Re: [ccp4bb] Which Coot for Scientific Linux 6.3
Hi Fred, on today's PC hardware, a 64bit Linux should be used. We have been using coot-0.7-pre-1-revision-3965-binary-Linux-x86_64-centos-5-python-gtk2 on our 64bit SL 6.3 systems without problems. I just now installed coot-0.7-pre-1-revision-4360-binary-Linux-x86_64-centos-6-python-gtk2 on these systems and it seems to run well. Is there an error message if you try that? HTH, Kay On Thu, 20 Sep 2012 17:05:04 +0200, vellieux frederic.velli...@ibs.fr wrote: Hi all, Well I did it the hard way, i.e. try all versions until I came across one version of Coot that runs. In my hands I did not get a single version to run on SL6.3, 64-bit version (Dirk Kostrewa had another experience with SL6.3 64 though). So I installed SL6.3, 32-bit version, and the version of Coot for Fedora core 12 runs and provides me with a proper graphics windows. I thought I'd keep the bb informed. F.V. -- Fred. Vellieux (B.Sc., Ph.D., hdr) IBS / ELMA 41 rue Jules Horowitz F-38027 Grenoble Cedex 01 Tel: +33 438789605 Fax: +33 438785494 email: frederic.velli...@ibs.fr
[ccp4bb] Program for map rotation
Dear Niu, MAIN can do it (http://www-bmb.ijs.si). dusan On Sep 21, 2012, at 1:06 AM, CCP4BB automatic digest system wrote: Date:Wed, 19 Sep 2012 15:25:50 -0700 From:Niu Tou niutou2...@gmail.com Subject: Program for map rotation Dear colleagues, Is there any program can rotate a density map (generated by FFT, could be read in Coot and Pymol) given the matrix? I have tried Extension-Maps- Transform map by LSQ model fit, it looks doesnot work. While the program Edit/Rotate map Mask in CCP4 gave an error message: mapmask: mapextend - input map does not contain a whole ASU. Thanks! Niu Dr. Dusan Turk, Prof. Head of Structural Biology Group Head of Centre for Protein and Structure Production Centre of excellence for Integrated Approaches in Chemistry and Biology of Proteins, Scientific Director Professor of Structural Biology at IPS Jozef Stefan e-mail: dusan.t...@ijs.sihttp://bio.ijs.si/sbl/ phone: +386 1 477 3857 Dept. of Biochem. Mol. Struct. Biol. fax: +386 1 477 3984 Jozef Stefan Institute Jamova 39, 1 000 Ljubljana,Slovenia Skype: dusan.turk (voice over internet: www.skype.com
[ccp4bb] Postdoctoral Fellow - University of Oklahoma
Postdoctoral Fellow – Protein CrystallographyUniversity of Oklahoma Health Sciences Center, USAA postdoctoral position is available immediately in the laboratory of Dr. Marie Hanigan for a highly motivated, creative individual with strong interest in the structure and function of enzymes relevant to redox stress and inflammation.The successful candidate will investigate the structure, catalytic mechanism and inhibition of the human gamma-glutamyl transpeptidase family of enzymes using macromolecular X-ray crystallography. This position is funded through a new NIH-sponsored Center of Biomedical Research Excellence in Structural Biology (OCSB) at The University of Oklahoma and the University of Oklahoma Health Sciences Center. The Center is directed by Dr. Ann West and is well equipped with state-of-the-art equipment for molecular biology, protein biochemistry, and crystallography, including a new protein production core facility, crystallization robot, and upgraded X-ray generator. The successful candidate will be actively involved in the Center including interaction and potential collaboration with all members of the OCSB.Candidates should have a Ph.D. in a field relevant to structural biology and a strong background in X-ray crystallography. The candidate should be familiar with the methods of determining protein X-ray structures including indexing/scaling of data, structure determination through molecular replacement and other techniques, refinement, and analysis of the resulting structure. Experience with molecular docking and/or modeling is advantageous. The candidate must have clear communication skills and fluency in the English language. Applicants should send a cover letter, a CV, a list of publications, a detailed summary of research experience and interests as well as the names and contact information of three references. The information should be sent via e-mail to marie-hani...@ouhsc.edu.the University of Oklahoma is an Equal Opportunity/Affirmative Action Employer.Marie Hanigan Marie H. Hanigan, Ph.D.Professor of Cell BiologyUniversity of Oklahoma Health Sciences CenterBiomedical Research Center, Room 264975 N.E. 10th StreetOklahoma City, Oklahoma 73104Phone: 405-271-3832FAX: 405-271-3758 -- Scanned by iCritical. Postdoc Ad.docx Description: application/vnd.openxmlformats-officedocument.wordprocessingml.document
