[ccp4bb] Cryo-EM
Hi everyone A bit off topic..but..I request you to please suggest me some good readings related to Cryo-EM.. Thanx in advance -- Regards Faisal School of Life Sciences JNU
Re: [ccp4bb] Gadolinium complexes- phosphate buffer
Alternatively, you can try soaking with Ln complexes, such as Tantalum-Br clusters (http://www.mitegen.com/mic_catalog.php?c=jenPhasingTantalum) Ln chelated in EDTA-like molecules. It does not bind covalently. Better used for soaking at high concentration (http://www.natx-ray.com/products/catalogue_consum_CSM002.html) Ln-(DPA)3 is a special case, that has to be used in co-crystallization, with new crystal forms with 3-fold axis JL On 05/18/2015 11:51 PM, Jurgen Bosch wrote: Also you can treat your SeMET as heavy atom derivative with your native dataset. Jrgen .. Jrgen Bosch Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Office:+1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-2926 http://lupo.jhsph.edu On May 18, 2015, at 13:37, Mark J van Raaij mjvanra...@cnb.csic.es wrote: Hi Isa, don't discard SeMet too rapidly if there are few Mets, modern beamlines, high-redundancy data collection techniques, and processing and phasing programs can extract and use small anomalous signal to get structures even if there are less SeMets than generally accepted by the "rule of thumb". Especially if you can rotate around more than one axis or merge data from different crystals. And even if the signal is not good enough and you then need additional phasing, the SeMet anomalous maps may be useful in tracing. If you have Cys, try Hg compounds, my favourite is methylmercury chloride. As it binds covalently, even if it precipitates in your drop, you may just get just enough soluble to react. We usually add a few grains of the mercury compound to the reservoir, mix, cover and let equilibrate with the drop for a few hours or overnight, then add a ul of the reservoir to the drop and fish crystals after different incubation times. Greetings, Mark Mark J van Raaij Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC c/Darwin 3 E-28049 Madrid, Spain tel. (+34) 91 585 4616 http://www.cnb.csic.es/~mjvanraaij On 18 May 2015, at 11:42, isabelle Lucet wrote: Hi All, We recently obtained a native data set to 2.8A. With no molecular replacement available we are now moving to heavy atom (not enough methionine coverage for seleno-met). Unfortunately crystals grow is in 1.4 Na/K H phosphate pH 8 and we do not have much room for improvement. Any literature you could point to or experience with for example gadolinium complexes, co-crystallization, soaking in phosphate buffer? Are we better off just focusing on class B metals? Thanks for your advise. Kind Regards, Isa __ The information in this email is confidential and intended solely for the addressee. You must not disclose, forward, print or use it without the permission of the sender. __ -- Jean-Luc Ferrer Institut de Biologie Structurale 71 Avenue des Martyrs CS 10090 38044 Grenoble Cedex 9 - FRANCE Ph.: +33 (0)4 57 42 85 22 Fax: +33 (0)4 76 50 63 14
Re: [ccp4bb] Low Phaser RFZ
Hi Eric For me it is perfectly normal Please check Phaser documentation : http://www.phaser.cimr.cam.ac.uk/index.php/Molecular_Replacement#Has_Phaser_Solved_It.3F All the best Carlos On 05/19/2015 02:36 AM, Eric Karg wrote: Hi all, Running Phaser using the apo protein as search model on a ~2.5 A dataset of a protein-DNA complex, I get a single solution but with low RFZ. The map looks reasonable but I was wondering why the RFZ is so low. Would this solution be acceptable? SOLU SET RFZ=3.2 TFZ=8.4 PAK=0 LLG=66 TFZ==10.6 RFZ=2.9 TFZ=13.7 PAK=0 LLG=203 TFZ==14.0 LLG=1440 TFZ==34.2 SOLU SPAC P 62 2 2 SOLU 6DIM ENSE ensemble1 EULER 181.8 55.7 74.8 FRAC 0.27 0.26 -0.40 BFAC -7.38 SOLU 6DIM ENSE ensemble1 EULER 4.5 120.2 7.9 FRAC -0.31 0.20 -0.09 BFAC 12.61 Ensemble ensemble1 RMS variance(s): 0.87 Thank you for your help! -- Carlos CONTRERAS MARTEL, Ph.D. (CR1 CNRS) carlos.contreras-mar...@ibs.fr Bacterial Pathogenesis Group Institut de Biologie Structurale UMR5075 CEA-CNRS-Université Joseph Fourier Grenoble 1 IBS 71, avenue des Martyrs CS 10090 38044 Grenoble CEDEX 9 FRANCE tel : (+33) (0)4 57 42 86 41 http://www.ibs.fr/groupes/groupe-pathogenie-bacterienne/?lang=fr http://www.ibs.fr/groups/bacterial-pathogenesis-group/?lang=en
Re: [ccp4bb] Protein precipitation
Thanks all for the suggestions. @ Pius, I used bacterial expression system.Yes I centrifuged precipitated protein sample and found more amount in soluble form itself, however within a day protein gets degraded. If I have to further purify the protein I have to concentrate the IMAC elutes and concentrate using filters. In this step protein degradation was more and filter used to block and could not complete the process . Do you use batch method of elution or gradient??? Also do you add PMSF in the elution buffer??? Yes Nikhil I did batch elution and included PMSF in all the buffers. and I tried using 500mM NaCl too but no change was observed. Thanks and Regards, Manjula R Research Scholar Department of Biophysics National Institute of Mental Health and Neurosciences Bengaluru-29, Karnataka INDIA E-mail: manjula@gmail.com Mobile no:+91-9538553356 http://www.nimhans.kar.nic.in/ https://www.nimhans.kar.nic.in/ On Tue, May 19, 2015 at 11:14 AM, PULSARSTRIAN bhanu.hydpri...@gmail.com wrote: Try increasing NaCl to 500 mM and glycerol to 10%..And try reduce bME to 1mM for IMAC using Ni-NTA. If your protein requires any additional co-factors (like Mg, Ca or Zn) add them as chloride salts upto 1 to 5 mM. On Tue, May 19, 2015 at 10:19 AM, Manjula Ramu manjula@gmail.com wrote: Hi all, I am purifying a basic protein with pI 7.8. I used 50mM tris 8.8, 300 mm NaCl, 5% glycerol, 0.1mM PMSFand 5mM beta ME in the buffer and performed affinity purification. Eluted with 200mM imidazole. While elution I could see slight turbid in eluted protein (I get pure protein, single band on SDS-PAGE). However, when I centrifuged I couldn't see any pellet. After some time(a day) protein got degraded. In other method I tried cation exchange purification of lysate with MES buffer pH 6.5. Here also I saw slight precipitation and later degradation. After this again I tried with MES buffer pH 5.5 and PIPES buffer pH 6.0, here also same problem I faced. Please suggest me a method where I can get stable protein. Thanks and Regards, Manjula R Research Scholar Department of Biophysics National Institute of Mental Health and Neurosciences Bengaluru-29, Karnataka INDIA E-mail: manjula@gmail.com Mobile no:+91-9538553356 http://www.nimhans.kar.nic.in/ https://www.nimhans.kar.nic.in/ -- B4U
Re: [ccp4bb] Low Phaser RFZ
Hi Eric, What does your map look like? Do you see features that don't come from the search model? That's the key. That said, with a TFZ of above 10, I'd be rather positive about my prospects. Andreas On Tue, May 19, 2015 at 2:36 AM, Eric Karg 052044071b36-dmarc-requ...@jiscmail.ac.uk wrote: Hi all, Running Phaser using the apo protein as search model on a ~2.5 A dataset of a protein-DNA complex, I get a single solution but with low RFZ. The map looks reasonable but I was wondering why the RFZ is so low. Would this solution be acceptable? SOLU SET RFZ=3.2 TFZ=8.4 PAK=0 LLG=66 TFZ==10.6 RFZ=2.9 TFZ=13.7 PAK=0 LLG=203 TFZ==14.0 LLG=1440 TFZ==34.2 SOLU SPAC P 62 2 2 SOLU 6DIM ENSE ensemble1 EULER 181.8 55.7 74.8 FRAC 0.27 0.26 -0.40 BFAC -7.38 SOLU 6DIM ENSE ensemble1 EULER 4.5 120.2 7.9 FRAC -0.31 0.20 -0.09 BFAC 12.61 Ensemble ensemble1 RMS variance(s): 0.87 Thank you for your help!
