Re: [ccp4bb] DNA analysis with Curves+
Hello Edward,
I am not really certain for my explanation, but your error message about
the namelist could be provoked by a problem in your input files. In fact
you have to oriented each strand and define limits of the two strands.
If you do a mistake with the orientation you can have this type of
message. You can try different combination with this part of your
command line :
2 1 -1 0 0
1: 12
24:13
Maybe the key could be in this part of your command line atless for the
input error message.
To my mind you have to edit your input file because its format is not
adaptated for this programm. The format wich is too recent or with to
much informations are not well suported.
I hope i help you.
Sincerly . Nicolas
Le 03/02/11 21:05, Eddie Pryor a écrit :
Hi, All,
I am trying to analyze DNA from a recent structure with the program
Curves+ (R. Lavery et al, Nuc. Acids. Res (2009) 37:17 5917;
http://gbio-pbil.ibcp.fr/Curves_plus/Curves+.html). I have downloaded
the files, and untarred them to a directory curves on my machine.
Running the Make command on these files yielded no errors, and I have
the executable file Cur+ in this directory. I am trying to run this
program, first using the example data that is provided (the
Drew-Dickerson Dodecamer), but am having some difficulties. The
resource for Curves gives the following command to run the program:
/Users/RL/Code/Cur+ !
inp file=str/1bna, lis=r+bdna,
lib=/Users/RL/Code/standard,
end
2 1 -1 0 0
1: 12
24:13
!
On my machine, the directory structure is slightly different:
- the executable Cur+ is in a folder named curves
- the files standard_b.lib and standard_s.lib are also in this folder
- the pdb file 1bna.pdb is in the subfolder data
I have tried to run the program by doing the following:
[x@zeus ~/curves]$ Cur+ !
? inp file=data/1bna, lis=r+bdna,
? lib=standard, end
? 2 1 -1 0 0
? 1:12
? 24:13
? !
The question mark prompts appear upon hitting enter after each line.
The only error message I get when I try to run this is:
Error in namelist input for
I have even tried the following (entering all if the input files on
the same line):
[x@zeus ~/curves]$ Cur+ ! inp file=data/1bna, lis=r+bdna,
lib=standard, end
? 2 1 -1 0 0
? 1:12
? 24:13
? !
Which gives the following errors:
inp: Command not found
end: Not in while/foreach
At line 28 of file nml.f
Fortran runtime error: End of file
I am hoping that some of you have had success with running this
program and can offer any advice. I would really appreciate it!
Thanks!
Edward Pryor
Ph.D. Candidate
Tom Hollis Lab
Department of Biochemistry
Center for Structural Biology
Wake Forest University School of Medicine
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[ccp4bb] adding gaussian noise to an mtz data column
Before re-inventing the wheel... Is there anywhere some software (freely available software, I mean) that can add some Gaussian noise to data. The data is currently stored in a data column in an mtz (not phase data, but amplitudes, sigma values...) but can be exported to another format if required. Before writing a computer program to do this, does anyone know if this can be done without writing any code. If it can then obviously I won't write new code. Thanks, Fred.
[ccp4bb] Post-Doctoral position available at Karolinska Institutet, Sweden
Post-Doctoral position available at Karolinska Institutet, Sweden Project description: A post-doctoral position is available at the Department of Medical Biochemistry and Biophysics (MBB), Karolinska Institutet, Stockholm. The project deals primarily with over-expression, purification, crystallization and structure determination of human enzymes involved in the generation of lipid mediators of inflammation. The successful candidate will join a multi-disciplinary research team and the position represents an excellent opportunity for a postdoctoral scientist to develop his/her expertise as well as broaden his/her experience. Qualifications: We are seeking an experienced crystallographer with a Ph.D. in protein crystallography. A proven track record of multiple successful structure determinations is required. Previous experience, apart from crystallography, with protein expression, purification and enzyme kinetics, is desirable. The candidate should be self-motivated, have interpersonal communication skills and ability to interact effectively and work productively in a team. How to Apply: Interested candidates should send a CV and letters of reference by either email to agnes.rinaldo-matt...@ki.semailto:agnes.rinaldo-matt...@ki.se or by normal post to Agnes Rinaldo-Matthis, MBB, Karolinska Institutet, Scheeles väg 2, S-171 77 Stockholm, Sweden.
