[ccp4bb] bug in Arp/wArp solvent?
Dear Arp/wArp developers, there seems to be a bug in the latest version of Arp/wArp Solvent (7.4 patch 1) shipped with ccp4 v 6.4.0: despite ticking the box For REFMAC 5 refinement do USE the Free R flag, the log file shows the message FreeR will not be used (and it clearly doesn't). Or am I missing something here? Cheers, Uli --- dr ulrich gohlke staff scientist - macromolecular structure and interaction max-delbrück-center for molecular medicine (mdc) +49 30 9406 - 2725 (w) +49 30 9406 - 2548 (fax) ulrich.goh...@mdc-berlin.demailto:ulrich.goh...@mdc-berlin.de http://www.mdc-berlin.de/en/research/research_teams/macromolecular_structure_and_interaction/
Re: [ccp4bb] bug in Arp/wArp solvent?
Dear Uli, thanks for letting us know - this is a bug that just happens in the CCP4i interface. If you use the command line, everything works fine. Here is an example how to use arp-solvent on the command line: # auto_solvent.sh datafile xxx.mtz protein xxx_start.pdb freelabin FREE We also just fixed the bug in the CCP4i interface, this will either come to you via the CCP4i updater or a near-future ARP/wARP patch ;) Cheers, Tim On 31 Jan 2014, at 09:30, ulrich.goh...@mdc-berlin.de ulrich.goh...@mdc-berlin.de wrote: Dear Arp/wArp developers, there seems to be a bug in the latest version of Arp/wArp Solvent (7.4 patch 1) shipped with ccp4 v 6.4.0: despite ticking the box For REFMAC 5 refinement do USE the Free R flag, the log file shows the message FreeR will not be used (and it clearly doesn't). Or am I missing something here? Cheers, Uli --- dr ulrich gohlke staff scientist - macromolecular structure and interaction max-delbrück-center for molecular medicine (mdc) +49 30 9406 - 2725 (w) +49 30 9406 - 2548 (fax) ulrich.goh...@mdc-berlin.de http://www.mdc-berlin.de/en/research/research_teams/macromolecular_structure_and_interaction/ __ Dr. Tim Wiegels Postdoc @ Lamzin Group, EMBL Hamburg __ EMBL Hamburg c/o DESY Notkestrasse 85 DE-22603 HAMBURG GERMANY Phone 0049 40 89902-184 Fax 0049 40 89902-149
Re: [ccp4bb] bug in Arp/wArp solvent?
Dear Tim, excellent. Thank you for the quick fix. Cheers, Uli From: Tim Wiegels [maxful...@gmail.com] Sent: 31 January 2014 12:24 To: Gohlke, Ulrich Cc: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] bug in Arp/wArp solvent? Dear Uli, thanks for letting us know - this is a bug that just happens in the CCP4i interface. If you use the command line, everything works fine. Here is an example how to use arp-solvent on the command line: # auto_solvent.sh datafile xxx.mtz protein xxx_start.pdb freelabin FREE We also just fixed the bug in the CCP4i interface, this will either come to you via the CCP4i updater or a near-future ARP/wARP patch ;) Cheers, Tim On 31 Jan 2014, at 09:30, ulrich.goh...@mdc-berlin.demailto:ulrich.goh...@mdc-berlin.de ulrich.goh...@mdc-berlin.demailto:ulrich.goh...@mdc-berlin.de wrote: Dear Arp/wArp developers, there seems to be a bug in the latest version of Arp/wArp Solvent (7.4 patch 1) shipped with ccp4 v 6.4.0: despite ticking the box For REFMAC 5 refinement do USE the Free R flag, the log file shows the message FreeR will not be used (and it clearly doesn't). Or am I missing something here? Cheers, Uli --- dr ulrich gohlke staff scientist - macromolecular structure and interaction max-delbrück-center for molecular medicine (mdc) +49 30 9406 - 2725 (w) +49 30 9406 - 2548 (fax) ulrich.goh...@mdc-berlin.demailto:ulrich.goh...@mdc-berlin.de http://www.mdc-berlin.de/en/research/research_teams/macromolecular_structure_and_interaction/ __ Dr. Tim Wiegels Postdoc @ Lamzin Group, EMBL Hamburg __ EMBL Hamburg c/o DESY Notkestrasse 85 DE-22603 HAMBURG GERMANY Phone 0049 40 89902-184 Fax 0049 40 89902-149
[ccp4bb] Ten days left, many seats available: Apply for RapiData 2014, a course on Data Collection and Structure Solving at the NSLS.