[ccp4bb] Protein precipitation
Hi Manjula, I had a similar problem: pH, salt, additives and protease inhibitors (I tried them all) didn't work. The protein degraded after lysis of bacteria within 20 min at 24°C to 50 %. I had luck after i cooled down all buffers and materials to less than 4 °C or used them icecold ... (1L bottle buffer stirred for 3-4h in icewaterbath). I performed IMAC, IEX and SEC to get rid of the degradation. Finally the Protein was stable for at least one month. You have to take care about temperature induced pH changes. Some buffers change their pH up to 0.5 (like Tris) when stirring from 24 to 2 °C. This can lead to precipitation if you are working close to the pI of your protein. Maybe you can try to characterize the protease to find a suitable protease inhibitor. Make some massspectrometry with your degraded sample. An other option is to test via westernblot. If you have some C- oder N-terminal monoclonal well characterized antibody. Greets Max Von: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] im Auftrag von Manjula Ramu [manjula@gmail.com] Gesendet: Dienstag, 19. Mai 2015 08:05 An: CCP4BB@JISCMAIL.AC.UK Betreff: Re: [ccp4bb] Protein precipitation Thanks all for the suggestions. @ Pius, I used bacterial expression system.Yes I centrifuged precipitated protein sample and found more amount in soluble form itself, however within a day protein gets degraded. If I have to further purify the protein I have to concentrate the IMAC elutes and concentrate using filters. In this step protein degradation was more and filter used to block and could not complete the process . Do you use batch method of elution or gradient??? Also do you add PMSF in the elution buffer??? Yes Nikhil I did batch elution and included PMSF in all the buffers. and I tried using 500mM NaCl too but no change was observed. Thanks and Regards, Manjula R Research Scholar Department of Biophysics National Institute of Mental Health and Neurosciences Bengaluru-29, Karnataka INDIA E-mail: manjula@gmail.commailto:manjula@gmail.com Mobile no:+91-9538553356 http://www.nimhans.kar.nic.in/ https://www.nimhans.kar.nic.in/ On Tue, May 19, 2015 at 11:14 AM, PULSARSTRIAN bhanu.hydpri...@gmail.commailto:bhanu.hydpri...@gmail.com wrote: Try increasing NaCl to 500 mM and glycerol to 10%..And try reduce bME to 1mM for IMAC using Ni-NTA. If your protein requires any additional co-factors (like Mg, Ca or Zn) add them as chloride salts upto 1 to 5 mM. On Tue, May 19, 2015 at 10:19 AM, Manjula Ramu manjula@gmail.commailto:manjula@gmail.com wrote: Hi all, I am purifying a basic protein with pI 7.8. I used 50mM tris 8.8, 300 mm NaCl, 5% glycerol, 0.1mM PMSFand 5mM beta ME in the buffer and performed affinity purification. Eluted with 200mM imidazole. While elution I could see slight turbid in eluted protein (I get pure protein, single band on SDS-PAGE). However, when I centrifuged I couldn't see any pellet. After some time(a day) protein got degraded. In other method I tried cation exchange purification of lysate with MES buffer pH 6.5. Here also I saw slight precipitation and later degradation. After this again I tried with MES buffer pH 5.5 and PIPES buffer pH 6.0, here also same problem I faced. Please suggest me a method where I can get stable protein. Thanks and Regards, Manjula R Research Scholar Department of Biophysics National Institute of Mental Health and Neurosciences Bengaluru-29, Karnataka INDIA E-mail: manjula@gmail.commailto:manjula@gmail.com Mobile no:+91-9538553356 http://www.nimhans.kar.nic.in/ https://www.nimhans.kar.nic.in/ -- B4U Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt
Re: [ccp4bb] Cryo-EM
Hi Faisal, I guess a start for you would be to go here: http://www.ccpem.ac.uk/ and subscribe to that mailing list :-) Best regards, Folmer 2015-05-19 9:01 GMT+02:00 Faisal Tarique faisaltari...@gmail.com: Hi everyone A bit off topic..but..I request you to please suggest me some good readings related to Cryo-EM.. Thanx in advance -- Regards Faisal School of Life Sciences JNU -- Folmer Fredslund
Re: [ccp4bb] Low Phaser RFZ
Dear Eric, I've just clarified the section in our documentation on how to tell if Phaser has solved your structure: http://www.phaser.cimr.cam.ac.uk/index.php/Molecular_Replacement#Has_Phaser_Solved_It.3F Briefly, the RFZ score is not that diagnostic of success or failure, particularly for high-symmetry space groups. For your space group, P6(2)22, the rotation function is evaluating the agreement between the observed data and the structure factors that you might get by adding up the contributions of 12 symmetry-related molecules. Because, at the rotation function stage, the relative phase angles of the contributions from symmetry-related molecules is not known, there's a lot of uncertainty so the signal-to-noise is low. That's why we emphasise the TFZ as the thing to look at. In your case, a TFZ of 8.4 for the first molecule is already pretty convincing, but even if the first molecule had a poor signal on its own, the TFZ of 13.7 for the second copy would tell you that the first one must have been right. I would say that you can be confident that this is basically right. (With the normal provisos: that doesn't rule out possible complications like pseudosymmetry, but as Phil Evans says the space group is a hypothesis, and you always have to be prepared to reconsider the hypothesis later if, say, it turns out to be difficult to refine the structure.) Best wishes, Randy Read On 19 May 2015, at 01:36, Eric Karg 052044071b36-dmarc-requ...@jiscmail.ac.uk wrote: Hi all, Running Phaser using the apo protein as search model on a ~2.5 A dataset of a protein-DNA complex, I get a single solution but with low RFZ. The map looks reasonable but I was wondering why the RFZ is so low. Would this solution be acceptable? SOLU SET RFZ=3.2 TFZ=8.4 PAK=0 LLG=66 TFZ==10.6 RFZ=2.9 TFZ=13.7 PAK=0 LLG=203 TFZ==14.0 LLG=1440 TFZ==34.2 SOLU SPAC P 62 2 2 SOLU 6DIM ENSE ensemble1 EULER 181.8 55.7 74.8 FRAC 0.27 0.26 -0.40 BFAC -7.38 SOLU 6DIM ENSE ensemble1 EULER 4.5 120.2 7.9 FRAC -0.31 0.20 -0.09 BFAC 12.61 Ensemble ensemble1 RMS variance(s): 0.87 Thank you for your help! -- Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: + 44 1223 336500 Wellcome Trust/MRC Building Fax: + 44 1223 336827 Hills RoadE-mail: rj...@cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk
Re: [ccp4bb] Cryo-EM
Hi Faisal, * This is a good introduction for a non-microscopist: Cryo-electron microscopy--a primer for the non-microscopist. Milne JL1, Borgnia MJ, Bartesaghi A, Tran EE, Earl LA, Schauder DM, Lengyel J, Pierson J, Patwardhan A, Subramaniam S. http://www.ncbi.nlm.nih.gov/pubmed/23181775 * A recent review: How cryo-EM is revolutionizing structural biology Xiao-chen Bai, Greg McMullan, Sjors H.W Scheres http://www.sciencedirect.com/science/article/pii/S096800041400187X * For background theory this is good place to start: Structural Analysis of Macromolecular Assemblies by Electron Microscopy E. V. Orlova and H. R. Saibil http://people.cryst.bbk.ac.uk/~ubcg16z/chemrevsmallfigs.pdf * And for tools for high-resolution modelling building: Tools for macromolecular model building and refinement into electron cryo-microscopy reconstructions Alan Brown, Fei Long, Robert A. Nicholls, Jaan Toots, Paul Emsley and Garib Murshudov http://www.ncbi.nlm.nih.gov/pubmed/25615868 Folmer beat me to it (thanks!). Please have a look at http://www.ccpem.ac. uk/ and subscribe to our mailing list: https://www.jiscmail.ac.uk/ccpem All the best, Tom On 19 May 2015 at 08:04, Folmer Fredslund folm...@gmail.com wrote: Hi Faisal, I guess a start for you would be to go here: http://www.ccpem.ac.uk/ and subscribe to that mailing list :-) Best regards, Folmer 2015-05-19 9:01 GMT+02:00 Faisal Tarique faisaltari...@gmail.com: Hi everyone A bit off topic..but..I request you to please suggest me some good readings related to Cryo-EM.. Thanx in advance -- Regards Faisal School of Life Sciences JNU -- Folmer Fredslund -- Dr Tom Burnley, PhD CCP-EM Science and Technology Facilities Council (STFC) The Research Complex At Harwell Rutherford Appleton Laboratory, R92 OX11 0FA 01235 56 7871
Re: [ccp4bb] MOLREP self-rotation matrix
