Re: [ccp4bb] What could these crystals be?
Hi Careina, Without knowing what's in your protein buffer or crystallisation condition it's hard to comment. Best wishes, Steve Dr Stephen Carr Research Complex at Harwell (RCaH) Rutherford Appleton Laboratory Harwell Oxford Didcot Oxon OX11 0FA United Kingdom Email stephen.c...@rc-harwell.ac.uk tel 01235 567717 From: CCP4 bulletin board on behalf of careinaedgo...@yahoo.com <02531c126adf-dmarc-requ...@jiscmail.ac.uk> Sent: 08 November 2023 15:00 To: ccp4bb Subject: [ccp4bb] What could these crystals be? Hi all We have been trying with no success to crystalize a protein. Recently we got these strange shape "crystals". They are hard and flat but they do not diffract at all. Any ideas as to what could cause this? Careina To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This email and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorized recipient of the addressee, please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to this email. Any views or opinions presented are solely those of the author and do not necessarily represent those of the Research Complex at Harwell. There is no guarantee that this email or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. We use an electronic filing system. Please send electronic versions of documents, unless paper is specifically requested. This email may have a protective marking, for an explanation, please see: http://www.mrc.ac.uk/About/informationandstandards/documentmarking/index.htm. To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] Question about CCP4 monomer dictionaries
Dear Boaz, You're quite right, in my haste to reply last night I only related part of the discussion relating to peroxide. In a bid to identify the diatomic ligand, which appears on oxygen exposure, I quoted the peroxide bond length as being too long, then went on to say it is much more like dioxygen in oxyhaemoglobin/myoglobin and referenced structures from yourself and Simon Phillips. Best wishes, Steve Dr Stephen Carr Research Complex at Harwell (RCaH) Rutherford Appleton Laboratory Harwell Oxford Didcot Oxon OX11 0FA United Kingdom Email stephen.c...@rc-harwell.ac.uk tel 01235 567717 From: Boaz Shaanan Sent: 28 November 2022 23:33 To: Carr, Stephen (MRC,RAL,RCAH) Subject: Re: [ccp4bb] Question about CCP4 monomer dictionaries Hi stephen, I obviously don't have the full context of your case, but I am not sure why you invoked peroxide as a reference for the O-O bond length in the context of oxygen-metal complex. In my good old oxy haemoglobin structure (1HHO) the O-O bond length in Fe-O-O is 1.22 A. It's also worth checking MbO2 with Fe and various metals which are most likely higher resolution structures. I could of course be completely wrong line of thought. Cheers, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaa...@bgu.ac.il Phone: 972-8-647-2220 Fax: 972-8-647-2992 or 972-8-646-1710 From: CCP4 bulletin board on behalf of stephen.c...@rc-harwell.ac.uk <8f3604def7f0-dmarc-requ...@jiscmail.ac.uk> Sent: Monday, November 28, 2022 10:03 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Question about CCP4 monomer dictionaries Dear BB, Thank you for all the helpful responses. To give a bit more context to my question, I have a 1.2 A structure with a diatomic ligand bound to a metal at the active site, which we believe is an oxygen species. The bond length is 1.22 A and I made a comment in the discussion that this was unlikely to be a peroxide species as the bond length was shorter than the 1.48 A typically observed. The referee has questioned the validity of the 1.48 A, which led to my original question. Best wishes, Steve PS I have tried Raman spectroscopy with no definitive result. Dr Stephen Carr Research Complex at Harwell (RCaH) Rutherford Appleton Laboratory Harwell Oxford Didcot Oxon OX11 0FA United Kingdom Email stephen.c...@rc-harwell.ac.uk tel 01235 567717 From: Paul Emsley Sent: 28 November 2022 19:20 To: Carr, Stephen (MRC,RAL,RCAH) Subject: Re: [ccp4bb] Question about CCP4 monomer dictionaries On 28/11/2022 17:29, stephen.c...@rc-harwell.ac.uk<mailto:stephen.c...@rc-harwell.ac.uk> wrote: Dear CCPBB, I have a question regarding the origin of the monomer libraries in CCP4. I ask because I have quoted the bond length listed in the monomer library describing peroxide in a manuscript and a referee has asked for a reference since they seem to disagree with the quoted value of ~1.48 A. My understanding is that parameters describing bond length, angles etc are derived from structures in the CSD is this the case? Is there an appropriate reference out there somewhere? When you say "peroxide," I presume that you mean H2O2. The entry for that in the monomer library is PEO. The bond length between the oxygen atoms in PEO is 1.461A. Perhaps your referee is thinking of the peroxide ion, which indeed would have a different bond length (1.15). Both PEO and PER would, to my mind, be susceptible to radiation damage, so one wonders what is actually in the crystal. To address question, one would make an "Fearly-Flate" map. One can (in principle) dig into the Acedrg table of bond lengths to examine how many examples, of this sort of chemistry exist (I did it a few years ago), but I don't recall now how to do it for this example. Regards, Paul. This email and any attachments may contain confidential, copyrightand or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorized recipient of the addressee, please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to this email. Any views or opinions presented are solely those of the author and do not necessarily represent those of the Research Complex at Harwell. There is no guarantee that this email or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. We use an electronic filing system. Please send electronic versions of documents, unless paper is specifically requested. This email may have a protective marking, for an explanation, please see: http://www.mrc.ac.
