[ccp4bb] Probleme with D-peptide cif dictionary with refmac5.8
Dear all, A quick note to report the problems I have experienced (and a solution) with the refinement of a peptide containing both D- and L-amino-acids with refmac5.8 (Refmac_5.8.0073). This refinement was done with high resolution data, with hydrogens included in the model (important to remember !). When using the standard dictionary for D-TRYPTOPHAN: $CLIBD_MON/d/DTR.cif, most of the geometrical definitions were altered after the inserted D-amino-acid. The geometrical Rms deviations are strongly increased already at the first cycle (see differences of two runs at the end of my message). The first solution was to generate a new cif dictionary from the standard TRP.cif file in the following way: sed -e 's/negativ/positiv/' -e 's/TRP/DTR/g' -e 's/L-peptide/D-peptide/' $CLIBD_MON/t/TRP.cif DTRP.cif Running again refmac5 with this cif file using the LIBIN DTRP.cif instruction produced the more sensible results. It looked to me that the TRP and DTR cif definitions have diverged at some point. Looking more closely at the differences in this two files, pointed me to this: Hydrogen on the indole NE1 is named HE1 in TRP and HNE1 for DRT... Using a pdb file with HE1 renamed as HNE1 worked with the current DRT file, but with slightly worst results. The DTR.cif file probably needs to be updated (and maybe the other D-amino-acids cifs also revisited). Best regards, Pierre PS1. I can send the log and pdb files to developers if they are interested. PS2. I haven't checked with other D-amino-acids, since I have only this one in my structure. With modified TRP as DTRP.cif: InitialFinal R factor0.0865 0.0847 R free0.0913 0.0896 Rms BondLength0.0181 0.0175 Rms BondAngle2.2555 2.2407 Rms ChirVolume0.1131 0.1154 With standard DRT.cif file: InitialFinal R factor0.0865 0.1916 R free0.0913 0.2006 Rms BondLength2.4522 1.7415 Rms BondAngle 33.3672 32.1460 Rms ChirVolume1.1972 1.0767 With DRT.cif and renamed HE1 as HNE1: InitialFinal R factor0.0865 0.0848 R free0.0913 0.0901 Rms BondLength0.0207 0.0200 Rms BondAngle2.4024 2.3884 Rms ChirVolume0.1122 0.1140
Re: [ccp4bb] Normal mode refinement
Dear All, Thank you very much for valuable suggestions and educating me on the normal mode refinement. Actually, I am trying to refine a protein (cytosolic domain and trans-membrane domain). I found a solution through PHASER and density looks really good in both domain but as i proceeds with refinement density remain great in both domain till Rfree around 38%. Interestingly, with further refinement cycle, Rfree reduced to 30% but the density in the trans-membrane domain becomes very weak. That is why i am wondering whether it is possible to improve the density in the trans-membrane domain by using Normal mode refinement. Conservatively speaking, it could be possible that trans-membrane is highly flexible or disordered and after much cerebration, i am thinking to incorporate the normal mode refinement to monitor if there is any improvement in electron density trans-membrane domain. I would follow suggestions of Dr, Mande and Dr. Ethan. Also, would give a try to what Arpita has suggested. I further, warmly welcome any suggestion on refinement procedure to improve electron density in flexible or disordered trans-membrane domain. Appu On 20 October 2014 23:41, Arpita Goswami bt.arp...@gmail.com wrote: Hello, You can also contact elNemo or NOMAD-Ref server developers about getting covariance/correlation matrices from normal mode analysis outputs to know the correctly coordinated mobile atoms. In this way you can compare with biological data also. In Shekhar's said paper K. Suhre (one of the developer of el-Nemo server) has done the same very correctly. best wishes, Arpita On Tue, Oct 21, 2014 at 5:40 AM, Appu kumar appu.kum...@gmail.com wrote: Dear CCP4 Users, I seek your valuable advice and suggestion in carrying out the normal mode structure refinement which manifest the dynamics of protein as linear combination of harmonic modes, used to describe the motion of protein structure in collective fashion. Studies suggest that it is highly useful in refining the protein structure which harbors a considerable magnitude of flexibility in atomic position owing to high thermal factors. Therefor I want to know is there any software/script available to execute the normal mode of refinement. Thanks a lot in advance for your imperative suggestions Appu -- Arpita -- Arpita Goswami Senior Research Fellow Structural Biology Laboratory Centre for DNA Fingerprinting and Diagnostics (CDFD) Tuljaguda (Opp MJ Market), Nampally, Hyderabad 500 001 INDIA Phone: +91- 40- 24749401/404 Mobile: 9390923667, 9502389184 Email: arp...@cdfd.org.in
Re: [ccp4bb] Normal mode refinement