Re: [ccp4bb] adding gaussian noise to an mtz data column
If you fancy using R (and its endless ways of generating random deviates), then you could use part of the crystallographic package we are developing here (cRy). Then you would carry out the following in R: source(cRy/all_load.R) mtz - readMTZ(test.mtz) # Load data from mtz file newF - mtz$reflections$Fnew+rnorm(mean=0,sd=1,n=length(mtz$reflections$H)) # Add gaussian deviates with mean 0 and standard dev 1 mtz$reflections$Fnew - newF # Replace new column writeMTZ(mtz,new_test.mtz) # Write modified file with a different name If you are interested I can provide you with my R code for doing this. J Dr James Foadi PhD Membrane Protein Laboratory Diamond Light Source Ltd. Diamond House Harwell Science and Innovation Campus Didcot Oxfordshire OX11 0DE United Kingdom office email: james.fo...@diamond.ac.uk alternative email: j.fo...@imperial.ac.uk - Original Message From: Vellieux Frederic frederic.velli...@ibs.fr To: CCP4BB@JISCMAIL.AC.UK Sent: Fri, 4 February, 2011 12:40:35 Subject: [ccp4bb] adding gaussian noise to an mtz data column Before re-inventing the wheel... Is there anywhere some software (freely available software, I mean) that can add some Gaussian noise to data. The data is currently stored in a data column in an mtz (not phase data, but amplitudes, sigma values...) but can be exported to another format if required. Before writing a computer program to do this, does anyone know if this can be done without writing any code. If it can then obviously I won't write new code. Thanks, Fred.
Re: [ccp4bb] adding gaussian noise to an mtz data column
Hi Fred Doesn't sftools do this - from 'man sftools': CALC F COL Fsimulated = COL Fcalc ran_g 10 * + Create a column with label Fsimulated which contains the value of column Fcalc plus 10 times a random number from a Gaussian distribution with average = 0 and variance = 1 Cheers -- Ian On Fri, Feb 4, 2011 at 12:40 PM, Vellieux Frederic frederic.velli...@ibs.fr wrote: Before re-inventing the wheel... Is there anywhere some software (freely available software, I mean) that can add some Gaussian noise to data. The data is currently stored in a data column in an mtz (not phase data, but amplitudes, sigma values...) but can be exported to another format if required. Before writing a computer program to do this, does anyone know if this can be done without writing any code. If it can then obviously I won't write new code. Thanks, Fred.
Re: [ccp4bb] adding gaussian noise to an mtz data column
Thanks Ian, I think this is good enough for what I have in mind. So I did not have to reinvent the wheel after all... Fred. Ian Tickle wrote: Hi Fred Doesn't sftools do this - from 'man sftools': CALC F COL Fsimulated = COL Fcalc ran_g 10 * + Create a column with label Fsimulated which contains the value of column Fcalc plus 10 times a random number from a Gaussian distribution with average = 0 and variance = 1 Cheers -- Ian On Fri, Feb 4, 2011 at 12:40 PM, Vellieux Frederic frederic.velli...@ibs.fr wrote: Before re-inventing the wheel... Is there anywhere some software (freely available software, I mean) that can add some Gaussian noise to data. The data is currently stored in a data column in an mtz (not phase data, but amplitudes, sigma values...) but can be exported to another format if required. Before writing a computer program to do this, does anyone know if this can be done without writing any code. If it can then obviously I won't write new code. Thanks, Fred.
Re: [ccp4bb] adding gaussian noise to an mtz data column
On 04/02/11 12:40, Vellieux Frederic wrote: Before re-inventing the wheel... Is there anywhere some software (freely available software, I mean) that can add some Gaussian noise to data. The data is currently stored in a data column in an mtz (not phase data, but amplitudes, sigma values...) but can be exported to another format if required. Before writing a computer program to do this, does anyone know if this can be done without writing any code. If it can then obviously I won't write new code. There's also the RAN_G function in SFTOOLS's CALC command (works on your MTZ directly, of course).
[ccp4bb] Fwd: Thesis at the Institut de BIologie Structurale in Grenoble, France
Please post the following message: --- As members of the IRTELIS graduate program of the French CEA we have obtained a three-year thesis fellowship. The candidate must have average grades better than or equal to 14/20 (in the French M-2 system) or the equivalent. Deadline: end of February Contact: Juan C. Fontecilla-Camps Structural Biology of Metalloproteins IBS-Grenoble e-mail: juan.fonteci...@ibs.fr To get information about the thesis subject please go to: http://www-instn.cea.fr/spip.php?page=Publication_SujetidSujet=6215lang=frlangue=frid_rubrique=70 http://www-instn.cea.fr/spip.php?page=Publication_SujetidSujet=6215lang=frlangue=frid_rubrique=70 To apply for the fellowship please go to: http://irtelis.cea.fr/phd_fr/ Thank you very much. Juan
Re: [ccp4bb] DNA analysis with Curves+
Hi Edward,
Have you tried just editing the short command script on a text editor so you
keep the formatting. You could also try the full path for the executable and
the lib files while you are at it.