Re: [ccp4bb] Question about CCP4 monomer dictionaries
Dear BB, Thank you for all the helpful responses. To give a bit more context to my question, I have a 1.2 A structure with a diatomic ligand bound to a metal at the active site, which we believe is an oxygen species. The bond length is 1.22 A and I made a comment in the discussion that this was unlikely to be a peroxide species as the bond length was shorter than the 1.48 A typically observed. The referee has questioned the validity of the 1.48 A, which led to my original question. Best wishes, Steve PS I have tried Raman spectroscopy with no definitive result. Dr Stephen Carr Research Complex at Harwell (RCaH) Rutherford Appleton Laboratory Harwell Oxford Didcot Oxon OX11 0FA United Kingdom Email stephen.c...@rc-harwell.ac.uk tel 01235 567717 From: Paul Emsley Sent: 28 November 2022 19:20 To: Carr, Stephen (MRC,RAL,RCAH) Subject: Re: [ccp4bb] Question about CCP4 monomer dictionaries On 28/11/2022 17:29, stephen.c...@rc-harwell.ac.uk<mailto:stephen.c...@rc-harwell.ac.uk> wrote: Dear CCPBB, I have a question regarding the origin of the monomer libraries in CCP4. I ask because I have quoted the bond length listed in the monomer library describing peroxide in a manuscript and a referee has asked for a reference since they seem to disagree with the quoted value of ~1.48 A. My understanding is that parameters describing bond length, angles etc are derived from structures in the CSD is this the case? Is there an appropriate reference out there somewhere? When you say "peroxide," I presume that you mean H2O2. The entry for that in the monomer library is PEO. The bond length between the oxygen atoms in PEO is 1.461A. Perhaps your referee is thinking of the peroxide ion, which indeed would have a different bond length (1.15). Both PEO and PER would, to my mind, be susceptible to radiation damage, so one wonders what is actually in the crystal. To address question, one would make an "Fearly-Flate" map. One can (in principle) dig into the Acedrg table of bond lengths to examine how many examples, of this sort of chemistry exist (I did it a few years ago), but I don't recall now how to do it for this example. Regards, Paul. This email and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorized recipient of the addressee, please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to this email. Any views or opinions presented are solely those of the author and do not necessarily represent those of the Research Complex at Harwell. There is no guarantee that this email or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. We use an electronic filing system. Please send electronic versions of documents, unless paper is specifically requested. This email may have a protective marking, for an explanation, please see: http://www.mrc.ac.uk/About/informationandstandards/documentmarking/index.htm. To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] Question about CCP4 monomer dictionaries
Dear CCPBB, I have a question regarding the origin of the monomer libraries in CCP4. I ask because I have quoted the bond length listed in the monomer library describing peroxide in a manuscript and a referee has asked for a reference since they seem to disagree with the quoted value of ~1.48 A. My understanding is that parameters describing bond length, angles etc are derived from structures in the CSD is this the case? Is there an appropriate reference out there somewhere? Thanks very much in advance, Steve Dr Stephen Carr Research Complex at Harwell (RCaH) Rutherford Appleton Laboratory Harwell Oxford Didcot Oxon OX11 0FA United Kingdom Email stephen.c...@rc-harwell.ac.uk tel 01235 567717 This email and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorized recipient of the addressee, please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to this email. Any views or opinions presented are solely those of the author and do not necessarily represent those of the Research Complex at Harwell. There is no guarantee that this email or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. We use an electronic filing system. Please send electronic versions of documents, unless paper is specifically requested. This email may have a protective marking, for an explanation, please see: http://www.mrc.ac.uk/About/informationandstandards/documentmarking/index.htm. To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] cation-aromatic database