We are offering RapiData 2014, the sixteenth offering of our popular course: Rapid Data Collection and Structure Solving at the NSLS: A Practical Course in Macromolecular X-Ray Diffraction Measurement The course will be held 27 April - 2 May 2014: http://www.bnl.gov/RapiData/. Students could be at any level from advanced undergraduate to full professor. The course should accommodate 48 students total. We encourage all students to bring their own specimens for data collection, and to bring old data for the data-reduction and structure-solving tutorials. Please read the Course Announcement at http://www.bnl.gov/RapiData/. You'll see that many experts in the field will be available for lectures and tutorials. In addition to MX there will be opportunity for learning about correlated MX and spectroscopy, and SAXS. You'll find the application materials on the Course Application tab at this site. For the twelfth time we will hold a short lecture course on the fundamentals of crystallography for roughly five hours on Sunday 27 April. The body of the RapiData course really requires that students have a healthy knowledge of crystallography. For potential students who have some experience but are shaky about fundamentals, this course will help. There will be an additional fee for the fundamentals course, to pay for Saturday night accomodations and food on Sunday morning and noon. Latin American Scientists: Several scholarships are available, from the International Union of Crystallography, to pay partial travel and subsistence costs for Latin-American students and junior faculty (no more than 30 yrs). Please apply for the course, and then contact R. Sweet (sw...@bnl.gov) if you are interested in applying for a scholarship. In accordance with the standards of the International Union of Crystallography, we observe the basic policy of non-discrimination, affirming the right and freedom of scientists to associate in international scientific activity without regard to such factors as citizenship, religion, creed, political stance, ethnic origin, race, colour, language, age, or gender, in accordance with the Statutes of the International Council for Science. At this course no barriers will exist beyond the application procedure that would prevent the participation of bona fide scientists. Please apply yourself, or send your students to our course, Bob Sweet, Sonya Kiss, and Alex Soares Course Announcement at http://www.bnl.gov/RapiData/ = Robert M. Sweet E-Dress: sw...@bnl.gov Group Leader, PXRR: Macromolecular ^ (that's L Crystallography Research Resource at NSLSnot 1) http://px.nsls.bnl.gov/ Photon Sciences and Biosciences Dept Office and mail, Bldg 745, a.k.a. LOB-5 Brookhaven Nat'l Lab. Phones: Upton, NY 11973631 344 3401 (Office) U.S.A. 631 344 2741 (Facsimile) =
[ccp4bb] MS analysis of frozen crystals after X-ray exposure
Hi ccp4bb, I would like to perform an MS analysis of the protein crystals after X-ray exposure. I'm interested in the characterization of the modifications on the cofactor (expected mass cca 400Da). I will need to wash the crystals before MS because they contain glycerol, long chain PEG and detergent. I'm trying to find a way how to wash these molecules out without losing the cofactor or breaking the crystal. As I don't have many crystals, I was wondering if some of you have tried such analysis and/or washing.. any advice would be greatly appreciated roman
[ccp4bb] resubmission of pdb
Dear all Dear Dr. PDB, Some time back i had submitted a coordinate in PDB but because of unacceptance of the manuscript we had to retract the submission. During this procedure i got few zipped file from the annotator such as 1. rcsb0.cif-public.gz, 2. rcsb0.pdb.gz and 3. rcsb0-sf.cif.gz..Now i want to submit the same ..My question is what is the best way to do it again..?? Should we start from the beginning through ADIT Deposition tool and resubmit it with a new PDB id or there is some way to submit again those zip files which the annotator sent us after retraction..May you please suggest what could be the easiest way to submit our structure to PDB without much efforts. -- Regards Faisal School of Life Sciences JNU
[ccp4bb] apologize
My earlier mail had an aberration where i began my mail by Dear Dr PDB..i am extremely sorry for this .. -- Regards Faisal School of Life Sciences JNU
Re: [ccp4bb] resubmission of pdb
I would write back to the annotator who send the processed files to you and ask if you can restart the deposition. The worst they can say is no and you're back to ADIT. On the other hand they will probably be as happy as you to save the work that has already been done. Dale Tronrud On 01/31/2014 01:04 PM, Faisal Tarique wrote: Dear all Dear Dr. PDB, Some time back i had submitted a coordinate in PDB but because of unacceptance of the manuscript we had to retract the submission. During this procedure i got few zipped file from the annotator such as 1. rcsb0.cif-public.gz, 2. rcsb0.pdb.gz and 3. rcsb0-sf.cif.gz..Now i want to submit the same ..My question is what is the best way to do it again..?? Should we start from the beginning through ADIT Deposition tool and resubmit it with a new PDB id or there is some way to submit again those zip files which the annotator sent us after retraction..May you please suggest what could be the easiest way to submit our structure to PDB without much efforts. -- Regards Faisal School of Life Sciences JNU
[ccp4bb] MSA with starting amino acid numbers
Dear users, I know one server for having the secondary structure over MSA i.e. Espript. But I want to incorporate the staring amino acid for protein. I could not find this option in the tutorial. Is it the post editing is the only way to add the amino acid numbers or there are other server which allow me to do so? Thanking you in advance. DCB -- Mr.Dilip C. Badgujar, Senior Research Fellow, ACTREC, Tata Memorial Center, Sector-22, Kharghar, Navi Mumbai. Pin-410210
