[ccp4bb] MOLREP fails when using input fixed model
Dear all, Recently, I used MOLREP to molecular replacement. My OS is fedora 14 and CCP4 version is the newest one ccp4-6.2.0 . When I run a pdb file and mtz by MOLREP without input fixed model, everything is right. However, when I run it by MOLREP when using input fixed model. The error is attached below. At line 1260 of file /usr/local/xtal/ccp4-6.2.0/src/molrep_/molrep.f Fortran runtime error: End of record Actually, my ccp4 is installed at /home/software/ccp4, not at /usr/local/xtal/ccp4-6.2.0/src/molrep_/molrep.f, which does not exist in my linux. In addition, I tried several published structures and tried to test MOLREP by input fixed model method .The error are same. Moreover, I tried to run it in windows XP using input fixed model, Molrep run well. I thought that it is a bug in this version of MOLREP. Any comments are welcome. with best wishes zhong chen -- zhongzhou chen Room 2071, research center in life sciences, No. 2 yuanmingyuan west road, Haidian District, Beijing, 100193 P.R. China Tel: (86)-10-62734078 15_molrep.log Description: Binary data
[ccp4bb] Position Available with Rigaku Europe - Scientific Support Engineer - Automation
Scientific Support Engineer – Automation Role: Rigaku Europe based in Sevenoaks UK is looking for a motivated scientist/engineer to join their service team. The primary responsibilities of the role will include the installation, customer training and maintenance of robotic crystallisation instruments from the Rigaku Automation range of products. Experience: 3+ years’ experience in the use and operation of scientific instrumentation. Experience in the maintenance and repair of electronic and mechanical systems. Knowledge of computer networking and databases is a pre-requisite. Experience in the use and maintenance of liquid handling instrumentation, automated crystal imaging systems and database software, in addition to practical experience with protein crystallization techniques is desirable. Excellent written and verbal communication skills. Location: This is a field based role requiring 75% travel. Ability to travel without restriction and at short notice to customer sites in Europe, USA and Far East is required. The candidate should hold a full clean driving licence. Closing Date: Applications should be received before 31st August 2011 Genuinely interested candidates should send a CV and covering letter by post or e-mail to: Dr. James Duncan Unit B6, Chaucer Business Park Watery Lane, Kemsing Sevenoaks, Kent TN15 6QY, England Tel: +44 1732 763 367 Informal enquiries or CVs can be sent to james.dun...@rigaku.com Rigaku Europe is an equal opportunities employer.
Re: [ccp4bb] TLS and ANISOU/RESIDUAL B-FACTORS - doubt
Thanks once again for all the suggestions. I managed to do it. Best regards, Catarina Silva On Fri, Aug 5, 2011 at 4:57 PM, Pavel Afonine pafon...@gmail.com wrote: Hi, On Fri, Aug 5, 2011 at 5:27 AM, Rachel Kramer Green kra...@rcsb.rutgers.edu wrote: ** (...) There are three ways to convert file so it contains full B factors: (...) in fact, more: 4. The command phenix.tls model.pdb combine_tls=true will combine TLS from PDB file header with 'residual' B from ATOM records. phenix.tls model.pdb extract_tls=true will split the total B-factor in ATOM records into TLS component and 'residual' part. Pavel.