I have a problem of a different nature. I get get the example data file to work
but no other file seems to work. I have tried editing other pdb files to make
them look more like the example pdb but none seems to work. I get an error
message in the .lis file which reads;
Base atom C1* missing in strand 2 level 1 (Necessary for analysis). I have
gotten the same error with a few files from the NDB and PDB as well as with
mine. Any suggestions on how to solve this problem will be highly appreciated.
Raymond.
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] On Behalf Of KAMESH
Narasimhan [kamesh...@gis.a-star.edu.sg]
Sent: Friday, February 04, 2011 4:44 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] DNA analysis with Curves+
Try and copy this on your command line and see if it works. The trick is to
shift first 3 lines by one space.
[x@zeus ~/curves]$ Cur+ !
inp file=data/1bna, lis=r+bdna,
lib=standard, end
2 1 -1 0 0
1:12
24:13
!
Curves is very handy once you get a hang of how to submit the input.
Alternatively, I use “3DNA to generate the curves input” --- which is less
cryptic.
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Eddie
Pryor
Sent: Friday, February 04, 2011 4:05 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] DNA analysis with Curves+
Hi, All,
I am trying to analyze DNA from a recent structure with the program Curves+ (R.
Lavery et al, Nuc. Acids. Res (2009) 37:17 5917;
http://gbio-pbil.ibcp.fr/Curves_plus/Curves+.html). I have downloaded the
files, and untarred them to a directory curves on my machine. Running the
Make command on these files yielded no errors, and I have the executable file
Cur+ in this directory. I am trying to run this program, first using the
example data that is provided (the Drew-Dickerson Dodecamer), but am having
some difficulties. The resource for Curves gives the following command to run
the program:
/Users/RL/Code/Cur+ !
inp file=str/1bna, lis=r+bdna,
lib=/Users/RL/Code/standard,
end
2 1 -1 0 0
1: 12
24:13
!
On my machine, the directory structure is slightly different:
- the executable Cur+ is in a folder named curves
- the files standard_b.lib and standard_s.lib are also in this folder
- the pdb file 1bna.pdb is in the subfolder data
I have tried to run the program by doing the following:
[x@zeus ~/curves]$ Cur+ !
? inp file=data/1bna, lis=r+bdna,
? lib=standard, end
? 2 1 -1 0 0
? 1:12
? 24:13
? !
The question mark prompts appear upon hitting enter after each line.
The only error message I get when I try to run this is:
Error in namelist input for
I have even tried the following (entering all if the input files on the same
line):
[x@zeus ~/curves]$ Cur+ ! inp file=data/1bna, lis=r+bdna, lib=standard,
end
? 2 1 -1 0 0
? 1:12
? 24:13
? !
Which gives the following errors:
inp: Command not found
end: Not in while/foreach
At line 28 of file nml.f
Fortran runtime error: End of file
I am hoping that some of you have had success with running this program and can
offer any advice. I would really appreciate it!
Thanks!
