RCUK Academic Research Fellow Astbury Centre for Structural Molecular Biology Astbury Building The University of Leeds LS2 9JT United Kingdom (t) +44 (0)113 34 33032 (e) a.r.pear...@leeds.ac.uk
Re: [ccp4bb] Strange density in arginine
The distance to your modelled water seems to be in agreement with an ionic interaction. What are the components of all buffers in the crystallisation components ? Fred. ruheng wrote: Dear all, Recently we are working on an archaebacteria protein which was expressed and purified from /E.coli /by conventional procedures. After we solved the structure, we found that there is an extra density in one of the argninine as shown in the attached picture. It seems that the density is larger than a methyl group and the atoms in the density are not on one plane. So we are curious about whether the density is a kind of posttranslational modification of arginine residues in the protein, if it is, what kind of modification could it be? And most important, what is the biological significance of this kind modification? Any suggestions and dicussions are appreciated! Best, Heng http://skydrive.live.com/redir.aspx?cid=2f5a8d98562e91e4page=playresid=2F5A8D98562E91E4%21199type=1Bpub=SDX.PhotosBsrc=Photomailparid=2F5A8D98562E91E4%21198authkey=S1J8JneduIs%24 Strange density in arginine http://skydrive.live.com/redir.aspx?cid=2f5a8d98562e91e4page=browseresid=2F5A8D98562E91E4%21198type=5Bpub=SDX.PhotosBsrc=Photomailauthkey=S1J8JneduIs%24 查看幻灯片 http://skydrive.live.com/redir.aspx?cid=2f5a8d98562e91e4page=playresid=2F5A8D98562E91E4%21198type=5Bpub=SDX.PhotosBsrc=Photomailauthkey=S1J8JneduIs%24 下载全部 http://skydrive.live.com/redir.aspx?cid=2f5a8d98562e91e4page=downloadaszipresid=2F5A8D98562E91E4%21198type=6Bpub=SDX.PhotosBsrc=Photomailauthkey=S1J8JneduIs%24 添加更多照片 http://skydrive.live.com/redir.aspx?cid=2f5a8d98562e91e4page=uploadresid=2F5A8D98562E91E4%21198type=5Bpub=SDX.PhotosBsrc=Photomailauthkey=S1J8JneduIs%24 此相册包含 1 张照片，并且将在 2011/10/02 之前在 SkyDrive 上提供。 通过 Hotmail 共享您自己的幻灯片 http://g.live.com/9wc9zh-cn/f_photos
Re: [ccp4bb] Strange density in arginine
Looks like an anion, possibly sulfate or phosphate. What's in the crystallization mix? Roger Rowlett On Jul 4, 2011 11:33 AM, ruheng rh_ibp2...@hotmail.com wrote: Dear all, Recently we are working on an archaebacteria protein which was expressed and purified from E.coli by conventional procedures. After we solved the structure, we found that there is an extra density in one of the argninine as shown in the attached picture. It seems that the density is larger than a methyl group and the atoms in the density are not on one plane. So we are curious about whether the density is a kind of posttranslational modification of arginine residues in the protein, if it is, what kind of modification could it be? And most important, what is the biological significance of this kind modification? Any suggestions and dicussions are appreciated! Best, Heng Strange density in arginine http://skydrive.live.com/redir.aspx?cid=2f5a8d98562e91e4page=browseresid=2F5A8D98562E91E4!198type=5Bpub=SDX.PhotosBsrc=Photomailauthkey=S1J8JneduIs%24
Re: [ccp4bb] Strange density in Arg
Mon. July 4th 2011 EBI Good evening, firstly, it could be something that came form the buffer/crystallisation soup etc. What about phosphate? Secondly, if you think it is a natural post-translation modification of your specific protein this is gene/source depended. Check the uniprot entry of your protein, UNP does lists the known modification. Is there a mass-spec analysis? Miri On Mon, 4 Jul 2011, Artem Evdokimov wrote: Before ruling this a covalent modification, did you check if a sulfate or some other tetrahedral ion (or a disordered acetate) fit the bill with respect to distances to the neighboring atoms? Artem 2011/7/4 ruheng rh_ibp2...@hotmail.com Dear all, Recently we are working on an archaebacteria protein which was expressed and purified from E.coli by conventional procedures. After we solved the structure, we found that there is an extra density in one of the argninine as shown in the attached picture. It seems that the density is larger than a methyl group and the atoms in the density are not on one plane. So we are curious about whether the density is a kind of posttranslational modification of arginine residues in the protein, if it is, what kind of modification could it be? And most important, what is the biological significance of this kind modification? Any suggestions and dicussions are appreciated! Best, Heng Mon. July 4th, 2011 EBI
Re: [ccp4bb] Strange density in arginine
Hi Ruheng, Curious to know what was in the crystallization cocktail, cryoprotectant? Did you collect the dataset at a synchrotron? Shiva 2011/7/4 ruheng rh_ibp2...@hotmail.com Dear all, Recently we are working on an archaebacteria protein which was expressed and purified from *E.coli *by conventional procedures. After we solved the structure, we found that there is an extra density in one of the argninine as shown in the attached picture. It seems that the density is larger than a methyl group and the atoms in the density are not on one plane. So we are curious about whether the density is a kind of posttranslational modification of arginine residues in the protein, if it is, what kind of modification could it be? And most important, what is the biological significance of this kind modification? Any suggestions and dicussions are appreciated! Best, Heng http://skydrive.live.com/redir.aspx?cid=2f5a8d98562e91e4page=playresid=2F5A8D98562E91E4!199type=1Bpub=SDX.PhotosBsrc=Photomailparid=2F5A8D98562E91E4%21198authkey=S1J8JneduIs%24 Strange density in arginine http://skydrive.live.com/redir.aspx?cid=2f5a8d98562e91e4page=browseresid=2F5A8D98562E91E4!198type=5Bpub=SDX.PhotosBsrc=Photomailauthkey=S1J8JneduIs%24 查看幻灯片http://skydrive.live.com/redir.aspx?cid=2f5a8d98562e91e4page=playresid=2F5A8D98562E91E4!198type=5Bpub=SDX.PhotosBsrc=Photomailauthkey=S1J8JneduIs%24 下载全部http://skydrive.live.com/redir.aspx?cid=2f5a8d98562e91e4page=downloadaszipresid=2F5A8D98562E91E4!198type=6Bpub=SDX.PhotosBsrc=Photomailauthkey=S1J8JneduIs%24 添加更多照片http://skydrive.live.com/redir.aspx?cid=2f5a8d98562e91e4page=uploadresid=2F5A8D98562E91E4!198type=5Bpub=SDX.PhotosBsrc=Photomailauthkey=S1J8JneduIs%24 此相册包含 1 张照片，并且将在 2011/10/02 之前在 SkyDrive 上提供。 通过 Hotmail 共享您自己的幻灯片 http://g.live.com/9wc9zh-cn/f_photos