Actually it is pretty easy: Here is the log of pdbset [ccp4@roo job_55]$ pdbset xyzin part.pdb ... Logical name: XYZIN File name: part.pdb PDB file is being opened on unit 1 for INPUT. MATRICES DERIVED FROM CRYST1 CARD IN COORDINATE FILE RF RO 0.016 0.009 -0.000 -0.000 61.922 -30.961 0.000 -0.000 -0.000 0.019 -0.000 0.0000.000 53.626 0.000 0.000 0.000 -0.000 0.004 0.0000.000 0.000 248.752 -0.000 -0.000 0.000 -0.000 1.000 -0.000 0.000 -0.000 1.000 rota euler 10 20 30 Data line--- rota euler 10 20 30 end Data line--- end Logical name: XYZOUT File name: XYZOUT PDB file is being opened on unit 2 for OUTPUT. Coordinates will be transformed as follows: ( 0.714610 -0.613092 0.336824 ) ( x ) ( 0.000 ) ( 0.633718 0.771281 0.059391 ) ( y ) + ( 0.000 ) ( -0.296198 0.171010 0.939693 ) ( z ) ( 0.000 ) Of course you still have to worry about the orthogonalisation code used for the SELFROT search. polarrfn tells you what is chosen For triclinic, orthorhombic ext the choice is usually Z || c* X || a and Y chosen to make an orthogonal set But for monoclinic it is often set Z || b* X || a and Y chosen to make an orthogonal set Eleanor On 18 May 2015 at 18:57, Chen Zhao c.z...@yale.edu wrote: Sorry for the spaming... Just want to correct that I plan to say covert the MOLREP self-RF Euler angle to RESOLVE (not SOLVE) orthogonal matrix... On Mon, May 18, 2015 at 1:44 PM, Chen Zhao c.z...@yale.edu wrote: I got some answers from the previous thread: https://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg36578.html But I just want to make sure what I am doing... Thanks a lot, Chen On Mon, May 18, 2015 at 1:36 PM, Chen Zhao c.z...@yale.edu wrote: Hi Eleanor, Yeah, the relationship of the XYZ with the unit cell axes is tricky too. Although I can get some clues by looking at the position of the crystallographic symmetry axes on the XY plane, it is better if I could find a definite answer... Thank you, Chen On Mon, May 18, 2015 at 1:24 PM, Eleanor Dodson eleanor.dod...@york.ac.uk wrote: Hmm - there are programs which give you the matrix associated with Eulerian or Polar angles. I think one is pdbset.. Or there is documentation in polarrfn or rotmat which describes how to do it.. But remember there are conventions about which axes correspond to the orthogonal X Y Z axes used to define the angles Eleanor On 18 May 2015 at 17:04, Chen Zhao c.z...@yale.edu wrote: Hi all, I am now trying to convert the NCS axis expressed by theta, phi, chi (or alpha, beta, gamma) from MOLREP to an orthogonal matrix in order to feed into SOLVE. Would anybody suggest me a correct way to do it? Thank you so much in advance! Best, Chen
[ccp4bb] Deletion of hydrogens
Dear all, I have added hydrogens on my molecule using the Refmac option in Coot. I now want to remove them. I tried various syntax but they didn't work. Is there a simple way to remove them from the pdb? Moreover, if I do my refinemnets with hydrogens in it, will it affect my results, other than maybe slowing down the process. Thank you Mohammad
Re: [ccp4bb] Deletion of hydrogens
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Mohammad, you can use e.g. the CCP4 tool pdbset with its keyword 'EXCLUDE HYDROGENS'. You could also repeat the refmac run but ask refmac not to include the hydrogen atoms in the output PDB. This is the default and available as option from the ccp4 GUI. I don't know how to steer this from Coot, though. You should always include hydrogen atoms during refinement. They improve the geometry restraints and they also have a small contribution to the X-ray scattering, especially at low resolution. Given their number approximately equals that of all other atoms in your structure, this small contribution may add up. You probably won't notice much of a slow down by including hydrogen atoms during refinement. There are probably other bottlenecks. Regards, Tim On 05/19/2015 12:55 PM, Mohammad Khan wrote: Dear all, I have added hydrogens on my molecule using the Refmac option in Coot. I now want to remove them. I tried various syntax but they didn't work. Is there a simple way to remove them from the pdb? Moreover, if I do my refinemnets with hydrogens in it, will it affect my results, other than maybe slowing down the process. Thank you Mohammad - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen phone: +49 (0)551 39 22149 GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1 iD8DBQFVWxtcUxlJ7aRr7hoRAgbGAJwJ24mkNXdBCkOiQ8angknihROamwCeLHTc lH3eHumFsNpBcsP2Q+xpbIE= =tAwF -END PGP SIGNATURE-
Re: [ccp4bb] Protein precipitation
Hi Manjula, I will lyse the bacterials cells and monitor the degradation of the lysed protein in lysis buffer over 4-5 days before proceeding with purification. What is the lifetime of this expressed protein once lysed? How long can it stay after lysis without degradation or aggregation? Does this protein contain disulfide bonds? How many? How big is this protein? Smita Smita Mohanty, Ph.D. Associate Professor Department of Chemistry447 Physical SciencesOklahoma State UniversityStillwater, OK 74078-3071 Phone: (405) 744 6636E-mail: Smita.Mohanty@okstate.eduWeb: chemistry.okstate.edu/mohanty On Monday, May 18, 2015 11:49 PM, Manjula Ramu manjula@gmail.com wrote: Hi all,I am purifying a basic protein with pI 7.8. I used 50mM tris 8.8, 300 mm NaCl, 5% glycerol, 0.1mM PMSFand 5mM beta ME in the buffer and performed affinity purification. Eluted with 200mM imidazole. While elution I could see slight turbid in eluted protein (I get pure protein, single band on SDS-PAGE). However, when I centrifuged I couldn't see any pellet. After some time(a day) protein got degraded. In other method I tried cation exchange purification of lysate with MES buffer pH 6.5. Here also I saw slight precipitation and later degradation.After this again I tried with MES buffer pH 5.5 and PIPES buffer pH 6.0, here also same problem I faced.Please suggest me a method where I can get stable protein. Thanks and Regards,Manjula R Research Scholar Department of Biophysics National Institute of Mental Health and Neurosciences Bengaluru-29, Karnataka INDIA E-mail: manjula.iob@gmail.comMobile no:+91-9538553356 http://www.nimhans.kar.nic.in/
Re: [ccp4bb] Deletion of hydrogens
On 19/05/15 11:55, Mohammad Khan wrote: Dear all, I have added hydrogens on my molecule using the Refmac option in Coot. I now want to remove them. I tried various syntax but they didn't work. Is there a simple way to remove them from the pdb? This will create a new molecule that is a copy of molecule number 0 without hydrogens: (new-molecule-by-atom-selection 0 //*//*[!H]) Moreover, if I do my refinemnets with hydrogens in it, will it affect my results, other than maybe slowing down the process. If you use hydrogens in refinement then no (or not much). Paul.
Re: [ccp4bb] MOLREP self-rotation matrix
Hi Eleanor, Thank you so much for your test! However, I am not starting with a PDB file. What I am doing self-RF on is just the Patterson map. So my problem is to convert the output Euler angles to orthogonal matrix. Thanks a lot for your time, Chen On Tue, May 19, 2015 at 5:26 AM, Eleanor Dodson eleanor.dod...@york.ac.uk wrote: Actually it is pretty easy: Here is the log of pdbset [ccp4@roo job_55]$ pdbset xyzin part.pdb ... Logical name: XYZIN File name: part.pdb PDB file is being opened on unit 1 for INPUT. MATRICES DERIVED FROM CRYST1 CARD IN COORDINATE FILE RF RO 0.016 0.009 -0.000 -0.000 61.922 -30.961 0.000 -0.000 -0.000 0.019 -0.000 0.0000.000 53.626 0.000 0.000 0.000 -0.000 0.004 0.0000.000 0.000 248.752 -0.000 -0.000 0.000 -0.000 1.000 -0.000 0.000 -0.000 1.000 rota euler 10 20 30 Data line--- rota euler 10 20 30 end Data line--- end Logical name: XYZOUT File name: XYZOUT PDB file is being opened on unit 2 for OUTPUT. Coordinates will be transformed as follows: ( 0.714610 -0.613092 0.336824 ) ( x ) ( 0.000 ) ( 0.633718 0.771281 0.059391 ) ( y ) + ( 0.000 ) ( -0.296198 0.171010 0.939693 ) ( z ) ( 0.000 ) Of course you still have to worry about the orthogonalisation code used for the SELFROT search. polarrfn tells you what is chosen For triclinic, orthorhombic ext the choice is usually Z || c* X || a and Y chosen to make an orthogonal set But for monoclinic it is often set Z || b* X || a and Y chosen to make an orthogonal set Eleanor On 18 May 2015 at 18:57, Chen Zhao c.z...@yale.edu wrote: Sorry for the spaming... Just want to correct that I plan to say covert the MOLREP self-RF Euler angle to RESOLVE (not SOLVE) orthogonal matrix... On Mon, May 18, 2015 at 1:44 PM, Chen Zhao c.z...@yale.edu wrote: I got some answers from the previous thread: https://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg36578.html https://urldefense.proofpoint.com/v2/url?u=https-3A__www.mail-2Darchive.com_ccp4bb-40jiscmail.ac.uk_msg36578.htmld=AwMFaQc=-dg2m7zWuuDZ0MUcV7Sdqwr=uV9bK9zAIvRZlk7q6-YllAm=7kauOiFgNMhDGRtA1PkMFhKOYJHao8bdY2NU84DO36Us=LWP0S_qlKqdAsniO09EK3o72dfTWMQ42_JzTShSCZvQe= But I just want to make sure what I am doing... Thanks a lot, Chen On Mon, May 18, 2015 at 1:36 PM, Chen Zhao c.z...@yale.edu wrote: Hi Eleanor, Yeah, the relationship of the XYZ with the unit cell axes is tricky too. Although I can get some clues by looking at the position of the crystallographic symmetry axes on the XY plane, it is better if I could find a definite answer... Thank you, Chen On Mon, May 18, 2015 at 1:24 PM, Eleanor Dodson eleanor.dod...@york.ac.uk wrote: Hmm - there are programs which give you the matrix associated with Eulerian or Polar angles. I think one is pdbset.. Or there is documentation in polarrfn or rotmat which describes how to do it.. But remember there are conventions about which axes correspond to the orthogonal X Y Z axes used to define the angles Eleanor On 18 May 2015 at 17:04, Chen Zhao c.z...@yale.edu wrote: Hi all, I am now trying to convert the NCS axis expressed by theta, phi, chi (or alpha, beta, gamma) from MOLREP to an orthogonal matrix in order to feed into SOLVE. Would anybody suggest me a correct way to do it? Thank you so much in advance! Best, Chen
Re: [ccp4bb] Protein precipitation