[ccp4bb] cTruncate fails after Scala - clipper::Message_fatal
Dear all, We have a problem where cTruncate generates an error message when trying to process data from Scala as part of a Scale and Merge Intensities task in the GUI. Scala appears to run ok. cTruncate produces *** * Information from CCP4Interface script *** The program run with command: /sw/share/xtal/ccp4-6.2.0/bin/ctruncate -hklin /tmp/foop/Scala_1_1_mtz.tmp -hklout /tmp/foop/Scala_1_3_mtz_MPS1-1624-118.tmp -colin /*/*/\[IMEAN,SIGIMEAN\] -colano /*/*/\[I(+),SIGI(+),I(-),SIGI(-)\] -colout MPS1-1624-118 has failed with error message CCP4MTZfile - internal error terminate called after throwing an instance of 'clipper::Message_fatal' *** #CCP4I TERMINATION STATUS 0 CCP4MTZfile - internal error terminate called after throwing an instance of 'clipper::Message_fatal' We're running CCP4 6.2.0 compiled by 32-bit fink on OS X 10.6.8. The GUI task runs to completion with other input MTZ files that I have tried. If I run the ctruncate command in a shell, it generates the same error. Dr Stephen Carr posted a similar query back in March 2011, but didn't get any replies on the bb. Does anyone know what's going on here? Regards, Chris -- Dr Chris Richardson :: Sysadmin, structural biology, icr.ac.uk 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] cTruncate fails after Scala - clipper::Message_fatal
Hi Chris In Stephen's case the problem was that the column names were too long. They are limited to 30 characters by the mtz standard running through it looks like the problem is name truncation on the output columns. Whether it is the total name, /crystal/dataset/column , or just the column name I do not know. If I reduce the length of colout it runs through successfully Charles Ballard CCP4 On 8 Aug 2011, at 15:27, Chris Richardson wrote: Dear all, We have a problem where cTruncate generates an error message when trying to process data from Scala as part of a Scale and Merge Intensities task in the GUI. Scala appears to run ok. cTruncate produces *** * Information from CCP4Interface script *** The program run with command: /sw/share/xtal/ccp4-6.2.0/bin/ctruncate -hklin /tmp/foop/Scala_1_1_mtz.tmp -hklout /tmp/foop/Scala_1_3_mtz_MPS1-1624-118.tmp -colin /*/*/\[IMEAN,SIGIMEAN\] -colano /*/*/\[I(+),SIGI(+),I(-),SIGI(-)\] -colout MPS1-1624-118 has failed with error message CCP4MTZfile - internal error terminate called after throwing an instance of 'clipper::Message_fatal' *** #CCP4I TERMINATION STATUS 0 CCP4MTZfile - internal error terminate called after throwing an instance of 'clipper::Message_fatal' We're running CCP4 6.2.0 compiled by 32-bit fink on OS X 10.6.8. The GUI task runs to completion with other input MTZ files that I have tried. If I run the ctruncate command in a shell, it generates the same error. Dr Stephen Carr posted a similar query back in March 2011, but didn't get any replies on the bb. Does anyone know what's going on here? Regards, Chris -- Dr Chris Richardson :: Sysadmin, structural biology, icr.ac.uk 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.
[ccp4bb] N-terminal sequencing facility?
Hello, Can anyone recommend a facility that does N-terminal protein sequencing very well? It has to be able to work with PVDF-blotted protein bands as a source. Relatively inexpensive would be a plus. Thanks! - Dima
[ccp4bb] postdoctoral position at SGC-Toronto
Posted on behalf of PI: We are looking for post-doctoral scientists with a strong background in protein biochemistry and a commitment to drug development for neglected diseases. The parasitology group at the Structural Genomics Consortium (SGC) focuses on structure and function of proteins from apicomplexan and kinetoplastid parasites, including pathogens responsible for malaria, African Sleeping Disease and toxoplasmosis. In collaboration with leading parasitology labs worldwide, we are actively pursuing potential drug leads. Since 2001, the SGC has leveraged an advanced high throughput protein expression system and state-of-the-art crystallography equipment to determine and deposit the largest number of parasite protein structures in the Protein Data Bank. With a natural curiosity and love for bench science, you will work with other SGC scientists to express and characterize important parasitic proteins, in search of knowledge that will advance the cause of the millions of patients of neglected diseases around the globe. Visit our Facebook page at https://www.facebook.com/pages/Structural-Parasitology/130918920299505 Interested candidates should submit their resume to: raymond@utoronto.ca http://raymond%2e...@utoronto.ca/. -- Amy K. Wernimont, PhD Structural Genomics Consortium University of Toronto MaRS South Tower, Suite 705 101 College Street Toronto, Ontario Canada M5G 1L7 Tel: 416.978.1859
[ccp4bb] Postdoctoral position at the University of Illinois at Chicago
Applications from recent graduates are invited for NIH-funded postdoctoral positions in structural biology at the University of Illinois at Chicago. The positions require a Ph.D. in structural biology, biochemistry or a closely related field. The ideal candidates will have interests in protein structure/function and will have extensive experience in protein chemistry and basic molecular biology proficiency. Prior X-ray crystallography experience is a plus but not required. Join an enthusiastic laboratory working on exciting projects that are aimed at translating structural data to improve and develop novel therapeutics. Specifically, you will explore structure-function relationships of enzymes involved pro-drug activation to allow for enzyme engineering of improved variants. In this position there will also be an option to be trained in cell biology methods to test the efficacy of the engineered enzymes. The laboratory is located in the new state-of-the-art Molecular Biology Research Building. Our 30 minute proximity to the Advanced Photon Source makes UIC an excellent environment for x-ray crystallographic studies. UIC, the largest University in the Chicago area and the largest medical school in the nation, is located near downtown Chicago, a city with great cultural and recreational offerings. Informal inquiries can be made via E-mail. (la...@uic.edu). -- *** Arnon Lavie, Professor Dept. of Biochemistry and Molecular Genetics University of Illinois at Chicago 900 S. Ashland Ave. Molecular Biology Research Building, Room 1108 (M/C 669) Chicago, IL 60607 U.S.A. Tel:(312) 355-5029 Fax:(312) 355-4535 E-mail: la...@uic.edu http://www.uic.edu/labs/lavie/ ***
[ccp4bb] Summary: N-terminal sequencing facility?