Dear All, Thank you very much for valuable suggestions and educating me on the normal mode refinement. Actually, I am trying to refine a protein (cytosolic domain and trans-membrane domain). I found a solution through PHASER and density looks really good in both domain but as i proceeds with refinement density remain great in both domain till Rfree around 38%. Interestingly, with further refinement cycle, Rfree reduced to 30% but the density in the trans-membrane domain becomes very weak. That is why i am wondering whether it is possible to improve the density in the trans-membrane domain by using Normal mode refinement. Conservatively speaking, it could be possible that trans-membrane is highly flexible or disordered and after much cerebration, i am thinking to incorporate the normal mode refinement to monitor if there is any improvement in electron density trans-membrane domain. I would follow suggestions of Dr, Mande and Dr. Ethan. Also, would give a try to what Arpita has suggested. I further, warmly welcome any suggestion on refinement procedure to improve electron density in flexible or disordered trans-membrane domain. Appu On 21 October 2014 07:39, Appu kumar appu.kum...@gmail.com wrote: Dear All, Thank you very much for valuable suggestions and educating me on the normal mode refinement. Actually, I am trying to refine a protein (cytosolic domain and trans-membrane domain). I found a solution through PHASER and density looks really good in both domain but as i proceeds with refinement density remain great in both domain till Rfree around 38%. Interestingly, with further refinement cycle, Rfree reduced to 30% but the density in the trans-membrane domain becomes very weak. That is why i am wondering whether it is possible to improve the density in the trans-membrane domain by using Normal mode refinement. Conservatively speaking, it could be possible that trans-membrane is highly flexible or disordered and after much cerebration, i am thinking to incorporate the normal mode refinement to monitor if there is any improvement in electron density trans-membrane domain. I would follow suggestions of Dr, Mande and Dr. Ethan. Also, would give a try to what Arpita has suggested. I further, warmly welcome any suggestion on refinement procedure to improve electron density in flexible or disordered trans-membrane domain. Appu On 20 October 2014 23:41, Arpita Goswami bt.arp...@gmail.com wrote: Hello, You can also contact elNemo or NOMAD-Ref server developers about getting covariance/correlation matrices from normal mode analysis outputs to know the correctly coordinated mobile atoms. In this way you can compare with biological data also. In Shekhar's said paper K. Suhre (one of the developer of el-Nemo server) has done the same very correctly. best wishes, Arpita On Tue, Oct 21, 2014 at 5:40 AM, Appu kumar appu.kum...@gmail.com wrote: Dear CCP4 Users, I seek your valuable advice and suggestion in carrying out the normal mode structure refinement which manifest the dynamics of protein as linear combination of harmonic modes, used to describe the motion of protein structure in collective fashion. Studies suggest that it is highly useful in refining the protein structure which harbors a considerable magnitude of flexibility in atomic position owing to high thermal factors. Therefor I want to know is there any software/script available to execute the normal mode of refinement. Thanks a lot in advance for your imperative suggestions Appu -- Arpita -- Arpita Goswami Senior Research Fellow Structural Biology Laboratory Centre for DNA Fingerprinting and Diagnostics (CDFD) Tuljaguda (Opp MJ Market), Nampally, Hyderabad 500 001 INDIA Phone: +91- 40- 24749401/404 Mobile: 9390923667, 9502389184 Email: arp...@cdfd.org.in
Re: [ccp4bb] Normal mode refinement
On Tuesday, 21 October 2014 07:39:53 AM Appu kumar wrote: Dear All, Thank you very much for valuable suggestions and educating me on the normal mode refinement. Actually, I am trying to refine a protein (cytosolic domain and trans-membrane domain). I found a solution through PHASER and density looks really good in both domain but as i proceeds with refinement density remain great in both domain till Rfree around 38%. Interestingly, with further refinement cycle, Rfree reduced to 30% but the density in the trans-membrane domain becomes very weak. That is why i am wondering whether it is possible to improve the density in the trans-membrane domain by using Normal mode refinement. Conservatively speaking, it could be possible that trans-membrane is highly flexible or disordered and after much cerebration, i am thinking to incorporate the normal mode refinement to monitor if there is any improvement in electron density trans-membrane domain. Please keep in mind that if the density is poor because the protein really is disordered, a perfect description of those disordered cell contents will perfectly reproduce that poor density. So improved description does not necessarily imply improved map quality. This is quite different from the case of a poor model for a well-ordered structure. Here also you will see a low quality map, but in this case it will improve as your description of the cell contents improves. Ethan I would follow suggestions of Dr, Mande and Dr. Ethan. Also, would give a try to what Arpita has suggested. I further, warmly welcome any suggestion on refinement procedure to improve electron density in flexible or disordered trans-membrane domain. Appu On 20 October 2014 23:41, Arpita Goswami bt.arp...@gmail.com wrote: Hello, You can also contact elNemo or NOMAD-Ref server developers about getting covariance/correlation matrices from normal mode analysis outputs to know the correctly coordinated mobile atoms. In this way you can compare with biological data also. In Shekhar's said paper K. Suhre (one of the developer of el-Nemo server) has done the same very correctly. best wishes, Arpita On Tue, Oct 21, 2014 at 5:40 AM, Appu kumar appu.kum...