Hi, Try using 100mM Ammonium Citrate pH 8.5 as the buffer for your lysis -add salts as well. The Citrate will inhibit metalloproteases and is Ni-NTA friendly. It solved our proteolysis problems and may help with yours. Best wishes, Reza Reza Khayat, PhD Assistant Professor City College of New York 85 St. Nicholas Dr. CDI 12308 New York, NY 10031 (212) 650-6070 www.khayatlab.orghttp://www.khayatlab.org On May 19, 2015, at 2:05 AM, Manjula Ramu manjula@gmail.commailto:manjula@gmail.com wrote: Thanks all for the suggestions. @ Pius, I used bacterial expression system.Yes I centrifuged precipitated protein sample and found more amount in soluble form itself, however within a day protein gets degraded. If I have to further purify the protein I have to concentrate the IMAC elutes and concentrate using filters. In this step protein degradation was more and filter used to block and could not complete the process . Do you use batch method of elution or gradient??? Also do you add PMSF in the elution buffer??? Yes Nikhil I did batch elution and included PMSF in all the buffers. and I tried using 500mM NaCl too but no change was observed. Thanks and Regards, Manjula R Research Scholar Department of Biophysics National Institute of Mental Health and Neurosciences Bengaluru-29, Karnataka INDIA E-mail: manjula@gmail.commailto:manjula@gmail.com Mobile no:+91-9538553356 http://www.nimhans.kar.nic.in/ https://www.nimhans.kar.nic.in/ On Tue, May 19, 2015 at 11:14 AM, PULSARSTRIAN bhanu.hydpri...@gmail.commailto:bhanu.hydpri...@gmail.com wrote: Try increasing NaCl to 500 mM and glycerol to 10%..And try reduce bME to 1mM for IMAC using Ni-NTA. If your protein requires any additional co-factors (like Mg, Ca or Zn) add them as chloride salts upto 1 to 5 mM. On Tue, May 19, 2015 at 10:19 AM, Manjula Ramu manjula@gmail.commailto:manjula@gmail.com wrote: Hi all, I am purifying a basic protein with pI 7.8. I used 50mM tris 8.8, 300 mm NaCl, 5% glycerol, 0.1mM PMSFand 5mM beta ME in the buffer and performed affinity purification. Eluted with 200mM imidazole. While elution I could see slight turbid in eluted protein (I get pure protein, single band on SDS-PAGE). However, when I centrifuged I couldn't see any pellet. After some time(a day) protein got degraded. In other method I tried cation exchange purification of lysate with MES buffer pH 6.5. Here also I saw slight precipitation and later degradation. After this again I tried with MES buffer pH 5.5 and PIPES buffer pH 6.0, here also same problem I faced. Please suggest me a method where I can get stable protein. Thanks and Regards, Manjula R Research Scholar Department of Biophysics National Institute of Mental Health and Neurosciences Bengaluru-29, Karnataka INDIA E-mail: manjula@gmail.commailto:manjula@gmail.com Mobile no:+91-9538553356 http://www.nimhans.kar.nic.in/ https://www.nimhans.kar.nic.in/ -- B4U
Re: [ccp4bb] Cryo-EM
Hi Faisal, There are some good video introduction available too: https://www.youtube.com/watch?v=nkGRhYv01ag HTH, Partha On Tue, May 19, 2015 at 3:01 AM, Faisal Tarique faisaltari...@gmail.com wrote: Hi everyone A bit off topic..but..I request you to please suggest me some good readings related to Cryo-EM.. Thanx in advance -- Regards Faisal School of Life Sciences JNU
Re: [ccp4bb] Equation Editor woes with Office 2011 for Mac
Dear Randy et al, May I suggest Lyx, an open-source wysiwyg editor that outputs Latex. The interface is so much like other word processors that it is a snap to learn quickly and you get those Latex files with equations that journals, at least math and physics journals, like. Maybe you could get your colleagues to try it--I did even though I was sure I didn't want to learn Latex. I use it in Linux, where you do one of those configure-make-install-from-source- code installs. Here is the online info for using it on a mac: http://wiki.lyx.org/Mac/Mac George Reeke On Mon, 2015-05-18 at 09:10 +0100, Randy Read wrote: Rather off-topic, but maybe someone on the list has found a way to work around this! There’s a problem with the Equation Editor in Office 2011 for Mac (i.e. the one that is based on a stripped-down version of MathType, which you get with Insert-Object-Microsoft Equation). You can insert an equation, re-open it and edit it several times, and then suddenly (and seemingly randomly) the equation object will be replaced by a picture showing the equation, which can no longer be edited. I’m writing a rather equation-heavy paper at the moment, and this is driving me crazy. This seems to be a known bug, which has existed from the release of Office 2011. Apparently it happens, unpredictably, when an AutoSave copy of the document is saved, so you can avoid it by turning off the AutoSave feature. The last time this drove me crazy, several years ago, I did try turning off AutoSave. For a while, I was very good about manually saving frequently, but I got into bad habits and eventually Word crashed after I had worked for several hours on a grant proposal without manually saving. So I turned AutoSave back on. At the moment, the least-bad solution seems to be to turn off AutoSave while I’m working on a document with lots of equations and then (hopefully) remember to turn it back on after that document is finished. But it would be great if someone has come up with a better cure for this problem. No doubt someone will suggest switching from Word to LaTeX, but I need to be able to collaborate on paper-writing, and even though I might be willing to invest the effort in learning LaTeX, I can’t really expect that of my collaborators. Most people in our field do use Microsoft Word, regardless of its failings. I’ve also tried using the professional version of MathType, but that requires your collaborators to install it as well — and I don’t think that cured the equation to picture problem anyway. Thanks! - Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical ResearchTel: +44 1223 336500 Wellcome Trust/MRC Building Fax: +44 1223 336827 Hills RoadE-mail: rj...@cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk
Re: [ccp4bb] MOLREP self-rotation matrix
Re: [ccp4bb] MOLREP self-rotation matrix
Hah, this sounds good. I will try it out! Thank you so much! Best, Chen On Tue, May 19, 2015 at 10:22 AM, Eleanor Dodson eleanor.dod...@york.ac.uk wrote: Any set of coordinates will do .. pdbset just converts the eulerian or polar angles to a matrix.. In the example I gave rota euler 10 20 30 corresponds to matrix. ( 0.714610 -0.613092 0.336824 ) ( x ) ( 0.000 ) ( 0.633718 0.771281 0.059391 ) ( y ) + ( 0.000 ) ( -0.296198 0.171010 0.939693 ) ( z ) ( 0.000 ) On 19 May 2015 at 15:11, Chen Zhao c.z...@yale.edu wrote: Hi Eleanor, Thank you so much for your test! However, I am not starting with a PDB file. What I am doing self-RF on is just the Patterson map. So my problem is to convert the output Euler angles to orthogonal matrix. Thanks a lot for your time, Chen On Tue, May 19, 2015 at 5:26 AM, Eleanor Dodson eleanor.dod...@york.ac.uk wrote: Actually it is pretty easy: Here is the log of pdbset [ccp4@roo job_55]$ pdbset xyzin part.pdb ... Logical name: XYZIN File name: part.pdb PDB file is being opened on unit 1 for INPUT. MATRICES DERIVED FROM CRYST1 CARD IN COORDINATE FILE RF RO 0.016 0.009 -0.000 -0.000 61.922 -30.961 0.000 -0.000 -0.000 0.019 -0.000 0.0000.000 53.626 0.000 0.000 0.000 -0.000 0.004 0.0000.000 0.000 248.752 -0.000 -0.000 0.000 -0.000 1.000 -0.000 0.000 -0.000 1.000 rota euler 10 20 30 Data line--- rota euler 10 20 30 end Data line--- end Logical name: XYZOUT File name: XYZOUT PDB file is being opened on unit 2 for OUTPUT. Coordinates will be transformed as follows: ( 0.714610 -0.613092 0.336824 ) ( x ) ( 0.000 ) ( 0.633718 0.771281 0.059391 ) ( y ) + ( 0.000 ) ( -0.296198 0.171010 0.939693 ) ( z ) ( 0.000 ) Of course you still have to worry about the orthogonalisation code used for the SELFROT search. polarrfn tells you what is chosen For triclinic, orthorhombic ext the choice is usually Z || c* X || a and Y chosen to make an orthogonal set But for monoclinic it is often set Z || b* X || a and Y chosen to make an orthogonal set Eleanor On 18 May 2015 at 18:57, Chen Zhao c.z...@yale.edu wrote: Sorry for the spaming... Just want to correct that I plan to say covert the MOLREP self-RF Euler angle to RESOLVE (not SOLVE) orthogonal matrix... On Mon, May 18, 2015 at 1:44 PM, Chen Zhao c.z...@yale.edu wrote: I got some answers from the previous thread: https://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg36578.html https://urldefense.proofpoint.com/v2/url?u=https-3A__www.mail-2Darchive.com_ccp4bb-40jiscmail.ac.uk_msg36578.htmld=AwMFaQc=-dg2m7zWuuDZ0MUcV7Sdqwr=uV9bK9zAIvRZlk7q6-YllAm=7kauOiFgNMhDGRtA1PkMFhKOYJHao8bdY2NU84DO36Us=LWP0S_qlKqdAsniO09EK3o72dfTWMQ42_JzTShSCZvQe= But I just want to make sure what I am doing... Thanks a lot, Chen On Mon, May 18, 2015 at 1:36 PM, Chen Zhao c.z...@yale.edu wrote: Hi Eleanor, Yeah, the relationship of the XYZ with the unit cell axes is tricky too. Although I can get some clues by looking at the position of the crystallographic symmetry axes on the XY plane, it is better if I could find a definite answer... Thank you, Chen On Mon, May 18, 2015 at 1:24 PM, Eleanor Dodson eleanor.dod...@york.ac.uk wrote: Hmm - there are programs which give you the matrix associated with Eulerian or Polar angles. I think one is pdbset.. Or there is documentation in polarrfn or rotmat which describes how to do it.. But remember there are conventions about which axes correspond to the orthogonal X Y Z axes used to define the angles Eleanor On 18 May 2015 at 17:04, Chen Zhao c.z...@yale.edu wrote: Hi all, I am now trying to convert the NCS axis expressed by theta, phi, chi (or alpha, beta, gamma) from MOLREP to an orthogonal matrix in order to feed into SOLVE. Would anybody suggest me a correct way to do it? Thank you so much in advance! Best, Chen