Thanks so much to everyone who replied! Just in case anyone needs a similar info in the future, here are the responses that I got: *** Peter Cherepanov: we had good experience with Pick 'n Post (Alphalyse: http://www.alphalyse.com/) Katya Heldwein: We've been happy with ours - Tufts University Core Facility, http://tucf.org/http://tucf.org/. They charge $50 startup fee and $10/cycle. John Pascal: I have used Dana Farber Cancer Center in the past with good results: http://mbcf.dfci.harvard.edu/http://mbcf.dfci.harvard.edu/ Debasish Chattopadhyay: I used the facility at Yale University; I think the name is Keck center. It was very good. Raji Edayathumangalam: I have used the facility at UTMB in the past and was very happy with their prompt service and good results. Daniel Bonsor: http://www.alphalyse.com/n-terminal-sequencing.html $400 6 cycles included. I used this last year though it was cheaper. I found this one but not used it, though it seems too cheap to be true. http://www.protein.iastate.edu/nsequence494.html $69 + $25 for each cycle. Thomas Brett: I use this guy here in town. He takes po's and can probably do out of town. He does an awesome job. We send all our samples to him. Does first 5 a.a. at $50 a pop (i.e., $250 for minimum). His name is Dave McCourt. Link: http://www.mastl.com/ Sangwon: I have used the service from Tufts core facility. It was relatively inexpensive and I was satisfied with the results. Thanks again! Good to know that the choice is still good. The two facilities that we used in the past are no longer doing it. - Dima
Re: [ccp4bb] gst-tag protein purify problem
Forgot to add, a 150aa dna binding protein should only need a minimal hexahistidine tagthese proteins are typically very soluble and express well. Adding a GST or sumo tag is overkill. Dr. Paul Kraft Structural Biologist cell 586-596-2770 email: haresea...@yahoo.com email: kraft_proteome_resea...@yahoo.com This communication and any attachments contain information which is confidential and may also be privileged. It is for the exclusive use of the intended recipient(s). If you are not the intended recipient(s) please note that any form of disclosure, distribution, copying or use of this communication or the information in it or in any attachments is strictly prohibited and may be unlawful. If you have received this communication in error, please notify the sender and delete the email and destroy any copies of it. E-mail communications cannot be guaranteed to be secure or error free, as information could be intercepted, corrupted, amended, lost, destroyed, arrive late or incomplete, or contain viruses. We do not accept liability for any such matters or their consequences. Anyone who communicates with us by e-mail is taken to accept the risks in doing so. --- On Sat, 8/6/11, Carlos Kikuti kik...@gmail.com wrote: From: Carlos Kikuti kik...@gmail.com Subject: Re: [ccp4bb] gst-tag protein purify problem To: CCP4BB@JISCMAIL.AC.UK Date: Saturday, August 6, 2011, 5:13 PM What happens if you load your elution fraction into a size exclusion column? If your protein of interest comes in the void volume together with most of its contaminants, you'd better test a different construct, and that's much more than only changing the tag from N- to C-terminus. Sumo and GST might be solubilizing things that shouldn't really be soluble... Carlos Em 06/08/2011, às 16:43, Paul Kraft escreveu: Hi Lisa, Have you compared your yield of purified protein of soluble protein per gram of pellet, 4M Guanidine solubilized pellet (wash and elute from Ni column with 8M urea .5M imidazole..otherwise the gel with run crappy), and and total protein in the pellet on a page gel? The main reason I would think you get high background of cellular proteins on you Ni purification is because your yield is too low (I know obvious..). There are a variety of methods to increase yield like expressing at RT (assuming your expressing in E.coli), or switching to yeast, insect, or mamallian cells if your protein is of human origin. The most helpful and easiest method to try first (after trying low temp), would be switching the tag from N to C terminus or vice versa. Otherwise switch to a thermophile version of your protein if possible (and try cysteine mutants or other bacterial organisms for source the source gene). Paul ps one thing I forgot, you mention it is a DNA binding protein, solublizing in 2M NaCl is much better than 1M NaCl, you could just be losing it...the protein that is :-) Dr. Paul Kraft Structural Biologist cell 586-596-2770 email: haresea...@yahoo.com email: kraft_proteome_resea...