@gmail.com wrote: Dear CCP4 Users, I seek your valuable advice and suggestion in carrying out the normal mode structure refinement which manifest the dynamics of protein as linear combination of harmonic modes, used to describe the motion of protein structure in collective fashion. Studies suggest that it is highly useful in refining the protein structure which harbors a considerable magnitude of flexibility in atomic position owing to high thermal factors. Therefor I want to know is there any software/script available to execute the normal mode of refinement. Thanks a lot in advance for your imperative suggestions Appu -- Arpita -- Arpita Goswami Senior Research Fellow Structural Biology Laboratory Centre for DNA Fingerprinting and Diagnostics (CDFD) Tuljaguda (Opp MJ Market), Nampally, Hyderabad 500 001 INDIA Phone: +91- 40- 24749401/404 Mobile: 9390923667, 9502389184 Email: arp...@cdfd.org.in -- mail: Biomolecular Structure Center, K-428 Health Sciences Bldg MS 357742, University of Washington, Seattle 98195-7742
[ccp4bb] 10 DAYS REMAIN to apply for the DLS/CCP4 data analysis workshop
Dear all, Please be aware that the application period for the first DLS/CCP4 data analysis workshop closes on the 31st October. Successful applicants will be notified shortly after that date. As a reminder, the workshop is intended for PhD students, postdocs and early career scientists who are *currently working on a project in MX, and who are able to bring crystals or data with them*. The workshop will consist of a mixture of lectures and tutorials, plus hands-on practical sessions, in which the students will work alongside the leading software developers and scientists on their own data. Applicants please note that you must provide the e-mail address of a supervisor who will write a letter in support of your application. More details may be found here: http://www.ccp4.ac.uk/schools/DLS-2014/index.php The online application form is at Diamond's Events site: http://www.diamond.ac.uk/Home/Events/2014/Diamond-CCP4-Data-Collection-and-Analysis-workshop.html Many thanks for your interest David Waterman, on behalf of the organisers.
[ccp4bb] Position available: Software Release Engineer - SBGrid
Apply at the Harvard https://sjobs.brassring.com/TGWebHost/jobdetails.aspx?SID=%5ejgFrmcPkboV4jePuRlvcNXlmX5_slp_rhc_uO148eWl8BHvn0%2fx4xqZEPHCOI9i2lie3nSAPjobId=1104142type=searchJobReqLang=1recordstart=1JobSiteId=5341JobSiteInfo=1104142_5341GQId=0 Auto req ID34021BRBusiness TitleSoftware Release EngineerSchool/UnitHarvard Medical SchoolLocationUSA - MA - Boston Job FunctionInformation TechnologyTime StatusFull-time Duties ResponsibilitiesThe SBGrid Consortium has an immediate opening for a Software Release Engineer. The primary responsibilities of the position will be installing, configuring and testing biomedical software on Linux and OS X for use in the Harvard Medical School laboratories as well as providing first level technical support for software users. The majority of user support occurs over email, so the ability to communicate clear English instructions is critical. Additional responsibilities include working with scientific software developers to integrate new applications into the software collection. The scientific software is written in a polyglot of languages (Fortran, C, C++, Python, Java, Perl, Tcl/Tk and many sh/csh scripts) and built with any one of a number of different build systems (autotools, cmake, scons, homebrew shell scripts/makefiles, setuptools, etc). This is a hybrid type position where some software development experience is useful, but it is not a traditional developer job in any sense. This individual will work as a member of a multidisciplinary research and computing environment that integrates a software consortium, research computing support, research laboratories, and teaching initiatives.Basic QualificationsBachelor’s degree in computer science, computer engineering or technology-related discipline; or PhD in biological sciences; or equivalent combination of education plus relevant experience. 5-7 years of research computing or related experience.Additional QualificationsRequires working knowledge of at least one programming or scripting language; sh or csh shell scripting experience. Knowledge of how to drive a compiler and linker as well as an understanding of shared libraries. Autodidact with strong attention to detail and enthusiasm for hard problems. Familiarity with Python or other programming languages; familiarity with biomedical software applications and structure determination/analysis workflows; strong knowledge of Linux and OS X operating systems. The successful candidate will have excellent organizational skills and particular ability to work independently and prioritize work. Proven project and/or program management skills. Excellent interpersonal and communications skills. Ability to work with discretion.Additional InformationThis is a 12 month term appointment with the possibility of extension.
[ccp4bb] Calculating over all bend in a DNA
Hello CCP4bb, May I know how can we calculate or use any server which can calculate the overall bend in a DNA (crystal structure)?