Re: [ccp4bb] Cryo-EM
Hi Faisal, Two recent reviews well worth reading are below: A Primer to Single-Particle Cryo-Electron Microscopy. Cheng Y, Grigorieff N, Penczek PA, Walz T http://www.ncbi.nlm.nih.gov/pubmed/25910204 Single-Particle Cryo-EM at Crystallographic Resolution. Cheng Y. http://www.ncbi.nlm.nih.gov/pubmed/25910205 Best wishes, Mo Dr. Mohammad W. Bahar Division of Structural Biology Wellcome Trust Centre for Human Genetics University of Oxford Roosevelt Drive, Oxford, OX3 7BN Phone: (+44) 1865 287549 ---BeginMessage--- Hi everyone A bit off topic..but..I request you to please suggest me some good readings related to Cryo-EM.. Thanx in advance -- Regards Faisal School of Life Sciences JNU ---End Message---
Re: [ccp4bb] MOLREP self-rotation matrix
Sorry for a bug with the previous (empty) mail . Here is the message : Dear Chen, there is a very old program CONVROT (Urzhumtseva Urzhumtsev, 1997, J.Appl.Cryst) that you can dowload from http://www-ibmc.u-strasbg.fr/arn/Site_UPR9002/Sites.html (or if you want I can send you a copy off-list). It converts any kind of angles (rotation description) to any other kind of rotation descriptions including the matrices. If you have difficulties to install it as a whole GUI program, for your particular problem you may use only the main fortran program convrot.for. A new python version will come soon I hope. Best regards, Sacha Urzhumtsev De : CCP4 bulletin board CCP4BB@JISCMAIL.AC.UK de la part de Chen Zhao c.z...@yale.edu Envoyé : mardi 19 mai 2015 16:11 À : CCP4BB@JISCMAIL.AC.UK Objet : Re: [ccp4bb] MOLREP self-rotation matrix Hi Eleanor, Thank you so much for your test! However, I am not starting with a PDB file. What I am doing self-RF on is just the Patterson map. So my problem is to convert the output Euler angles to orthogonal matrix. Thanks a lot for your time, Chen On Tue, May 19, 2015 at 5:26 AM, Eleanor Dodson eleanor.dod...@york.ac.ukmailto:eleanor.dod...@york.ac.uk wrote: Actually it is pretty easy: Here is the log of pdbset [ccp4@roo job_55]$ pdbset xyzin part.pdb ... Logical name: XYZIN File name: part.pdb PDB file is being opened on unit 1 for INPUT. MATRICES DERIVED FROM CRYST1 CARD IN COORDINATE FILE RF RO 0.016 0.009 -0.000 -0.000 61.922 -30.961 0.000 -0.000 -0.000 0.019 -0.000 0.0000.000 53.626 0.000 0.000 0.000 -0.000 0.004 0.0000.000 0.000 248.752 -0.000 -0.000 0.000 -0.000 1.000 -0.000 0.000 -0.000 1.000 rota euler 10 20 30 Data line--- rota euler 10 20 30 end Data line--- end Logical name: XYZOUT File name: XYZOUT PDB file is being opened on unit 2 for OUTPUT. Coordinates will be transformed as follows: ( 0.714610 -0.613092 0.336824 ) ( x ) ( 0.000 ) ( 0.633718 0.771281 0.059391 ) ( y ) + ( 0.000 ) ( -0.296198 0.171010 0.939693 ) ( z ) ( 0.000 ) Of course you still have to worry about the orthogonalisation code used for the SELFROT search. polarrfn tells you what is chosen For triclinic, orthorhombic ext the choice is usually Z || c* X || a and Y chosen to make an orthogonal set But for monoclinic it is often set Z || b* X || a and Y chosen to make an orthogonal set Eleanor On 18 May 2015 at 18:57, Chen Zhao c.z...@yale.edumailto:c.z...@yale.edu wrote: Sorry for the spaming... Just want to correct that I plan to say covert the MOLREP self-RF Euler angle to RESOLVE (not SOLVE) orthogonal matrix... On Mon, May 18, 2015 at 1:44 PM, Chen Zhao c.z...@yale.edumailto:c.z...@yale.edu wrote: I got some answers from the previous thread: https://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg36578.htmlhttps://urldefense.proofpoint.com/v2/url?u=https-3A__www.mail-2Darchive.com_ccp4bb-40jiscmail.ac.uk_msg36578.htmld=AwMFaQc=-dg2m7zWuuDZ0MUcV7Sdqwr=uV9bK9zAIvRZlk7q6-YllAm=7kauOiFgNMhDGRtA1PkMFhKOYJHao8bdY2NU84DO36Us=LWP0S_qlKqdAsniO09EK3o72dfTWMQ42_JzTShSCZvQe= But I just want to make sure what I am doing... Thanks a lot, Chen On Mon, May 18, 2015 at 1:36 PM, Chen Zhao c.z...@yale.edumailto:c.z...@yale.edu wrote: Hi Eleanor, Yeah, the relationship of the XYZ with the unit cell axes is tricky too. Although I can get some clues by looking at the position of the crystallographic symmetry axes on the XY plane, it is better if I could find a definite answer... Thank you, Chen On Mon, May 18, 2015 at 1:24 PM, Eleanor Dodson eleanor.dod...@york.ac.ukmailto:eleanor.dod...@york.ac.uk wrote: Hmm - there are programs which give you the matrix associated with Eulerian or Polar angles. I think one is pdbset.. Or there is documentation in polarrfn or rotmat which describes how to do it.. But remember there are conventions about which axes correspond to the orthogonal X Y Z axes used to define the angles Eleanor On 18 May 2015 at 17:04, Chen Zhao c.z...@yale.edumailto:c.z...@yale.edu wrote: Hi all, I am now trying to convert the NCS axis expressed by theta, phi, chi (or alpha, beta, gamma) from MOLREP to an orthogonal matrix in order to feed into SOLVE. Would anybody suggest me a correct way to do it? Thank you so much in advance! Best, Chen
Re: [ccp4bb] Cryo-EM
Hi Faisal, if you are particularly interested in refinement of atomic models into cryo-EM maps then you may check this too: http://phenix-online.org/presentations/real_space_refine.pdf (Of course by no means I claim this being a good reading!) Good luck, Pavel On Tue, May 19, 2015 at 12:01 AM, Faisal Tarique faisaltari...@gmail.com wrote: Hi everyone A bit off topic..but..I request you to please suggest me some good readings related to Cryo-EM.. Thanx in advance -- Regards Faisal School of Life Sciences JNU
Re: [ccp4bb] Equation Editor woes with Office 2011 for Mac
Hi Randy, You could use a LyX--LaTeXiT--MS Word workflow to solve the equation editing issue without anyone learning LaTeX syntax. The LyX document with equations can be exported to a LaTeX *.tex file, and you can open this tex file in any text editor to copy the equations encoded in LaTeX syntax for pasting into the LaTeXiT gui. Alternatively, you can select and copy the equation in the LyX document and paste it directly into the LaTeXiT gui to get back the LaTeX encoding. LyX gui is very easy to start using productively without reading the manual. However, I do not know of a way to directly use ENDNOTE with LyX. I use LyX to assemble my early drafts, and then I move the draft into MS Word when I need to start adding citations. In MS Word 2011 on a Mac, it is painful to scroll through a large document (10 pages) with tables and figures, whereas a 1000 page document in LyX can be scrolled through in a flash. LyX has been used to assemble books. Best regards, Blaine Blaine Mooers, Ph.D. Assistant Professor Director of the Laboratory of Biomolecular Structure and Function Department of Biochemistry and Molecular Biology University of Oklahoma Health Sciences Center S.L. Young Biomedical Research Center Rm. 466 Shipping address: 975 NE 10th Street, BRC 466 Oklahoma City, OK 73104-5419 Letter address: P.O. Box 26901, BRC 466 Oklahoma City, OK 73190 office: (405) 271-8300 lab: (405) 271-8313 fax: (405) 271-3910 e-mail: blaine-moo...@ouhsc.edu Faculty webpage: http://www.oumedicine.com/department-of-biochemistry-and-molecular-biology/faculty/blaine-mooers-ph-d- Small Angle Scattering webpage: http://www.oumedicine.com/docs/default-source/ad-biochemistry-workfiles/small-angle-scattering-links-27aug2014.html?sfvrsn=0 X-ray lab webpage: http://www.oumedicine.com/department-of-biochemistry-and-molecular-biology/department-facilities/macromolecular-crystallography-laboratory From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of George Reeke [re...