Re: [ccp4bb] [phenixbb] Calculate average B-factor?
Dear Jose,
the question came up again because I did not receive an answer to my
question. The thread discussed benefits and malefits of PDB vs. mmCIF,
which was not my question.
This time, Nat Echolls gave a very reasonable answer (at least for
phenix) on the phenixbb, i.e., that there are no plans to abandon the
PDB format (as working format), but very likely a smooth transition will
take place - I guess this will be more slowly than the enforcement of
the PDB to upload PDBx/mmCIF files for archiving. I agree that for
archiving mmCIF is a reasonable format, but I guess less than 1% of all
structures in the PDB hit the limits of the PDB format.
I greatly appreciate Nat's answer and I would appreciate an answer from
the responsibles for the other refinement programs.
Best,
Tim
On 10/05/2014 08:05 PM, Jose Manuel Duarte wrote:
Thanks Frances for the explanation. Indeed mmCIF format is a lot more
complicated and grep can be a dangerous tool to use with them. But for
most cases it can do the job and thus it maintains some sort of
backwards compatibility. I can't agree more that using specialised tools
(for either PDB files or mmCIF files) that deal with the formats
properly is the best solution (see for instance
http://mmcif.wwpdb.org/docs/software-resources.html for some of the
mmCIF readers).
In any case I find it most surprising that this topic came yet again to
this BB, when it was thoroughly discussed last year in this thread:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1308L=ccp4bbD=0P=26939
I'm not sure why this kind of urban legends on the evilness of the mmCIF
format keep coming back to the list...
As explained there and elsewhere endless times, the PDB format is
inadequate to represent the complexity of macromolecules and has been
needing a replacement for a long time. The decision to move on to mmCIF
has been made and in my opinion the sooner we move forward the better.
Cheers
Jose
On 05.10.2014 15:52, Frances C. Bernstein wrote:
mmCIF is a very general format with tag-value pairs, and loops
so that tags do not need to be repeated endlessly. It was
designed so that there is the flexibility of defining new terms
easily and presenting the data in any order and with any kind
of spacing.
I understand that there are 10+ files in cyberspace prepared
by the PDB and that they all have the 'same' format.
It is tempting to write software that treats these files as fixed
format and hope that all software packages that generate coordinate
files will use the same fixed format. But that loses the generality
and flexibility of mmCIF, and software written that way will fail
when some field requires more characters or a new field is added.
There are software tools to allow one to read and extract data from
any mmCIF file; using these is more complicated than using grep but
using these assures that one's software will not fail when it encounters
a date file that is not exactly what the PDB is currently producing.
Note that mmCIf was defined when the limitations of the fixed-format
PDB format became apparent with large structures. Let's not repeat
the mistakes of the past.
Frances
=
Bernstein + Sons
* * Information Systems Consultants
5 Brewster Lane, Bellport, NY 11713-2803
* * ***
*Frances C. Bernstein
* *** f...@bernstein-plus-sons.com
*** *
* *** 1-631-286-1339FAX: 1-631-286-1999
=
On Sun, 5 Oct 2014, Tim Gruene wrote:
Hi Jose,
I see. In the example on page
http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v40.dic/Categories/atom_site.html,
it is in field 12, though, and I would have thought that mmCIF allows
line breaks.
But as long as all developers writing PDBx/mmCIF with their programs
follow the PDB constraints (``styling plans'' in their FAQ), everything
is fine.
Cheers,
Tim
On 10/05/2014 01:13 PM, Jose Manuel Duarte wrote:
Well, if you simply replace that beauty by this one:
grep ^ATOM filename.cif | awk '{print $15}' | awk '{s+=$1;} END
{print
s/NR;}'
You will achieve exactly the same result (the b-factors are in the 15th
field of the _atom_site section in deposited mmCIF files). I'm not an
expert in awk, but I'm sure that can be made even shorter ;)
It is important to keep in mind that mmCIF files are designed to be
usable with grep-like tools, so I don't see any problems in moving
forward to that format. Whilst I see a lot of problems in staying with
the classic PDB format.