Dear BB, Does anyone know if the cation-aromatic database (Reddy, 2007, Prot Sci) is still available? The link listed in the manuscript (http://203.199.182.73/gnsmmg/databases/cad/) no longer appears to work. Thanks, Steve Dr Stephen Carr Research Complex at Harwell (RCaH) Rutherford Appleton Laboratory Harwell Oxford Didcot Oxon OX11 0FA United Kingdom Email stephen.c...@rc-harwell.ac.uk tel 01235 567717 This email and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorized recipient of the addressee, please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to this email. Any views or opinions presented are solely those of the author and do not necessarily represent those of the Research Complex at Harwell. There is no guarantee that this email or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. We use an electronic filing system. Please send electronic versions of documents, unless paper is specifically requested. This email may have a protective marking, for an explanation, please see: http://www.mrc.ac.uk/About/informationandstandards/documentmarking/index.htm. To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] Shipping samples for neutron diffraction
Dear Roberto, John, Jahaun, Harry, Thank you all for the useful suggestions regarding how to transport crystals for neutron work. The bulletin board is once again shown to be an invaluable source of information for all things crystallographic. Best wishes, Steve Dr Stephen Carr Research Complex at Harwell (RCaH) Rutherford Appleton Laboratory Harwell Oxford Didcot Oxon OX11 0FA United Kingdom Email stephen.c...@rc-harwell.ac.uk tel 01235 567717 From: CCP4 bulletin board on behalf of Randy Read Sent: 20 February 2020 08:48:47 To: ccp4bb Subject: Re: [ccp4bb] Shipping samples for neutron diffraction Hi Gloria, While we're confessing to minor economies with the truth, I never travelled to the Photon Factory in Japan with crystals of pertussis toxin: they were crystals of Bordetella pertussis ADP-ribosyltransferase. Randy On 20 Feb 2020, at 02:47, Gloria Borgstahl mailto:gborgst...@gmail.com>> wrote: Actually we don't declare anything to TSA, Jahaun just carries them in his carryon and it is fine. Easy peasy? On Wed, Feb 19, 2020 at 3:48 PM <0c2488af9525-dmarc-requ...@jiscmail.ac.uk<mailto:0c2488af9525-dmarc-requ...@jiscmail.ac.uk>> wrote: ... and don't say you're travelling with heavy water! Jon Cooper On 19 Feb 2020 17:12, "Azadmanesh, Jahaun" mailto:jahaun.azadman...@unmc.edu>> wrote: Hello, I have traveled to a neutron beamline ~6 times over the past several years. I have had awful luck shipping crystals, so I decided to hand-carry and I found this best. I'm not sure what conditions you plan to shoot your crystals. I mount my crystals in a sturdy quartz capillary (from vitrocom), seal the ends with a layer of wax, then two coats of nail polish (choose your favorite prettiest color!) I would then wrap the capillary in cotton from a cottonball, then "stuff" the capillary-cotton combination in a 15 mL falcon tube for a snug fit. For extra assurance, the falcon tubes were placed inside a generous amount of bubble-wrap that was then taped inside a small cardboard box. I have sought anaerobic conditions for several of my samples to acquire a desired redox state of my metallo-protein. This was tough, so instead I used a high-ish concentration of my redox agent dissolved in my reservoir solution "slugs" in the capillary. These would be replaced in intervals with fresh slugs prior to the beamtime, and for sure right before the beamtime. The redox state held for my ~10 days of beamtime and several months after. For cryo-conditions, I just placed a bunch of my crystals in a capillary filled with reservoir solution and sealed as above. I would do my chemical manipulations and freezing at the beamline. Much more details are found in our publication: https://www.ncbi.nlm.nih.gov/pubmed/30279321 Hope this helps! From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> on behalf of stephen.c...@rc-harwell.ac.uk<mailto:stephen.c...@rc-harwell.ac.uk> mailto:stephen.c...