[ccp4bb] sequencing
Dear all , my job is to clone part of the gene already carried on pJC40 vector .i sent this vector for sequencing . i made also squence alignment, i have found only 97% identity . this mean about five nuclutides are not matching with original sequence . when i made protein blast i also found 4 amino acid were altered . this is sequencing result 10285313.seq - ID: 130912 Amr-T7 on 2012/9/17-4:14:28 automatically edited with PhredPhrap, start with base no.: 10 Internal Params: Windowsize: 20, Goodqual: 19, Badqual: 10, Minseqlength: 50, nbadelimit: 1 tnaaaTaTTTtgTTTtaCTTtAGanngagaTATACCatggGGcCATCATCATCATCATCATCATCATCATCACAGCAGCGGCCATATCGAAgGTCGTCATATGATAAAcgtCGCCAACAACAACAACAACAACAACAGCAACAACAACgtGatgAACGTgGAATACCACCACGGAAGgtGCACCACCAAgtgTTATCGATGAAATAATTTGCTACTGATGTCTGATCAACAAACtgAAGCTGATGTTGAAGCATTCATCAATAGACTTGGTGGCAGTTACAAGGTTCGATTTACTCAATTCATGGAAGAAGTAAAGAAAGCTAGAGCTGATTATGAAAGAATCCATCAGCAGGCAGTAGCAAGACGCCAGCAGCGATGCTGACGCAAGGATGTCCGCTATTGCTGGTTCGCCGCATCTAACTACGCGACATCGCAGCAAATTCAAGCCATCATGGATTCATTATCTGAGAGCGTTCGAGGagaGATCATTAAGGCATTGAGCCCACAAGAATAAGGATCCCGGGCCCTAGCTAACTGATCCGGCTGCTAACAAAGCCCGAAAGGAAGCTGAGTTGGCTGCTGCCACCGCTGAGCAATAACTAGCATAATTCCTCTAAACGGGTCTTGATTGCTGAAAGGAGGAACTATATCCGGATAATTCTTGAAGACGAAAGGGCCTCGTGATACGCCTATtTTTATAGGTTAATGTCATGATAATAATGGTTTCTTAGACGTCAGGTGGCACCAAATGTGCGCGGAACCcCTATTTGTTTATCTAAATACATTCAAATATGTATCCGCTCATGAGACAATAACCCTGATAAATGCTTCAATAATATTGAaGGAAGAGTATGAGTATTCAACATTTCCGTGTCGCC this is DNA alignment. gb|U00693.1|OVU00693 Onchocerca volvulus Rainforest immunodominant hypodermal antigen mRNA, complete cds Length=880 Score = 798 bits (432), Expect = 0.0 Identities = 442/447 (99%), Gaps = 0/447 (0%) Strand=Plus/Plus Query 48 ATAAACGTCGCcaacaacaacaacaacaacaacagcaacaacaacGTGATGAACGT 107 Sbjct 117 ATAAACGTCGCCAACAACAACAACAACAACAACAGCAACAACAACGTGATGAACGT 176 Query 108 GGAATACCACCACGGAAGGTGCACCACCAAGTGTTATCGATGAAATAATTTG 167 | || ||| Sbjct 177 GAAATACCACCATGGAAGGTGCACCACCAAGTGTTATCGATGAAATAATTTG 236 Query 168 CTACTGATGTCTGATCAACAAACTGAAGCTGATGTTGAAGCATTCATC 227 Sbjct 237 CTACTGATGTCTGATCAACAAACTGAAGCTGATGTTGAAGCATTCATC 296 Query 228 AATAGACTTGGTGGCAGTTACAAGGTTCGATTTACTCAATTCATGGAAGAAGTAAAGAAA 287 Sbjct 297 AATAGACTTGGTGGCAGTTACAAGGTTCGATTTACTCAATTCATGGAAGAAGTAAAGAAA 356 Query 288 GCTAGAGCTGATTATGAAAGAATCCATCAGCAGGCAGTAGCAAGACGCCAGCAGCA 347 Sbjct 357 GCTAGAGCTGATTATGAAAGAATCCATCAGCAGGCAGTAGCAAGACGCCAGCAGCA 416 Query 348 AAAGATGCTGACGCAAGGATGTCCGCTATTGCTGGTTCGCCGCATCTAACTACGCGACAA 407 || | Sbjct 417 AAAGATGCTGACGCAAGGATGTCCGCTATTGCTGATTCGCCGCATCTAACTACGCGACAA 476 Query 408 AAATCGCAGCAAATTCAAGCCATCATGGATTCATTATCTGAGAGCGTTCGAGGAGAGATC 467 ||| Sbjct 477 AAATCGCAGCAAATTCAAGCCATCATGGATTCATTATCTGAGAGCGTTCGAAGAGAGATC 536 Query 468 ATTAAGGCATTGAGCCCACAAGAATAA 494 | | Sbjct 537 ATTAATGCATTGAGCCCACAAGAATAA 563 and this is amino acid sequence alignment . lcl|8325 unnamed protein product Length=148 Score = 256 bits (655), Expect = 7e-93, Method: Compositional matrix adjust. Identities = 143/148 (97%), Positives = 143/148 (97%), Gaps = 0/148 (0%) Query 1 IPQRRQQQRDEREIPPFLEGAPPSVIDEFYNLLKTDENKTDQQTEADVEAFI 60 IPQRRQQQRDER IPPF EGAPPSVIDEFYNLLKTDENKTDQQTEADVEAFI Sbjct 1 IPQRRQQQRDERGIPPFSEGAPPSVIDEFYNLLKTDENKTDQQTEADVEAFI 60 Query 61 NRLGGSYKVRFTQFMEEVKKARADYERIHQQAVARFSPAAKDADARMSAIADSPHLTTRQ 120 NRLGGSYKVRFTQFMEEVKKARADYERIHQQAVARFSPAAKDADARMSAIA SPHLTTRQ Sbjct 61 NRLGGSYKVRFTQFMEEVKKARADYERIHQQAVARFSPAAKDADARMSAIAGSPHLTTRQ 120 Query 121 KSQQIQAIMDSLSESVRREIINALSPQE 148 KSQQIQAIMDSLSESVR EII ALSPQE Sbjct 121 KSQQIQAIMDSLSESVRGEIIKALSPQE 148. now what should i do? continue and design primers or repeat the sequencing again or begin every thing from zero point . best regards Amr