@mail.rockefeller.edu] Sent: Tuesday, May 19, 2015 10:17 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Equation Editor woes with Office 2011 for Mac Dear Randy et al, May I suggest Lyx, an open-source wysiwyg editor that outputs Latex. The interface is so much like other word processors that it is a snap to learn quickly and you get those Latex files with equations that journals, at least math and physics journals, like. Maybe you could get your colleagues to try it--I did even though I was sure I didn't want to learn Latex. I use it in Linux, where you do one of those configure-make-install-from-source- code installs. Here is the online info for using it on a mac: https://urldefense.proofpoint.com/v2/url?u=http-3A__wiki.lyx.org_Mac_Macd=AwIFaQc=qRnFByZajCb3ogDwk-HidsbrxD-31vTsTBEIa6TCCEkr=39ovrj_9gtbpqLqHj52qObHez22uGBx1oHrj21rIdIIm=LcTP6vjD81n8gdU8pO7MO0O_G5V4cd6IYIjH5HR5LAQs=ZKNr8DjE1hiSYE6bjdgorDpAUWU_3gUFfRH9urzCZxIe= George Reeke On Mon, 2015-05-18 at 09:10 +0100, Randy Read wrote: Rather off-topic, but maybe someone on the list has found a way to work around this! There’s a problem with the Equation Editor in Office 2011 for Mac (i.e. the one that is based on a stripped-down version of MathType, which you get with Insert-Object-Microsoft Equation). You can insert an equation, re-open it and edit it several times, and then suddenly (and seemingly randomly) the equation object will be replaced by a picture showing the equation, which can no longer be edited. I’m writing a rather equation-heavy paper at the moment, and this is driving me crazy. This seems to be a known bug, which has existed from the release of Office 2011. Apparently it happens, unpredictably, when an AutoSave copy of the document is saved, so you can avoid it by turning off the AutoSave feature. The last time this drove me crazy, several years ago, I did try turning off AutoSave. For a while, I was very good about manually saving frequently, but I got into bad habits and eventually Word crashed after I had worked for several hours on a grant proposal without manually saving. So I turned AutoSave back on. At the moment, the least-bad solution seems to be to turn off AutoSave while I’m working on a document with lots of equations and then (hopefully) remember to turn it back on after that document is finished. But it would be great if someone has come up with a better cure for this problem. No doubt someone will suggest switching from Word to LaTeX, but I need to be able to collaborate on paper-writing, and even though I might be willing to invest the effort in learning LaTeX, I can’t really expect that of my collaborators. Most people in our field do use Microsoft Word, regardless of its failings. I’ve also tried using the professional version of MathType, but that requires your collaborators to install it as well — and I don’t think that
Re: [ccp4bb] Deletion of hydrogens
Dear Mohammad, You can use 'modify pdb' tool in phenix utilities and select remove hydrogen option. Also, if you are familiar with Vim editor in linux then there is easy command (:g/ H/d). Regards, NIKHIL G BHARAMBE, Ph.D Student, Prof. K. Suguna's Lab Molecular Biophysics Unit (MBU) IISc, Bangalore. -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.
[ccp4bb] 2015 Asian Crystallographic Association Meeting - Kolkata India
Dear CCP4 Community, We cordially invite you to attend the 2015 Asian Crystallographic Association Meeting (AsCA 2015 http://www.asca2015.org/) at Science City, Kolkata (old name Calcutta) to be held from December 5-8, 2015. The sessions are arranged under three broad headings – Chemical Crystallography, Structural Biology, and Specialized Techniques. In total there are eighteen microsymposia, organized in three parallel sessions. Additionally there are two Crystallogrpahic Software sessions – dealing with the structure solution/analysis of small and macromolecules. Finally there will be a General Interest Session covering different aspects of pharmaceuticals. Registration and abstract submission are now open. Please visit the conference webpage:http://www.asca2015.org/ for information on registration, abstract submission and accommodation. Please book your accommodation as soon as possible since availability is limited. Important Dates • Conference dates: Dec 5-8, 2015 • Call for papers and Registration opening May 11, 2015 • Abstract submission deadline Sept 15, 2015 • Travel support application deadline Aug 31, 2015 • Travel support announcement Sept 30, 2015 • Early registration deadline Sept 5, 2015 • Regular registration deadline Nov 20, 2015 • Final program Nov 27, 2015 To support excellence in crystallographic research carried out by young scientists the organizers are seeking application for the AsCA Rising Star Award. The details are available at the conference website. The six finalists will be invited to present their work in a special session. A limited number of young scientists will be provided partial travel support from the grant received from IUCr. Participants from outside India are requested to register early so that all the visa formalities can be completed well ahead of the conference date. We look forward to welcoming you in Kolkata. Kind regards Alice Vrielink Pinak Chakrabarti Chair of the International Program Committee Chair of the Local Organizing Committee ** Alice Vrielink Professor of Structural Biology Head of Discipline - Biochemistry and Molecular Biology School of Chemistry and Biochemistry M310 University of Western Australia 35 Stirling Highway Crawley, WA, 6009 Australia Email: alice.vriel...@uwa.edu.aumailto:alice.vriel...@uwa.edu.au Phone: +61 08 6488 3162 Fax:+61 08 6488 1005 Webpage: http://www.crystal.uwa.edu.au/alice/ We are what we repeatedly do. Excellence, then, is not an act, but a habit. Aristotle ** [cid:14BE597D-3D25-4D8F-8C78-836E103224C5@bcs.uwa.edu.au]
Re: [ccp4bb] Protein precipitation
The information about of the cleavage site can be used in two ways : possibly identify the protease - as it has already been suggested - or introduce a mutation at the cleavage site which would prevent clipping from occurring. The caveat of introducing a mutation is that there is always the possibility that the mutated residue plays a key role. Good luck Thierry From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Phoebe A. Rice Sent: Tuesday, May 19, 2015 12:23 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Protein precipitation For one of our more easily-degraded proteins, we added a mix of protease inhibitors (those expensive tablets you can buy) and also put a drop of EDTA into each tube in the fraction collector so that any contaminating metal-dependent proteases would be knocked out as soon as the protein came off the metal affinity column. That seemed to help. Also, if you can get your protein to stick to the next column in whatever buffer it comes off the IMAC column in, there's no need to dialyze or concentration between columns - the faster you get it clean, the better. Good luck! Phoebe Rice From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Michel, Max [m.mic...@fz-juelich.de] Sent: Tuesday, May 19, 2015 1:32 AM To: CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Protein precipitation Hi Manjula, I had a similar problem: pH, salt, additives and protease inhibitors (I tried them all) didn't work. The protein degraded after lysis of bacteria within 20 min at 24°C to 50 %. I had luck after i cooled down all buffers and materials to less than 4 °C or used them icecold ... (1L bottle buffer stirred for 3-4h in icewaterbath). I performed IMAC, IEX and SEC to get rid of the degradation. Finally the Protein was stable for at least one month. You have to take care about temperature induced pH changes. Some buffers change their pH up to 0.5 (like Tris) when stirring from 24 to 2 °C. This can lead to precipitation if you are working close to the pI of your protein. Maybe you can try to characterize the protease to find a suitable protease inhibitor. Make some massspectrometry with your degraded sample. An other option is to test via westernblot. If you have some C- oder N-terminal monoclonal well characterized antibody. Greets Max Von: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] im Auftrag von Manjula Ramu [manjula@gmail.com] Gesendet: Dienstag, 19. Mai 2015 08:05 An: CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK Betreff: Re: [ccp4bb] Protein precipitation Thanks all for the suggestions. @ Pius, I used bacterial expression system.Yes I centrifuged precipitated protein sample and found more amount in soluble form itself, however within a day protein gets degraded. If I have to further purify the protein I have to concentrate the IMAC elutes and concentrate using filters. In this step protein degradation was more and filter used to block and could not complete the process . Do you use batch method of elution or gradient??? Also do you add PMSF in the elution buffer??? Yes Nikhil I did batch elution and included PMSF in all the buffers. and I tried using 500mM NaCl too but no change was observed. Thanks and Regards, Manjula R Research Scholar Department of Biophysics National Institute of Mental Health and Neurosciences Bengaluru-29, Karnataka INDIA E-mail: manjula@gmail.commailto:manjula@gmail.com Mobile no:+91-9538553356 http://www.nimhans.kar.nic.in/ https://www.nimhans.kar.nic.in/ On Tue, May 19, 2015 at 11:14 AM, PULSARSTRIAN bhanu.hydpri...@gmail.commailto:bhanu.hydpri...@gmail.com wrote: Try increasing NaCl to 500 mM and glycerol to 10%..And try reduce bME to 1mM for IMAC using Ni-NTA. If your protein requires any additional co-factors (like Mg, Ca or Zn) add them as chloride salts upto 1 to 5 mM. On Tue, May 19, 2015 at 10:19 AM, Manjula Ramu manjula@gmail.commailto:manjula@gmail.com wrote: Hi all, I am purifying a basic protein with pI 7.8. I used 50mM tris 8.8, 300 mm NaCl, 5% glycerol, 0.1mM PMSFand 5mM beta ME in the buffer and performed affinity purification. Eluted with 200mM imidazole. While elution I could see slight turbid in eluted protein (I get pure protein, single band on SDS-PAGE). However, when I centrifuged I couldn't see any pellet. After some time(a day) protein got degraded. In other method I tried cation exchange purification of lysate with MES buffer pH 6.5. Here also I saw slight precipitation and later degradation. After this again I tried with MES buffer pH 5.5 and PIPES buffer pH 6.0, here also same problem I faced. Please suggest me a method where I can get stable protein. Thanks and Regards, Manjula R Research Scholar Department of Biophysics National Institute of Mental Health and Neurosciences Bengaluru-29, Karnataka INDIA E-mail:
Re: [ccp4bb] Cryo-EM
Hi Faisal, Recordings of MRC-LMB EM-course last year are available at http://www2.mrc-lmb.cam.ac.uk/groups/scheres/impact.html Best regards, Takanori Nakane On 2015/05/20 2:36, Yi-Wei Chang wrote: Hi Faisal, Here is a new series of lecture video called Getting Started in Cryo-EM made by Prof. Grant Jensen at Caltech/HHMI. http://cryo-em-course.caltech.edu/ There are 14.5 hours of lecture total, which starts with the basic anatomy of electron microscopes, an introduction to Fourier transforms, and the principles of image formation. Building upon that foundation, the lecture then covers sample preparation issues, data collection strategies, and basic image processing workflows for tomography, single particle analysis, and 2-D crystallography. It is an excellent introduction that will prepare people for real practical training on the microscope or to engage in serious conversations about cryo-EM: a great way to get started for anyone just joining a cryo-EM lab, or anyone who wants to be sure they have the basic concepts down. Cheers, Yi-Wei
Re: [ccp4bb] Equation Editor woes with Office 2011 for Mac
Hi All, what happened to Randy happened to me several times in the past, with one most remarkable example being editing the 47 page long text that were mostly formulas. While most responses so far suggest using latex or flavors thereof, I for one would still be using MS Word mostly because I find it impractical to convince collaborators to use something else. The only solution that works for me so far is being disciplined about this issue by periodically checking to make sure this trouble did not occur (which is annoying to say the least!). All the best, Pavel On Mon, May 18, 2015 at 1:10 AM, Randy Read rj...@cam.ac.uk wrote: Rather off-topic, but maybe someone on the list has found a way to work around this! There’s a problem with the Equation Editor in Office 2011 for Mac (i.e. the one that is based on a stripped-down version of MathType, which you get with Insert-Object-Microsoft Equation). You can insert an equation, re-open it and edit it several times, and then suddenly (and seemingly randomly) the equation object will be replaced by a picture showing the equation, which can no longer be edited. I’m writing a rather equation-heavy paper at the moment, and this is driving me crazy. This seems to be a known bug, which has existed from the release of Office 2011. Apparently it happens, unpredictably, when an AutoSave copy of the document is saved, so you can avoid it by turning off the AutoSave feature. The last time this drove me crazy, several years ago, I did try turning off AutoSave. For a while, I was very good about manually saving frequently, but I got into bad habits and eventually Word crashed after I had worked for several hours on a grant proposal without manually saving. So I turned AutoSave back on. At the moment, the least-bad solution seems to be to turn off AutoSave while I’m working on a document with lots of equations and then (hopefully) remember to turn it back on after that document is finished. But it would be great if someone has come up with a better cure for this problem. No doubt someone will suggest switching from Word to LaTeX, but I need to be able to collaborate on paper-writing, and even though I might be willing to invest the effort in learning LaTeX, I can’t really expect that of my collaborators. Most people in our field do use Microsoft Word, regardless of its failings. I’ve also tried using the professional version of MathType, but that requires your collaborators to install it as well — and I don’t think that cured the equation to picture problem anyway. Thanks! - Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical ResearchTel: +44 1223 336500 Wellcome Trust/MRC Building Fax: +44 1223 336827 Hills Road E-mail: rj...@cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk
Re: [ccp4bb] Protein precipitation
For one of our more easily-degraded proteins, we added a mix of protease inhibitors (those expensive tablets you can buy) and also put a drop of EDTA into each tube in the fraction collector so that any contaminating metal-dependent proteases would be knocked out as soon as the protein came off the metal affinity column. That seemed to help. Also, if you can get your protein to stick to the next column in whatever buffer it comes off the IMAC column in, there's no need to dialyze or concentration between columns - the faster you get it clean, the better. Good luck! Phoebe Rice From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Michel, Max [m.mic...@fz-juelich.de] Sent: Tuesday, May 19, 2015 1:32 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Protein precipitation Hi Manjula, I had a similar problem: pH, salt, additives and protease inhibitors (I tried them all) didn't work. The protein degraded after lysis of bacteria within 20 min at 24°C to 50 %. I had luck after i cooled down all buffers and materials to less than 4 °C or used them icecold ... (1L bottle buffer stirred for 3-4h in icewaterbath). I performed IMAC, IEX and SEC to get rid of the degradation. Finally the Protein was stable for at least one month. You have to take care about temperature induced pH changes. Some buffers change their pH up to 0.5 (like Tris) when stirring from 24 to 2 °C. This can lead to precipitation if you are working close to the pI of your protein. Maybe you can try to characterize the protease to find a suitable protease inhibitor. Make some massspectrometry with your degraded sample. An other option is to test via westernblot. If you have some C- oder N-terminal monoclonal well characterized antibody. Greets Max Von: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] im Auftrag von Manjula Ramu [manjula@gmail.com] Gesendet: Dienstag, 19. Mai 2015 08:05 An: CCP4BB@JISCMAIL.AC.UK Betreff: Re: [ccp4bb] Protein precipitation Thanks all for the suggestions. @ Pius, I used bacterial expression system.Yes I centrifuged precipitated protein sample and found more amount in soluble form itself, however within a day protein gets degraded. If I have to further purify the protein I have to concentrate the IMAC elutes and concentrate using filters. In this step protein degradation was more and filter used to block and could not complete the process . Do you use batch method of elution or gradient??? Also do you add PMSF in the elution buffer??? Yes Nikhil I did batch elution and included PMSF in all the buffers. and I tried using 500mM NaCl too but no change was observed. Thanks and Regards, Manjula R Research Scholar Department of Biophysics National Institute of Mental Health and Neurosciences Bengaluru-29, Karnataka INDIA E-mail: manjula@gmail.commailto:manjula@gmail.com Mobile no:+91-9538553356 http://www.nimhans.kar.nic.in/ https://www.nimhans.kar.nic.in/ On Tue, May 19, 2015 at 11:14 AM, PULSARSTRIAN bhanu.hydpri...@gmail.commailto:bhanu.hydpri...@gmail.com wrote: Try increasing NaCl to 500 mM and glycerol to 10%..And try reduce bME to 1mM for IMAC using Ni-NTA. If your protein requires any additional co-factors (like Mg, Ca or Zn) add them as chloride salts upto 1 to 5 mM. On Tue, May 19, 2015 at 10:19 AM, Manjula Ramu manjula@gmail.commailto:manjula@gmail.com wrote: Hi all, I am purifying a basic protein with pI 7.8. I used 50mM tris 8.8, 300 mm NaCl, 5% glycerol, 0.1mM PMSFand 5mM beta ME in the buffer and performed affinity purification. Eluted with 200mM imidazole. While elution I could see slight turbid in eluted protein (I get pure protein, single band on SDS-PAGE). However, when I centrifuged I couldn't see any pellet. After some time(a day) protein got degraded. In other method I tried cation exchange purification of lysate with MES buffer pH 6.5. Here also I saw slight precipitation and later degradation. After this again I tried with MES buffer pH 5.5 and PIPES buffer pH 6.0, here also same problem I faced. Please suggest me a method where I can get stable protein. Thanks and Regards, Manjula R Research Scholar Department of Biophysics National Institute of Mental Health and Neurosciences Bengaluru-29, Karnataka INDIA E-mail: manjula@gmail.commailto:manjula@gmail.com Mobile no:+91-9538553356 http://www.nimhans.kar.nic.in/ https://www.nimhans.kar.nic.in/ -- B4U Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), Karsten Beneke (stellv.