@rc-harwell.ac.uk>> Sent: Wednesday, February 19, 2020 4:22 AM To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> mailto:CCP4BB@JISCMAIL.AC.UK>> Subject: [ccp4bb] Shipping samples for neutron diffraction Non-UNMC email Dear CCP4 community, I have an impending trip to a neutron source and was wondering how people tend to ship their samples prior to beam time? Is sending something frozen best or is sealed in a capillary more sensible or is there another better way? One caveat is that ideally my sample should remain anaerobic which has me leaning towards frozen, but I guess in pcr type tubes sealed in gas tight vessels is also a viable option? Any thoughts or suggestions are very much appreciated. Best wishes, Steve Dr Stephen Carr Research Complex at Harwell (RCaH) Rutherford Appleton Laboratory Harwell Oxford Didcot Oxon OX11 0FA United Kingdom Email stephen.c...@rc-harwell.ac.uk<mailto:stephen.c...@rc-harwell.ac.uk> tel 01235 567717 This email and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorized recipient of the addressee, please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to this email. Any views or opinions presented are solely those of the author and do not necessarily represent those of the Research Complex at Harwell. There is no guarantee that this email or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. We use an electronic filing system. Please send electronic versions of documents, unless paper is specifically requested. This email may h
[ccp4bb] Shipping samples for neutron diffraction
Dear CCP4 community, I have an impending trip to a neutron source and was wondering how people tend to ship their samples prior to beam time? Is sending something frozen best or is sealed in a capillary more sensible or is there another better way? One caveat is that ideally my sample should remain anaerobic which has me leaning towards frozen, but I guess in pcr type tubes sealed in gas tight vessels is also a viable option? Any thoughts or suggestions are very much appreciated. Best wishes, Steve Dr Stephen Carr Research Complex at Harwell (RCaH) Rutherford Appleton Laboratory Harwell Oxford Didcot Oxon OX11 0FA United Kingdom Email stephen.c...@rc-harwell.ac.uk tel 01235 567717 This email and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorized recipient of the addressee, please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to this email. Any views or opinions presented are solely those of the author and do not necessarily represent those of the Research Complex at Harwell. There is no guarantee that this email or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. We use an electronic filing system. Please send electronic versions of documents, unless paper is specifically requested. This email may have a protective marking, for an explanation, please see: http://www.mrc.ac.uk/About/informationandstandards/documentmarking/index.htm. To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] Errors reading mmcif files when trying to deposit coordinates to pdb
Dear Roberto, I am using ccp4i at the moment, but am trying i2 to see if this corrects the problem. I have also tried pdb-extract as suggested by Isobel, but am still awaiting the results. Thanks fir the suggestions so far, Steve Dr Stephen Carr Research Complex at Harwell (RCaH) Rutherford Appleton Laboratory Harwell Oxford Didcot Oxon OX11 0FA United Kingdom Email stephen.c...@rc-harwell.ac.uk tel 01235 567717 From: Steiner, Roberto Sent: 25 September 2019 15:08:11 To: Carr, Stephen (MRC,RAL,RCAH) Cc: ccp4bb Subject: Re: [ccp4bb] Errors reading mmcif files when trying to deposit coordinates to pdb I assume you’re using ccp4i and not i2. If you use the latter the mmcif coords file produced should be ok. I have had the same problem a few days ago. Best wishes Roberto On 25 Sep 2019, at 15:00, stephen.c...@rc-harwell.ac.uk<mailto:stephen.c...@rc-harwell.ac.uk> mailto:stephen.c...@rc-harwell.ac.uk>> wrote: Dear ccp4ers, I have refined several structures using refmac5 within ccp4i and tried to upload the output mmcif files to the pdb in order to deposit the coordinates/structure factors. However, during the initial upload process when the files are scanned I get the following errors: ERROR - Read file 'input_file_1' failed: syntax error at line 30421 ERROR - syntax error at line 30426 Warning - Duplicate category name chem_comp_atom at line 30428 Warning - Duplicate category name chem_comp_bond at line 30446 Warning - Duplicate category name chem_comp_angle at line 30467 ERROR - syntax error at line 30581 ERROR - syntax error at line 30585 These all lie after the coordinates in the dictionary part of the file. When I have investigated this I cannot see any duplicated category names that would result in the above warnings and the syntax errors are not a result of anything obvious. I have checked for hidden characters, found none, and can see nothing else wrong. Finally, line 30585 does not exist, the file stops at 30584. Has anyone had similar problems or any suggestions that might solve this? Thanks, Steve Dr Stephen Carr Research Complex at Harwell (RCaH) Rutherford Appleton Laboratory Harwell Oxford Didcot Oxon OX11 0FA United Kingdom Email stephen.c...