Cheers
Jose
On 05.10.2014 11:18, Tim Gruene wrote:
Hi all,
reading this beauty I would like to ask a question to the respective
developers:
Will the PDB format remain the working format for the users and only
upon deposition will it be converted to PDBml for archiving
purposes, or
are the
[ccp4bb] Faculty Position in Structural Biology at Purdue
Dear Colleagues, I wanted to draw your attention to the following position announcement (Below) advertised in Science on Friday, October 3rd. http://jobs.sciencecareers.org/job/343203/position-in-structural-biology/ PURDUE UNIVERSITY Faculty Position in Structural Biology The Purdue University Department of Biological Sciences in conjunction with the Center for Cancer Research and the Walther Cancer Foundation are seeking an outstanding scientist with a proven track record of excellence in the science of cancer structural biology to join our faculty as a Walther Professor in Structural Biology. A Walther Professor is expected to conduct research in the area of structural biology to address fundamental questions in cancer biology; teach undergraduate and/or graduate students, and participate in ongoing programs in the Department of Biological Sciences and the Center for Cancer Research. Preference will be given to candidates utilizing modern cryo-EM approaches combined with other structural approaches such as X-ray crystallography to determine structures of cancer-relevant macromolecules and macromolecular complexes, and/or X-ray crystallography of cancer-relevant drug targets as part of a structure-based drug design program. Candidates should hold the rank of associate or full professor and have a PhD in Biological Sciences or related field, have an excellent track record of publications and extramural funding and a strong commitment to excellence in teaching. The Department of Biological Sciences offers a dynamic research environment in structural biology research and education. The Markey Center for Structural Biology at Purdue is recognized worldwide for its leadership in structural biology of viruses, membrane proteins, receptors, signaling proteins, enzymes and nucleic acids in addition to methods development in X-ray crystallography, cryo-electron microscopy and NMR. The Purdue Center for Cancer Research is among an elite group of NCI-designated Cancer Centers nationwide and one of only seven centers focused exclusively on basic and translational research. The Walther Professor will have laboratory space in the newly constructed Hockmeyer Hall of Structural Biology, which houses a Titan Krios cryo-TEM, X-ray generators and detectors, and crystallization and imaging robots. Other state-of-the-art shared resources across Purdue such as a Bruker Avance-III 800 MHz NMR and other advanced biophysical instrumentation are available through the Bindley Biosciences and Birck Nanotechnology Centers. Applications must be submitted electronically to http://hiring.science.purdue.eduhttp://hiring.science.purdue.edu/ as a PDF file that includes; a detailed curriculum vitae, names and addresses of three referees, a 2 - 3 page summary of research interests, and a one-page statement of teaching experience and interests. Inquiries should be directed tosea...@bio.purdue.edumailto:sea...@bio.purdue.edu or Structural Biology Search Committee, Department of Biological Sciences, Purdue University, 915 W. State St., West Lafayette, IN 47907-2054. Confidential review of applications will begin October 1, 2014 and will continue until the position is filled. Further information about the Department is available at http://www.bio.purdue.edu/. A background check will be required for employment in this position. Purdue University is an ADVANCE institution and a dual career friendly employer. Purdue University in EEO/AA Employer. All individuals, including minorities, women, individuals with disabilities, and protected veterans are encouraged to apply. Andrew D. Mesecar Walther Professor of Cancer Structural Biology Deputy Director, Purdue University Center for Cancer Research Departments of Biological Sciences and Chemistry Hockmeyer Hall of Structural Biology Room 311 240 S. Martin Jischke Drive West Lafayette, IN 47907-1971 Ear Mail: 765-494-1924 E-Mail: amese...@purdue.edu
[ccp4bb] REMINDER: apply now for the first 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
Re: [ccp4bb] [phenixbb] Calculate average B-factor?
