[ccp4bb] RP-LC validation paper
for our research project we are on the lookout of following full text paper if anyone can kindly assist me in this Validation of an RP-LC Method and Assessment of rhG-CSF in Pharmaceutical Formulations by Liquid Chromatography and Biological Assay Authors: Sergio Luiz Dalmora a; Silvia Maria Krug Masiero b; Paulo Renato de Oliveira a; Maximiliano da Silva Sangoi a; Liberato Brum Junior a Journal of Liquid Chromatography Related Technologies, Volume 29, Issue 12 June 2006 , pages 1753 - 1767 Method validation requirements and approaches in biotechnology Auteur(s) / Author(s) KRULL I. (1) ; SWARTZ M. (2) ; Affiliation(s) du ou des auteurs / Author(s) Affiliation(s) (1) Northeastern University, Boston, Massachusetts, ETATS-UNIS (2) Waters Corp., Milford, Massachusetts, ETATS-UNIS Revue / Journal Title LC GC (LC GC) ISSN 0888-9090 thanks and regards
[ccp4bb] Using the BB for file sharing
Dear All, There seems to be an increasing number of requests for articles on the BB. Can we assume that those supplying articles hold the necessary copyright permissions? Since the BB is visible and archived, I just want to be sure everything is nice and legal. regards Martyn -- *** * * * Dr. Martyn Winn * * * * STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K. * * Tel: +44 1925 603455E-mail: [EMAIL PROTECTED] * * Fax: +44 1925 603825Skype name: martyn.winn * * URL: http://www.ccp4.ac.uk/martyn/ * ***
[ccp4bb] PEPCAT or similar software
Dear All Sorry for the off-topic question. I am trying to classify peptides by populations in a molecular dynamics simulation. I got the reference to the PEPCAT software that can do that, but the web site is down (http://www.ludwig.edu.au/pepcat/index.html). Do you know if this software is still available or any alternatives to do this peptide classification ?. Thanks a lot Cheers Francisco -- - Francisco J. Enguita, Ph.D. Host-pathogen Interactions Group Macromolecular Crystallography Laboratory ITQB EAN, Av. da República 2781-901 Oeiras Portugal Phone : +351-21-4469663 Fax : +351-21-4433644 E-mail : [EMAIL PROTECTED] -
Re: [ccp4bb] PST in refinement
One question - do you have two pairs of molecules, each related by the PST or is there extra non-crystallographic translation ? Averaging or NCS restraints dont give much extra information for molecules in the same orientation. Certainly any pseudo translation will generate sets of weak and strong reflections but unless you have a simple fraction in each direction it is not easy to try to select a sub-set for refinement. Do all the data sets merge together reasonably? You probably just have to slog it through - do you have any experimental phasing at all? Eleanor Maruf Ali wrote: Dear all I have recently collected several datasets on different crystals of a particular protein with a resolution range form 2.4 - 3.2A. All datasets seem to process well in p21 with a unit cell of 109.6 83.1 115.87 90 94.8 90, and this space group is further supported by analysis with the program pointless. The dataset have very reasonable statistics and Rmerge values, with no indication of twinning. Analysis of the self patterson indicated a 43% off origin peak at 0.3 0.5 0.47. This was further flagged by pointless and molrep as a Psuedo cell translation (PST). Looking at the systematic absences there are some unusually strong and weak peaks. Initially after some toiling with molecular replacement, there was a clear solution with four molecules in the asymmetric unit. The maps generated were good enough to build the core of the protein but do not look like maps generated from data at 2.4A-3.2. Further more the free R is stuck at around 40%, and there is no difference in free R when I apply ncs or not or any difference in the maps. After building by hand and with phenix autobuild there is still no difference in maps and Rfree. I have read papers where labs have successfully refined PST data by separating the reflections according to the PST. Oksanen et al 2006 acta D62 1369-1374: Poy et al 2001 NSMB Vol 8 no12 pg 1053: VajDos et al protein science 1997 6;2297 My specific question are Firstly how would I deal with refining PST data? (assuming this is the problem). Second with off origin peak of 0.3 0.5 0.47 how would I separate the reflections? Thirdly any comments would be valued Thank you in advance Maruf Dr Maruf Ali Section of Structural Biology, Institute of Cancer Research, 237 Fulham road, London. SW3 6JB The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network.