@rc-harwell.ac.uk<mailto:stephen.c...@rc-harwell.ac.uk> tel 01235 567717 This email and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorized recipient of the addressee, please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to this email. Any views or opinions presented are solely those of the author and do not necessarily represent those of the Research Complex at Harwell. There is no guarantee that this email or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. We use an electronic filing system. Please send electronic versions of documents, unless paper is specifically requested. This email may have a protective marking, for an explanation, please see: https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.mrc.ac.uk%2FAbout%2Finformationandstandards%2Fdocumentmarking%2Findex.htmdata=01%7C01%7Croberto.steiner%40KCL.AC.UK%7C03ca2e3ed7d84887dd7f08d741c0deb8%7C8370cf1416f34c16b83c724071654356%7C0sdata=Sis5qLyK7eNOUxiQpjsL54rExJ54OW80OtGRKFqh1w4%3Dreserved=0. To unsubscribe from the CCP4BB list, click the following link: https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2Fwebadmin%3FSUBED1%3DCCP4BB%26A%3D1data=01%7C01%7Croberto.steiner%40KCL.AC.UK%7C03ca2e3ed7d84887dd7f08d741c0deb8%7C8370cf1416f34c16b83c724071654356%7C0sdata=dCJFqMW5iC6wJN3eZV1EHuCS0I5dPQKgLsLwGtxI07g%3Dreserved=0 Professor Roberto Steiner Randall Centre for Cell and Molecular Biophysics Faculty of Life Sciences and Medicine King's College London roberto.stei...@kcl.ac.uk<mailto:roberto.stei...@kcl.ac.uk> Phone 0044 20 78488216 Fax0044 20 78486435 Room 3.10A New Hunt's House Guy's Campus SE1 1UL London This email and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorized recipient of the addressee, please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to this email. Any views or opinions presented are solely those of the author and do not necessarily represent those of the Research Complex at Harwell. There is no guarantee that this email or any attachments are f
[ccp4bb] Errors reading mmcif files when trying to deposit coordinates to pdb
Dear ccp4ers, I have refined several structures using refmac5 within ccp4i and tried to upload the output mmcif files to the pdb in order to deposit the coordinates/structure factors. However, during the initial upload process when the files are scanned I get the following errors: ERROR - Read file 'input_file_1' failed: syntax error at line 30421 ERROR - syntax error at line 30426 Warning - Duplicate category name chem_comp_atom at line 30428 Warning - Duplicate category name chem_comp_bond at line 30446 Warning - Duplicate category name chem_comp_angle at line 30467 ERROR - syntax error at line 30581 ERROR - syntax error at line 30585 These all lie after the coordinates in the dictionary part of the file. When I have investigated this I cannot see any duplicated category names that would result in the above warnings and the syntax errors are not a result of anything obvious. I have checked for hidden characters, found none, and can see nothing else wrong. Finally, line 30585 does not exist, the file stops at 30584. Has anyone had similar problems or any suggestions that might solve this? Thanks, Steve Dr Stephen Carr Research Complex at Harwell (RCaH) Rutherford Appleton Laboratory Harwell Oxford Didcot Oxon OX11 0FA United Kingdom Email stephen.c...@rc-harwell.ac.uk tel 01235 567717 This email and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorized recipient of the addressee, please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to this email. Any views or opinions presented are solely those of the author and do not necessarily represent those of the Research Complex at Harwell. There is no guarantee that this email or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. We use an electronic filing system. Please send electronic versions of documents, unless paper is specifically requested. This email may have a protective marking, for an explanation, please see: http://www.mrc.ac.uk/About/informationandstandards/documentmarking/index.htm. To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] KCl in SDS-PAGE workarounds?