[ccp4bb] Off Topic: help locating CNS data
I have been presented with the problem of locating protein data for a structure which was refined here ten years ago with the CNS program. Unfortunately I have never used this program so do not know what type of files I am looking for (or how many files). Any suggestions please Rex Palmer http://www.bbk.ac.uk/biology/our-staff/emeritus-staff http://rexpalmer2010.homestead.com
Re: [ccp4bb] Off Topic: help locating CNS data
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Rex, CNS uses input files, which are listed e.g. at http://cns.csb.yale.edu/v1.2/ When I used CNS I always had to use 'generate.inp' so i would start search for this. However, they can be freely renamed, I am afraid. Good luck, Tim On 09/21/2012 12:10 PM, Rex Palmer wrote: I have been presented with the problem of locating protein data for a structure which was refined here ten years ago with the CNS program. Unfortunately I have never used this program so do not know what type of files I am looking for (or how many files). Any suggestions please Rex Palmer http://www.bbk.ac.uk/biology/our-staff/emeritus-staff http://rexpalmer2010.homestead.com - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFQXEDhUxlJ7aRr7hoRAs5rAKD5w3VlVFECMzVgPU56G/biy6AsfwCgxM41 1vG/TghWgjLKNb9qp3NDHtU= =LegZ -END PGP SIGNATURE-
Re: [ccp4bb] Off Topic: help locating CNS data
As was mentioned, the diffraction data files can be named according to the user's wish. But I'd try to locate files with extensions .hkl, .xpl, .cv (and .cns? although I have never seen that extension used myself) Fred. On 21/09/12 12:10, Rex Palmer wrote: I have been presented with the problem of locating protein data for a structure which was refined here ten years ago with the CNS program. Unfortunately I have never used this program so do not know what type of files I am looking for (or how many files). Any suggestions please Rex Palmer http://www.bbk.ac.uk/biology/our-staff/emeritus-staff http://rexpalmer2010.homestead.com -- Fred. Vellieux (B.Sc., Ph.D., hdr) IBS / ELMA 41 rue Jules Horowitz F-38027 Grenoble Cedex 01 Tel: +33 438789605 Fax: +33 438785494
Re: [ccp4bb] Off Topic: help locating CNS data
Add another extension to your search: *.mtf If your structure was refined with CNS, chances are you'll find its Molecular Topology File somewhere. Best of luck, Jon 2012/9/21 vellieux frederic.velli...@ibs.fr As was mentioned, the diffraction data files can be named according to the user's wish. But I'd try to locate files with extensions .hkl, .xpl, .cv (and .cns? although I have never seen that extension used myself) Fred. On 21/09/12 12:10, Rex Palmer wrote: I have been presented with the problem of locating protein data for a structure which was refined here ten years ago with the CNS program. Unfortunately I have never used this program so do not know what type of files I am looking for (or how many files). Any suggestions please Rex Palmer http://www.bbk.ac.uk/biology/our-staff/emeritus-staff http://rexpalmer2010.homestead.com -- Fred. Vellieux (B.Sc., Ph.D., hdr) IBS / ELMA 41 rue Jules Horowitz F-38027 Grenoble Cedex 01 Tel: +33 438789605 Fax: +33 438785494 -- Jon Agirre, PhD Unit of Biophysics (CSIC-UPV/EHU) http://www.ehu.es/jon.agirre http://sourceforge.net/projects/projectrecon/ +34656756888
Re: [ccp4bb] Off Topic: help locating CNS data
If you are looking for reflection files, the tricky part is that in CNS
format they did not include the unit cell parameters. Just to locate
them, it may be helpful to know that they contain a header that looks
like this
NREFlection= 49238
ANOMalous=FALSe { equiv. to HERMitian=TRUE}
DECLare NAME=FOBS DOMAin=RECIprocal TYPE=REAL END
DECLare NAME=SIGMA DOMAin=RECIprocal TYPE=REAL END
DECLare NAME=TEST DOMAin=RECIprocal TYPE=INTE END
so if you are in *nix environment something like this
egrep -rl '^[ ]DECLare NAME.*DOMAin=RECIprocal' .