Re: [ccp4bb] Using the BB for file sharing
May I also suggest that the more traditional avenue - requesting the reprint from the corresponding author - is always tried first? I used to do this back in time when I was a poor russian grad student with zero access to full-text articles. Also handy if you collect stamps :) On Tue, 2008-07-15 at 10:40 +0100, Martyn Winn wrote: Dear All, There seems to be an increasing number of requests for articles on the BB. Can we assume that those supplying articles hold the necessary copyright permissions? Since the BB is visible and archived, I just want to be sure everything is nice and legal. regards Martyn -- Edwin Pozharski, PhD, Assistant Professor University of Maryland, Baltimore -- When the Way is forgotten duty and justice appear; Then knowledge and wisdom are born along with hypocrisy. When harmonious relationships dissolve then respect and devotion arise; When a nation falls to chaos then loyalty and patriotism are born. -- / Lao Tse /
Re: [ccp4bb] PST in refinement
I have four molecules arranged such that molecules a and b are related by PST and adopt the same orientation as do molecules c and d, but there is no pst between the two pairs. All molecules lie in the same plane. A B top view C D from side view / X \ I hope that the description is clear. Any further comments would be appreciated. Maruf On 15 Jul 2008, at 12:28, Eleanor Dodson wrote: One question - do you have two pairs of molecules, each related by the PST or is there extra non-crystallographic translation ? Averaging or NCS restraints dont give much extra information for molecules in the same orientation. Certainly any pseudo translation will generate sets of weak and strong reflections but unless you have a simple fraction in each direction it is not easy to try to select a sub-set for refinement. Do all the data sets merge together reasonably? You probably just have to slog it through - do you have any experimental phasing at all? Eleanor Maruf Ali wrote: Dear all I have recently collected several datasets on different crystals of a particular protein with a resolution range form 2.4 - 3.2A. All datasets seem to process well in p21 with a unit cell of 109.6 83.1 115.87 90 94.8 90, and this space group is further supported by analysis with the program pointless. The dataset have very reasonable statistics and Rmerge values, with no indication of twinning. Analysis of the self patterson indicated a 43% off origin peak at 0.3 0.5 0.47. This was further flagged by pointless and molrep as a Psuedo cell translation (PST). Looking at the systematic absences there are some unusually strong and weak peaks. Initially after some toiling with molecular replacement, there was a clear solution with four molecules in the asymmetric unit. The maps generated were good enough to build the core of the protein but do not look like maps generated from data at 2.4A-3.2. Further more the free R is stuck at around 40%, and there is no difference in free R when I apply ncs or not or any difference in the maps. After building by hand and with phenix autobuild there is still no difference in maps and Rfree. I have read papers where labs have successfully refined PST data by separating the reflections according to the PST. Oksanen et al 2006 acta D62 1369-1374: Poy et al 2001 NSMB Vol 8 no12 pg 1053: VajDos et al protein science 1997 6;2297 My specific question are Firstly how would I deal with refining PST data? (assuming this is the problem). Second with off origin peak of 0.3 0.5 0.47 how would I separate the reflections? Thirdly any comments would be valued Thank you in advance Maruf Dr Maruf Ali Section of Structural Biology, Institute of Cancer Research, 237 Fulham road, London. SW3 6JB The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network. Dr Maruf Ali Section of Structural Biology, Institute of Cancer Research, 237 Fulham road, London. SW3 6JB The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network.