Hi Jacob, If you keep the protein solution warm the KDS remains soluble. Just load the sample on the gel immediately after heating to denature. This has allowed me to load samples containing up to 1.5M KCl with no problems. Best wishes, Steve Dr Stephen Carr Research Complex at Harwell (RCaH) Rutherford Appleton Laboratory Harwell Oxford Didcot Oxon OX11 0FA United Kingdom Email stephen.c...@rc-harwell.ac.uk tel 01235 567717 From: CCP4 bulletin board on behalf of Bonsor, Daniel Sent: 03 March 2019 03:19:34 To: ccp4bb Subject: Re: [ccp4bb] KCl in SDS-PAGE workarounds? SDS is soluble, whereas the potassium salt of dodecyl sulphate is insoluble. You could try 18-Crown-6 ether to chelate the potassium, though I don't know if the crown ether would then affect the gel. Dan Daniel A. Bonsor PhD Institute of Human Virology, University of Maryland at Baltimore 725 W. Lombard Street N571 Baltimore MD 21201 From: CCP4 bulletin board on behalf of Keller, Jacob Sent: Saturday, March 2, 2019 9:52 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] KCl in SDS-PAGE workarounds? Dear crystallographers, It has been my experience that KCl does nasty things when loading SDS-PAGE gels. Does anyone have an easy workaround, perhaps TCA precipitation? Ideally this would be something nicely quantitative yet quick and easy…. Any suggestions appreciated. All the best, Jacob Keller + Jacob Pearson Keller Research Scientist / Looger Lab HHMI Janelia Research Campus 19700 Helix Dr, Ashburn, VA 20147 Desk: (571)209-4000 x3159 Cell: (301)592-7004 + The content of this email is confidential and intended for the recipient specified in message only. It is strictly forbidden to share any part of this message with any third party, without a written consent of the sender. If you received this message by mistake, please reply to this message and follow with its deletion, so that we can ensure such a mistake does not occur in the future. From: CCP4 bulletin board On Behalf Of Artem Evdokimov Sent: Saturday, March 2, 2019 8:32 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] ionic strength for extraction buffer of membrane proteins Hi Alex, In my experience you just have to experiment with these parameters (in however of a limited space that is afforded by your experimental set-up). If you have the right tools you can slog through semifactorial or DoE-based scouting of various parameters with relative ease. These parameters typically include pH, salinity, detergent(s), and other variables (e.g. the nature of the buffer and salt(s) - many cases exist where the 'standard' choices do not work well). Literature-based analogies do help on occasion. For example, membrane-spanning p450-type proteins often prefer high salt, and often would do better in sodium acetate as opposed to chloride. I've worked with ion channels that preferred 3M NaCl, or 2M MgCl2 and other fairly weird conditions... Artem - Cosmic Cats approve of this message On Fri, Mar 1, 2019 at 7:27 AM Alex Perálvarez Marín mailto:aperalva...@gmail.com>> wrote: Dear all, any reference as a guide for selecting the appropriate salt and concentration for membrane proteins extraction buffer? Best, Alex -- Alex Perálvarez-Marín, Ph.D. Centre d'Estudis en Biofísica / Unitat de Biofísica Edifici M Universitat Autònoma de Barcelona 08193 Cerdanyola del Vallés Barcelona Spain Phone: +34 93 581 4504 FAX: +34 93 581 1907 e-mail: aperalva...@gmail.com<mailto:aperalva...@gmail.com> LinkedIn: es.linkedin.com/in/aperalvarez/<http://es.linkedin.com/in/aperalvarez/> To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 This email and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorized recipient of the addressee, please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to this email. Any views or opinions presented are solely those of the author and do not necessarily represent those of the Research