@yahoo.com This communication and any attachments contain information which is confidential and may also be privileged. It is for the exclusive use of the intended recipient(s). If you are not the intended recipient(s) please note that any form of disclosure, distribution, copying or use of this communication or the information in it or in any attachments is strictly prohibited and may be unlawful. If you have received this communication in error, please notify the sender and delete the email and destroy any copies of it. E-mail communications cannot be guaranteed to be secure or error free, as information could be intercepted, corrupted, amended, lost, destroyed, arrive late or incomplete, or contain viruses. We do not accept liability for any such matters or their consequences. Anyone who communicates with us by e-mail is taken to accept the risks in doing so. From: LISA science...@gmail.com To: CCP4BB@JISCMAIL.AC.UK Sent: Thursday, August 4, 2011 11:51 AM Subject: [ccp4bb] gst-tag protein purify problem hi guys, I have a DNA binding protein and expressed the DNA binding domain (150 aa) with his-sumo tag or gst tag at the n-terminal. I tried to purified it with Ni column or Gst column separately. But purity is lower than 50% after Ni or GST column. This protein only stable with 1M Nacl or higher. I worked on it almost half year. But I still can not get the pure protein. please give me some suggestions. Thank you. Lisa
[ccp4bb] Installation of ccp4 on 64bit fedora core 13
Dear all, First I’m a beginner of linux and I’m trying to install CCP4 on my 64bit Fedora 13. If there is anyone who successfully installed ccp4 on 64bit fedora13, please, instruct me how to install this program in detail. I’m very desperate Sangheon Yu Rm. 1053 Bldg. 200 School of Agricultural Biotechnology College of Agriculture Life Sciences Seoul National University Seoul 151-921, KOREA
[ccp4bb] Installation of ccp4 on 64bit fedora core 13
Dear all, First I’m a beginner of linux and I’m trying to install CCP4 on my 64bit Fedora 13. If there is anyone who successfully installed ccp4 on 64bit fedora13, please, instruct me how to install this program in detail. I’m very desperate Sangheon Yu Rm. 1053 Bldg. 200 School of Agricultural Biotechnology College of Agriculture Life Sciences Seoul National University Seoul 151-921, KOREA
Re: [ccp4bb] Installation of ccp4 on 64bit fedora core 13
유상헌 wrote: Dear all, First I’m a beginner of linux and I’m trying to install CCP4 on my 64bit Fedora 13. If there is anyone who successfully installed ccp4 on 64bit fedora13, please, instruct me how to install this program in detail. I recently installed CCP4-6.1.3 from source on fedora 14, 64-bit. After googling solved a few problems it went easily. Maybe the problems are all fixed in 6.2 so try that first. Un-tar the package- read INSTALL (or INSTALL.html or .ps) in the top directory Try to follow the instructions for installing from source and see where you get stuck. Check the list of problems reported and see if there are solutions at http://www.ccp4.ac.uk/problems.php For me, this site had most of the answers: http://bioscreencastwiki.com/Crystallography_Howtos/Installing_ccp4-6.0.99e_on_64_bit_Ubuntu For fedora, use yum install instead of apt-get install and yum provides (or whatprovides) instead of apt-file search (And unless you are a mac person, you might be more comfortable becoming root rather than prepending every privilege-requiring command with sudo) If you have trouble with TCL/TK read below-quoted message. Mosflm site has more suggestions. better yet: http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/CCP4_on_Fedora_12 Mark Del Campo wrote: Okay, I got the problem resolved in the following way (thanks go to Clint Leysath): 1. removed the tcltk++ directory that came with my ccp4 download 2. installed Activestate's tcltk 8.4.19.2 from https://www.activestate.com/activetcl/downloads/ 3. downloaded blt2.4z.tar.gz and the blt2.4z-patch-2 from http://sourceforge.net/projects/blt/files/ 4. unpacked blt2.4z.tar.gz and moved the patch file into the blt2.4z directory 5. patched the blt installation (patch -p1 -i blt2.4z-patch-2) 6. then reordered statements in blt2.4z/src/bltTree.c [this is detailed at http://www.ccp4.ac.uk/ccp4i/install_tcltkblt.html under the heading Compilation failure in bltTree on 64-bit machines] 7. configured the blt install (./configure --with-tcl=/path/to/ActiveTcl-8.4) 8. installed blt (make) 9. for some reason bltwish did not end up in /path/to/ActiveTcl-8.4/bin even though the configure script said that is where it would be put, so I moved it to /path/to/ActiveTcl-8.4/bin 10. edited 1 line in ccp4.setup-bash (setenv CCP4I_TCLTK /path/to/ActiveTcl-8.4/bin/) 11. opened a new terminal window ccp4i works