Re: [ccp4bb] Using the BB for file sharing
It is impossible to know when someone has an anonymous user name and email address. I would suggest, minimally, that if someone asks us to send a paper, they need to sign their correspondence unambiguously (name and institution). Also, several requests in the span of three weeks from the same user gets really annoying. On Jul 15, 2008, at 2:40 AM, Martyn Winn wrote: Dear All, There seems to be an increasing number of requests for articles on the BB. Can we assume that those supplying articles hold the necessary copyright permissions? Since the BB is visible and archived, I just want to be sure everything is nice and legal. regards Martyn
[ccp4bb] Question re: ice rings in diffraction data
Hello all, I have a query re: processing data. I have some lovely diffraction data that has been marred by ice rings (so...not as lovely as it could be). I was told it may be possible to mask the regions of the ice rings (obviously sacrificing completeness) during processing. I have been using HKL2000 to process data. Is this feature available with this program? Otherwise, we also have Mosfilm. Any advice would be greatly appreciated. Thank you. Sincerely in anticipation Mona Rahman --- Mona N. Rahman, Ph.D. Dept. of Biochemistry/Pharmacology Toxicology Botterell Hall, Rooms 623 and 634 (lab) Queen's University, Kingston, ON, K7L 3N6 Phone: 613-533-2993, 613-533-6293 (lab) E-mail: [EMAIL PROTECTED]
Re: [ccp4bb] RP-LC validation paper
Also, I wonder if word has gotten out that we've become a literature search service rather than a crystallography bulletin board. A lot of these papers seemingly have little to do with what we do... On Jul 15, 2008, at 1:24 AM, Meg wrote: for our research project we are on the lookout of following full text paper if anyone can kindly assist me in this Validation of an RP-LC Method and Assessment of rhG-CSF in Pharmaceutical Formulations by Liquid Chromatography and Biological Assay Authors: Sergio Luiz Dalmora a; Silvia Maria Krug Masiero b; Paulo Renato de Oliveira a; Maximiliano da Silva Sangoi a; Liberato Brum Junior a Journal of Liquid Chromatography Related Technologies, Volume 29, Issue 12 June 2006 , pages 1753 - 1767 Method validation requirements and approaches in biotechnology Auteur(s) / Author(s) KRULL I. (1) ; SWARTZ M. (2) ; Affiliation(s) du ou des auteurs / Author(s) Affiliation(s) (1) Northeastern University, Boston, Massachusetts, ETATS-UNIS (2) Waters Corp., Milford, Massachusetts, ETATS-UNIS Revue / Journal Title LC GC (LC GC) ISSN 0888-9090 thanks and regards
Re: [ccp4bb] Question re: ice rings in diffraction data
One can try to set the high resolution to exlude the ice ring ONLY during autoindexing. Once Denzo picks the correct lattice, then you can include the highest resolution available during the refinement. or One can pick fewer peaks during the peak search in hope that the ice ring will be dropped. In this case, if only a few ice ring reflections are picked, one can manually Pick(Remove) reflections also. Good luck, Jeff Quoting Mona Rahman [EMAIL PROTECTED]: Hello all, I have a query re: processing data. I have some lovely diffraction data that has been marred by ice rings (so...not as lovely as it could be). I was told it may be possible to mask the regions of the ice rings (obviously sacrificing completeness) during processing. I have been using HKL2000 to process data. Is this feature available with this program? Otherwise, we also have Mosfilm. Any advice would be greatly appreciated. Thank you. Sincerely in anticipation Mona Rahman --- Mona N. Rahman, Ph.D. Dept. of Biochemistry/Pharmacology Toxicology Botterell Hall, Rooms 623 and 634 (lab) Queen's University, Kingston, ON, K7L 3N6 Phone: 613-533-2993, 613-533-6293 (lab) E-mail: [EMAIL PROTECTED]
Re: [ccp4bb] Question re: ice rings in diffraction data