I am sure perl masters will laugh at my awkward attempts at using
regular expressions.
Cheers,
Ed.
On 09/21/2012 06:10 AM, Rex Palmer wrote:
I have been presented with the problem of locating protein data for a
structure which was refined here ten years ago with the CNS program.
Unfortunately I have never used this program so do not know what type
of files I am looking for (or how many files).
Any suggestions please
Rex Palmer
http://www.bbk.ac.uk/biology/our-staff/emeritus-staff
http://rexpalmer2010.homestead.com
[ccp4bb] CCP4 update
Dear CCP4 Users, A CCP4 update has just been released, consisting of the following changes. For Linux and Mac: - *areaimol*: fixed segmentation fault due to a bug in dynamic memory allocation - *cprodrg*: HETATM notations synchronised with refmac - *ccp4i*: fixes in refmac harvesting In addition to the above, on Windows: - *ccp4i*: added kill job functionality The easiest way to obtain the update is to install the CCP4 update clienthttp://www.ccp4.ac.uk/download/update_manual.html, if you have not done so already. Note that autoupdates will work correctly only with CCP4 release 6.3.0, therefore upgrade if necessary. Report bugs to c...@stfc.ac.uk. Many thanks for using CCP4, -- David Waterman
[ccp4bb] Post-doctoral Position in Structural Biology
Post-doctoral Position in Structural Biology A post-doctoral position is available for a person with experience in protein or virus crystallography. Some experience in electron microscopy would be desirable but not essential. The work of the laboratory centers on the structure and function of viruses. Salary will depend on experience. A starting post-doc salary is around $39,000/year. Applications should be send by e-mail to Michael Rossmann (m...@purdue.edumailto:m...@purdue.edu). Michael G. Rossmann Hanley Professor of Biological Sciences Hockmeyer Hall of Structural Biology 240 S. Martin Jischke DriveTel: 765-494-4911 Purdue University,FAX: 765-496-1189 West Lafayette,e-mail: m...@purdue.edu IN 47907-1971, USA. web site http://bilbo.bio.purdue.edu/~viruswww/Rossmann_home/
[ccp4bb] dmmulti cross-crystal averaging question
We are working with two crystals. Both crystals have a domain that is not in the other. Both crystals have one domain that is the same in each. We'd like the average the one domain between the crystals, but leave the other domains unaveraged. How do we describe that to dmmulti? thanks, Dave --
Re: [ccp4bb] dmmulti cross-crystal averaging question
The domain common to both crystals constitutes the averaging mask. (you can make it around the pdb using ncsmask). As for describing it to dmmulti, you need the rotation matrix which maps it from crystal 1 to crystal 2. The rotation matrix for crystal one is always the identity matrix. You will put the matrix mapping the domain from 1 to 2 as the rotation matrix for the second crystal. You may want to obtain a rotation matrix optimized against your current density first before supplying it to dmmulti (the rave utilities will do this for you). When you get to dmmulti, output the solvent masks and make sure they're accurate (or alternatively you can supply a solvent mask for each crystal separately). F On Sep 21, 2012, at 9:47 AM, Garboczi, David (NIH/NIAID) [E] wrote: We are working with two crystals. Both crystals have a domain that is not in the other. Both crystals have one domain that is the same in each. We'd like the average the one domain between the crystals, but leave the other domains unaveraged. How do we describe that to dmmulti? thanks, Dave -- - Francis E. Reyes PhD 215 UCB University of Colorado at Boulder