Edward Pryor
Ph.D. Candidate
Tom Hollis Lab
Department of Biochemistry
Center for Structural Biology
Wake Forest University School of Medicine
[ccp4bb] UNESCO/IUPAC course 2011/12
Call for new participants of a graduate student course at the Institute of Macromolecular Chemistry in Prague, Czech Republic. Within this annual training program for graduate students UNESCO/IUPAC Postgraduate Course in Polymer Science a project focused on biochemistry-structural biology of chitinolytic enzymes is open: Unraveling the details of chitinolytic complex from human symbiotic bacterium influencing immunity. Interested potential candidates, please, follow this link to find out more: http://www.imc.cas.cz/unesco/projects.html#dohnalek General information on the course and participants status, etc. can be found at: http://www.imc.cas.cz/unesco/index.html as well as instructions regarding conditions and applications. Jan Dohnalek IMC Prague -- Jan Dohnalek, Ph.D Institute of Macromolecular Chemistry Academy of Sciences of the Czech Republic Heyrovskeho nam. 2 16206 Praha 6 Czech Republic Tel: +420 296 809 390 Fax: +420 296 809 410
[ccp4bb] ICSG 2011 Abstract Deadline Feb 28, 2011: International Conference on Structural Genomics
Dear Colleagues, We hope that you are planning to attend the International Conference on Structural Genomics 2011, which will be held in Toronto, Canada on May 10-14, 2011. The meeting is designed to serve as a forum to discuss the most recent developments in structural genomics, structural/chemical biology, and their impact on research in biology, medicine and disease. There are many speaking slots still open that will be chosen from submitted poster abstracts. We invite you to submit your abstract by February 28, 2011. Please visit http://www.icsg2011.org for ICSG 2011 meeting and workshop registration details and to submit your abstract. In addition to the main ICSG meeting, there will be a whole day of free concurrent satellite workshops (May 10, 2011), including: Small Molecule Screening Workshop- This hands-on workshop will allow participants to screen a protein of their choice for binding of selected compounds, using thermal shift assays. Eukaryotic Gene Expression Systems Workshop - This workshop will provide participants with a detailed understanding of the state-of-the-art for production of eukaryotic proteins destined for biochemical, biophysical, and structural analyses. iSee: Interactive 3D Documents for the Dissemination of Structural Biology This hands-on workshop will familiarize participants with the iSEE 3D graphical software which allows interactive viewing of 3 dimensional molecular structures and is currently used by journals such as Nature Structural Molecular Biology and PLoS Biology and PLoS ONE. Workshop on NMR Methods for Structural Biology- This workshop will survey technologies for structure/function investigations of proteins, developed in (or in collaboration with) structural genomics projects, that are ready for widespread use by the wider biological community. Phenix Crystallography Software Workshop This workshop will introduce the PHENIX software for macromolecular structure determination and the core algorithms that it uses. It will provide hands-on tutorials for crystallographers of all levels. We hope to see you there! Best regards, Cheryl Arrowsmith ICSG 2011 Organizer Ted Baker Stephen Burley Dino Moras Joel Sussman Shigeyuki Yokoyama Tom Terwilliger ISGO Executive Committee
[ccp4bb] REMINDER - 9th Carbohydrate Bioengineering Meeting, Lisboa, Portugal, 15-18 May 2011
Dear one, two, three and all, Just a quick reminder: Only one month left to send your poster abstracts and benefit from the early registration fee for the 9th Carbohydrate Bioengineering Meeting to be held in the fabulous city of Lisboa. For more details check out: http://www.cbm9.org/ScientificTopics.htm As well as a full scientific fest on offer, come and sample the beautiful and enchantingly decadent city of Lisboa. I came here for just six months initially, and I am still here after over six years! Cheers Shabir Najmudin CISSA-FMV-UTL. Lisboa
[ccp4bb] Postdoctoral Position in 2D and 3D crystallography
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[ccp4bb] how to use mac to solve structures
Hi all, I just start to install crystallography software on my new mac. My os X version is 10.6. Can some one show me how to install phenix, cns , ccp4 and so on? Thank you. Lisa
Re: [ccp4bb] how to use mac to solve structures
Just google for crystallography on os x and you will find Bill Scott's excellent guide through the galaxy. Jürgen .. Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Phone: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-3655 http://web.mac.com/bosch_lab/ On Feb 5, 2011, at 0:33, LISA science...@gmail.com wrote: Hi all, I just start to install crystallography software on my new mac. My os X version is 10.6. Can some one show me how to install phenix, cns , ccp4 and so on? Thank you. Lisa
Re: [ccp4bb] how to use mac to solve structures
Thank you for responds. Dr. Scott asked to install xcode before install fink. Does my new mac pro has xcode already? How to check it? I find xcode 3.25 is 3G on apple site. It is very big. On Sat, Feb 5, 2011 at 1:37 PM, Jürgen Bosch jubo...@jhsph.edu wrote: Just google for crystallography on os x and you will find Bill Scott's excellent guide through the galaxy. Jürgen .. Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Phone: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-3655 http://web.mac.com/bosch_lab/ On Feb 5, 2011, at 0:33, LISA science...@gmail.com wrote: Hi all, I just start to install crystallography software on my new mac. My os X version is 10.6. Can some one show me how to install phenix, cns , ccp4 and so on? Thank you. Lisa
Re: [ccp4bb] how to use mac to solve structures
Hi Lisa, Can some one show me how to install phenix (...)? how to install phenix: http://www.phenix-online.org/ I afraid you will need to have a look at this page before you know how to get and install it (hint#1: click on Full Documentation link; hint#2: the link is located at the upper-right part of the web page). Good luck! Pavel.