Dear Mona, If you used XDS to process the data you could use the EXCLUDE_RESOLUTION_RANGE keyword to exactly do what you describe. Best regards, Alexander Mit freundlichen Grüßen / Best regards / Cordialement Alexander Schiffer Sanofi-Aventis Deutschland GmbH RD CAS Structural Biology FFM Industriepark Hoechst Bldg. G877, Room 029 D-65926 Frankfurt am Main f: +49 69 305 24896 f: +49 69 305 80169 w:www.sanofi-aventis.de 125 Jahre Arzneimittel aus Deutschland von sanofi-aventis ** Sanofi-Aventis Deutschland GmbH · Sitz der Gesellschaft: Frankfurt am Main · Handelsregister: Frankfurt am Main, Abt. B Nr. 40661 Vorsitzender des Aufsichtsrats: Hanspeter Spek - Geschäftsführer: Dr. Heinz-Werner Meier (Vorsitzender),Dr. Matthias Braun, Hervé Gisserot, Prof. Dr. Dr. Werner Kramer, Dr. Klaus Menken, Dr. Martin Siewert ** From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Mona Rahman Sent: Tuesday, July 15, 2008 4:14 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Question re: ice rings in diffraction data Hello all, I have a query re: processing data. I have some lovely diffraction data that has been marred by ice rings (so...not as lovely as it could be). I was told it may be possible to mask the regions of the ice rings (obviously sacrificing completeness) during processing. I have been using HKL2000 to process data. Is this feature available with this program? Otherwise, we also have Mosfilm. Any advice would be greatly appreciated. Thank you. Sincerely in anticipation Mona Rahman --- Mona N. Rahman, Ph.D. Dept. of Biochemistry/Pharmacology Toxicology Botterell Hall, Rooms 623 and 634 (lab) Queen's University, Kingston, ON, K7L 3N6 Phone: 613-533-2993, 613-533-6293 (lab) E-mail: [EMAIL PROTECTED]
Re: [ccp4bb] Question re: ice rings in diffraction data
Look at the reject fraction keyword and increase the value, as described on pp 39-40 of the manual Pete From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Mona Rahman Sent: Tuesday, July 15, 2008 7:14 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Question re: ice rings in diffraction data Hello all, I have a query re: processing data. I have some lovely diffraction data that has been marred by ice rings (so...not as lovely as it could be). I was told it may be possible to mask the regions of the ice rings (obviously sacrificing completeness) during processing. I have been using HKL2000 to process data. Is this feature available with this program? Otherwise, we also have Mosfilm. Any advice would be greatly appreciated. Thank you. Sincerely in anticipation Mona Rahman --- Mona N. Rahman, Ph.D. Dept. of Biochemistry/Pharmacology Toxicology Botterell Hall, Rooms 623 and 634 (lab) Queen's University, Kingston, ON, K7L 3N6 Phone: 613-533-2993, 613-533-6293 (lab) E-mail: [EMAIL PROTECTED]
Re: [ccp4bb] PST in refinement
Hi Maruf, 1) Why the low-resolution data was collected to 3.2 Å? 2) Is it possible the real space group is P2 with a NCS which making it look like P21, especially when the PST has a value of exact 0.5. Lijun On Jul 14, 2008, at 5:42 AM, Maruf Ali wrote: Dear all I have recently collected several datasets on different crystals of a particular protein with a resolution range form 2.4 - 3.2A. All datasets seem to process well in p21 with a unit cell of 109.6 83.1 115.87 90 94.8 90, and this space group is further supported by analysis with the program pointless. The dataset have very reasonable statistics and Rmerge values, with no indication of twinning. Analysis of the self patterson indicated a 43% off origin peak at 0.3 0.5 0.47. This was further flagged by pointless and molrep as a Psuedo cell translation (PST). Looking at the systematic absences there are some unusually strong and weak peaks. Initially after some toiling with molecular replacement, there was a clear solution with four molecules in the asymmetric unit. The maps generated were good enough to build the core of the protein but do not look like maps generated from data at 2.4A-3.2. Further more the free R is stuck at around 40%, and there is no difference in free R when I apply ncs or not or any difference in the maps. After building by hand and with phenix autobuild there is still no difference in maps and Rfree. I have read papers where labs have successfully refined PST data by separating the reflections according to the PST. Oksanen et al 2006 acta D62 1369-1374: Poy et al 2001 NSMB Vol 8 no12 pg 1053: VajDos et al protein science 1997 6;2297 My specific question are Firstly how would I deal with refining PST data? (assuming this is the problem). Second with off origin peak of 0.3 0.5 0.47 how would I separate the reflections? Thirdly any comments would be valued Thank you in advance Maruf Dr Maruf Ali Section of Structural Biology, Institute of Cancer Research, 237 Fulham road, London. SW3 6JB The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network. Lijun Liu, PhD Institute of Molecular Biology HHMI Department of Physics University of Oregon Eugene, OR 97403 541-346-4080
[ccp4bb] obtaining hkl2map