Re: [ccp4bb] Protein precipitation
a third way to use the information would be to reclone the part before and/or after the protease cleavage site, i.e. you may have identified (a) stable domain(s) that may crystallize much better than the full-length protein. Mark J van Raaij Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC c/Darwin 3 E-28049 Madrid, Spain tel. (+34) 91 585 4616 http://www.cnb.csic.es/~mjvanraaij On 19 May 2015, at 18:48, Fischmann, Thierry wrote: The information about of the cleavage site can be used in two ways : possibly identify the protease - as it has already been suggested - or introduce a mutation at the cleavage site which would prevent clipping from occurring. The caveat of introducing a mutation is that there is always the possibility that the mutated residue plays a key role. Good luck Thierry From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Phoebe A. Rice Sent: Tuesday, May 19, 2015 12:23 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Protein precipitation For one of our more easily-degraded proteins, we added a mix of protease inhibitors (those expensive tablets you can buy) and also put a drop of EDTA into each tube in the fraction collector so that any contaminating metal-dependent proteases would be knocked out as soon as the protein came off the metal affinity column. That seemed to help. Also, if you can get your protein to stick to the next column in whatever buffer it comes off the IMAC column in, there's no need to dialyze or concentration between columns - the faster you get it clean, the better. Good luck! Phoebe Rice From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Michel, Max [m.mic...@fz-juelich.de] Sent: Tuesday, May 19, 2015 1:32 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Protein precipitation Hi Manjula, I had a similar problem: pH, salt, additives and protease inhibitors (I tried them all) didn't work. The protein degraded after lysis of bacteria within 20 min at 24°C to 50 %. I had luck after i cooled down all buffers and materials to less than 4 °C or used them icecold ... (1L bottle buffer stirred for 3-4h in icewaterbath). I performed IMAC, IEX and SEC to get rid of the degradation. Finally the Protein was stable for at least one month. You have to take care about temperature induced pH changes. Some buffers change their pH up to 0.5 (like Tris) when stirring from 24 to 2 °C. This can lead to precipitation if you are working close to the pI of your protein. Maybe you can try to characterize the protease to find a suitable protease inhibitor. Make some massspectrometry with your degraded sample. An other option is to test via westernblot. If you have some C- oder N-terminal monoclonal well characterized antibody. Greets Max Von: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] im Auftrag von Manjula Ramu [manjula@gmail.com] Gesendet: Dienstag, 19. Mai 2015 08:05 An: CCP4BB@JISCMAIL.AC.UK Betreff: Re: [ccp4bb] Protein precipitation Thanks all for the suggestions. @ Pius, I used bacterial expression system.Yes I centrifuged precipitated protein sample and found more amount in soluble form itself, however within a day protein gets degraded. If I have to further purify the protein I have to concentrate the IMAC elutes and concentrate using filters. In this step protein degradation was more and filter used to block and could not complete the process . Do you use batch method of elution or gradient??? Also do you add PMSF in the elution buffer??? Yes Nikhil I did batch elution and included PMSF in all the buffers. and I tried using 500mM NaCl too but no change was observed. Thanks and Regards, Manjula R Research Scholar Department of Biophysics National Institute of Mental Health and Neurosciences Bengaluru-29, Karnataka INDIA E-mail: manjula@gmail.com Mobile no:+91-9538553356 http://www.nimhans.kar.nic.in/ On Tue, May 19, 2015 at 11:14 AM, PULSARSTRIAN bhanu.hydpri...@gmail.com wrote: Try increasing NaCl to 500 mM and glycerol to 10%..And try reduce bME to 1mM for IMAC using Ni-NTA. If your protein requires any additional co-factors (like Mg, Ca or Zn) add them as chloride salts upto 1 to 5 mM. On Tue, May 19, 2015 at 10:19 AM, Manjula Ramu manjula@gmail.com wrote: Hi all, I am purifying a basic protein with pI 7.8. I used 50mM tris 8.8, 300 mm NaCl, 5% glycerol, 0.1mM PMSFand 5mM beta ME in the buffer and performed affinity purification. Eluted with 200mM imidazole. While elution I could see slight turbid in eluted protein (I get pure protein, single band on SDS-PAGE). However, when I centrifuged I couldn't see any pellet. After some time(a day) protein got degraded. In other method I tried cation exchange purification of lysate with MES buffer pH 6.5. Here also I saw slight precipitation and later degradation. After this again I
Re: [ccp4bb] Equation Editor woes with Office 2011 for Mac
Certainly LyX is very nice for beginners, and yes you can start typing
without reading the manual (Although I do recommend reading the manual).
But there are lots of problems with compatibility (like Lyx 2.X cannot open
Lyx 1.6.x files or something like that). And sometimes if you do
\usepackage{whatever} in the preamble and that package was going to be
loaded by LyX, then you wil end up with a package clash... and there is
where the beginner gets lost. The citation manager that I like to use with
LyX (or LaTeX) is called Jabref (F5 to open the look for dialog; choose
database -pubmed; input pubmed id; click on import and generate key; and
finally with one button you can push that reference into LyX).
Why I like about sharelatex is that you can start by a minimum input,
others can watch you in real time...far away...and then they can be as good
..as you (limiting factor) in a couple of days.
2015-05-19 11:39 GMT-05:00 Mooers, Blaine H.M. (HSC)
blaine-moo...@ouhsc.edu:
Hi Randy,
You could use a LyX--LaTeXiT--MS Word workflow to solve the equation
editing issue without anyone learning LaTeX syntax.
The LyX document with equations can be exported to a LaTeX *.tex file,
and you can open this tex file in any text editor to copy the equations
encoded in LaTeX syntax for pasting into the LaTeXiT gui. Alternatively,
you can select and copy the equation in the LyX document and paste it
directly into the LaTeXiT gui to get back the LaTeX encoding.
LyX gui is very easy to start using productively without reading the
manual. However, I do not know of a way to directly use ENDNOTE with LyX. I
use LyX to assemble my early drafts, and then I move the draft into MS Word
when I need to start adding citations. In MS Word 2011 on a Mac, it is
painful to scroll through a large document (10 pages) with tables and
figures, whereas a 1000 page document in LyX can be scrolled through in a
flash. LyX has been used to assemble books.
Best regards,
Blaine
Blaine Mooers, Ph.D.
Assistant Professor
Director of the Laboratory of Biomolecular Structure and Function
Department of Biochemistry and Molecular Biology
University of Oklahoma Health Sciences Center
S.L. Young Biomedical Research Center Rm. 466
Shipping address:
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419
Letter address:
P.O. Box 26901, BRC 466
Oklahoma City, OK 73190
office: (405) 271-8300 lab: (405) 271-8313 fax: (405) 271-3910
e-mail: blaine-moo...@ouhsc.edu
Faculty webpage:
http://www.oumedicine.com/department-of-biochemistry-and-molecular-biology/faculty/blaine-mooers-ph-d-
Small Angle Scattering webpage:
http://www.oumedicine.com/docs/default-source/ad-biochemistry-workfiles/small-angle-scattering-links-27aug2014.html?sfvrsn=0
X-ray lab webpage:
http://www.oumedicine.com/department-of-biochemistry-and-molecular-biology/department-facilities/macromolecular-crystallography-laboratory
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of George
Reeke [re...@mail.rockefeller.edu]
Sent: Tuesday, May 19, 2015 10:17 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Equation Editor woes with Office 2011 for Mac
Dear Randy et al,
May I suggest Lyx, an open-source wysiwyg editor that outputs
Latex. The interface is so much like other word processors that
it is a snap to learn quickly and you get those Latex files with
equations that journals, at least math and physics journals, like.
Maybe you could get your colleagues to try it--I did even though
I was sure I didn't want to learn Latex. I use it in Linux,
where you do one of those configure-make-install-from-source-
code installs. Here is the online info for using it on a mac:
https://urldefense.proofpoint.com/v2/url?u=http-3A__wiki.lyx.org_Mac_Macd=AwIFaQc=qRnFByZajCb3ogDwk-HidsbrxD-31vTsTBEIa6TCCEkr=39ovrj_9gtbpqLqHj52qObHez22uGBx1oHrj21rIdIIm=LcTP6vjD81n8gdU8pO7MO0O_G5V4cd6IYIjH5HR5LAQs=ZKNr8DjE1hiSYE6bjdgorDpAUWU_3gUFfRH9urzCZxIe=
George Reeke
On Mon, 2015-05-18 at 09:10 +0100, Randy Read wrote:
Rather off-topic, but maybe someone on the list has found a way to work
around this!
There’s a problem with the Equation Editor in Office 2011 for Mac (i.e.
the one that is based on a stripped-down version of MathType, which you get
with Insert-Object-Microsoft Equation). You can insert an equation,
re-open it and edit it several times, and then suddenly (and seemingly
randomly) the equation object will be replaced by a picture showing the
equation, which can no longer be edited. I’m writing a rather
equation-heavy paper at the moment, and this is driving me crazy.
This seems to be a known bug, which has existed from the release of
Office 2011. Apparently it happens, unpredictably, when an AutoSave copy
of the document is saved, so you can avoid it by turning off the AutoSave
feature. The last time this drove me crazy, several years ago, I did try
turning off