Hi, I am trying to reach Thomas Schneider [EMAIL PROTECTED] to request a copy of hkl2map and his email server keeps on bouncing my message. Would somebody, by chance, have more recent contact info for him or have another suggestion on obtaining this program? Much appreciate your help, Vlad
Re: [ccp4bb] obtaining hkl2map
Thank to all the responders! I successfully obtained the program. Now all that's left is solving structures :). Cheers and thanks again, Vlad
Re: [ccp4bb] Question re: ice rings in diffraction data
Hi You can exclude the ice rings easily in Mosflm - from the command line - (a) Autoindexing - AUTOINDEX EXCLUDE ICE (but see user guide for more on this) (b) Processing - RESOLUTION EXCLUDE ICE Or if you try iMosflm, just check the button that says exclude ice rings (Indexing pane) or Do not integrate near ice rings (Processing pane). These are good for hexagonal ice (what you probably have), but if you've got cubic (or other) ice, you need to exclude the rings by their explicit resolution. On 15 Jul 2008, at 15:14, Mona Rahman wrote: Hello all, I have a query re: processing data. I have some lovely diffraction data that has been marred by ice rings (so...not as lovely as it could be). I was told it may be possible to mask the regions of the ice rings (obviously sacrificing completeness) during processing. I have been using HKL2000 to process data. Is this feature available with this program? Otherwise, we also have Mosfilm. Any advice would be greatly appreciated. Thank you. Sincerely in anticipation Mona Rahman --- Mona N. Rahman, Ph.D. Dept. of Biochemistry/Pharmacology Toxicology Botterell Hall, Rooms 623 and 634 (lab) Queen's University, Kingston, ON, K7L 3N6 Phone: 613-533-2993, 613-533-6293 (lab) E-mail: [EMAIL PROTECTED] Harry -- Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road, Cambridge, CB2 2QH
Re: [ccp4bb] Question re: ice rings in diffraction data
Dear Mona, Yes. You can get Denzo to reject reflections on or close to ice rings, or any other features with highly irregular background variations, by increasing the value of the REJECT keyword (see p. 40 of the HKL2000 manual by D. Gerwith, http://www.hkl-xray.com/hkl_web1/hkl/manual_online.pdf). HTH, Joe Hello all, I have a query re: processing data. I have some lovely diffraction data that has been marred by ice rings (so...not as lovely as it could be). I was told it may be possible to mask the regions of the ice rings (obviously sacrificing completeness) during processing. I have been using HKL2000 to process data. Is this feature available with this program? Otherwise, we also have Mosfilm. Any advice would be greatly appreciated. Thank you. Sincerely in anticipation Mona Rahman --- Mona N. Rahman, Ph.D. Dept. of Biochemistry/Pharmacology Toxicology Botterell Hall, Rooms 623 and 634 (lab) Queen's University, Kingston, ON, K7L 3N6 Phone: 613-533-2993, 613-533-6293 (lab) E-mail: [EMAIL PROTECTED]
[ccp4bb] Coiled Coils
Hi all, I was wondering if anyone knows a good website/software for prediction of coiled coil regions within proteins based on the amino acid sequence. Also does anyone know of examples where coiled coil regions can cause secondary structural changes by influencing the oligomeric state of proteins. I would be grateful for any help i can get. thanks neeraj -- Neeraj Kapoor TPCB Graduate Fellow Sakmar Lab/ Molecular Biology Biochemistry The Rockefeller University 1230 York Avenue, RRB 510 New York, NY 10021 lab.1.212.327.8284:fax.7904 mobile: 917.535.2030 http://www.rockefeller.edu/labheads/sakmar/sakmar-lab.html
Re: [ccp4bb] Coiled Coils
How about Coils ? http://www.ch.embnet.org/software/COILS_form.html jürgen On 15 Jul 2008, at 14:38, Neeraj wrote: Hi all, I was wondering if anyone knows a good website/software for prediction of coiled coil regions within proteins based on the amino acid sequence. Also does anyone know of examples where coiled coil regions can cause secondary structural changes by influencing the oligomeric state of proteins. I would be grateful for any help i can get. thanks neeraj -- Neeraj Kapoor TPCB Graduate Fellow Sakmar Lab/ Molecular Biology Biochemistry The Rockefeller University 1230 York Avenue, RRB 510 New York, NY 10021 lab.1.212.327.8284:fax.7904 mobile: 917.535.2030 http://www.rockefeller.edu/labheads/sakmar/sakmar-lab.html - Jürgen Bosch University of Washington Dept. of Biochemistry, K-426 1705 NE Pacific Street Seattle, WA 98195 Box 357742 Phone: +1-206-616-4510 FAX: +1-206-685-7002 Web: http://faculty.washington.edu/jbosch