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 On 10/6/2014 4:20 AM, Tim Gruene wrote: Dear Jose, the question came up again because I did not receive an answer to my question. The thread discussed benefits and malefits of PDB vs. mmCIF, which was not my question. This time, Nat Echolls gave a very reasonable answer (at least for phenix) on the phenixbb, i.e., that there are no plans to abandon the PDB format (as working format), but very likely a smooth transition will take place - I guess this will be more slowly than the enforcement of the PDB to upload PDBx/mmCIF files for archiving. I agree that for archiving mmCIF is a reasonable format, but I guess less than 1% of all structures in the PDB hit the limits of the PDB format. That's odd. I've found that just about every structure I've worked on in the last couple decades has not been able to be expressed in the PDB format without loss of information. A primary example? Try expressing a pair of side chains that have alternative conformation in a PDB file. Okay, one conformation is A and the other is B. That allows me a total of twelve pairs of side chains before I run out of upper case letters. Most people hack their model by reusing A and B but of course that is ambiguous about where you mean the A's are the same and where they are different. A realistic model of the surface of a protein cannot be expressed in the PDB format. How many models are refined with TLS B factors? There still is no way to describe TLS in the PDB format. Don't tell me it's stuffed in REMARK! What kind of a file format is that? I believe that 100% of the models that we should be building can't be described in the PDB file format, and that has been true for a great many years. Dale Tronrud I greatly appreciate Nat's answer and I would appreciate an answer from the responsibles for the other refinement programs. Best, Tim On 10/05/2014 08:05 PM, Jose Manuel Duarte wrote: Thanks Frances for the explanation. Indeed mmCIF format is a lot more complicated and grep can be a dangerous tool to use with them. But for most cases it can do the job and thus it maintains some sort of backwards compatibility. I can't agree more that using specialised tools (for either PDB files or mmCIF files) that deal with the formats properly is the best solution (see for instance http://mmcif.wwpdb.org/docs/software-resources.html for some of the mmCIF readers). In any case I find it most surprising that this topic came yet again to this BB, when it was thoroughly discussed last year in this thread: https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1308L=ccp4bbD=0P=26939 I'm not sure why this kind of urban legends on the evilness of the mmCIF format keep coming back to the list... As explained there and elsewhere endless times, the PDB format is inadequate to represent the complexity of macromolecules and has been needing a replacement for a long time. The decision to move on to mmCIF has been made and in my opinion the sooner we move forward the better. Cheers Jose On 05.10.2014 15:52, Frances C. Bernstein wrote: mmCIF is a very general format with tag-value pairs, and loops so that tags do not need to be repeated endlessly. It was designed so that there is the flexibility of defining new terms easily and presenting the data in any order and with any kind of spacing. I understand that there are 10+ files in cyberspace prepared by the PDB and that they all have the 'same' format. It is tempting to write software that treats these files as fixed format and hope that all software packages that generate coordinate files will use the same fixed format. But that loses the generality and flexibility of mmCIF, and software written that way will fail when some field requires more characters or a new field is added. There are software tools to allow one to read and extract data from any mmCIF file; using these is more complicated than using grep but using these assures that one's software will not fail when it encounters a date file that is not exactly what the PDB is currently producing. Note that mmCIf was defined when the limitations of the fixed-format PDB format became apparent with large structures. Let's not repeat the mistakes of the past. Frances = Bernstein + Sons * * Information Systems Consultants 5 Brewster Lane, Bellport, NY 11713-2803 * * *** *Frances C. Bernstein * *** f...@bernstein-plus-sons.com *** * * *** 1-631-286-1339 FAX: 1-631-286-1999 = On Sun, 5 Oct 2014, Tim Gruene wrote: Hi Jose, I see. In the example on page http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v40.dic/Categories/atom_site.html, it is in field 12, though, and I would have thought that mmCIF allows line breaks. But as
[ccp4bb] Chicago Symposium in Honor of the International Year of Crystallography
Dear Colleagues, On Friday October 10th, the University of Illinois at Chicago is hosting a symposium and poster session to celebrate the 100th year of crystallography. (Location: Herman Auditorium, MBRB 900 S. Ashland Ave., Chicago) Please send a copy of the abstract for your poster to cjeff...@uic.edu by 5pm Tuesday, Oct. 7. Please indicate in the email if you are an undergraduate, graduate student, or postdoc, to be entered in the poster contest. * Please note the posters are not limited to projects involving X-ray crystallography. For example, projects involving NMR, Molecular Dynamics, Bioinformatics, and related methods are also welcome. The schedule of the symposium will be as follows, with lunch provided for those who register: 9:30am Registration 10:00-10:15 Welcome and IYCR Overview (C. Jeffery, University of Illinois at Chicago) 10:15-11:00 Prof. Phoebe Rice (University of Chicago) 11:00-11:45 Prof. Andrejz Joachimiak (Argonne National Labs) 12noon-1:00 Lunch 1:15 - 2:00Prof. Bernie Santarsiero (University of Illinois at Chicago) 2:00 - 2:45 Prof. Heather Pinkett (Northwestern University) 2:45 - 4:30pm Poster session For more information and to register, please visit the webpage: http://www.uic.edu/labs/smxrd/IYCR/Welcome.html ***To help us plan for lunch and the reception, please indicate on the Doodle poll if you will be able to attend (check box) or not (click on Cannot make it button). Here is the link: http://doodle.com/qzuswpz2qpzy7dgm We hope to see you all there! -Constance Jeffery Associate Professor Dept. Biological Sciences UIC
Re: [ccp4bb] Molecular Replacement model preparation
That document is fairly old and is in dire need of revision to reflect the modern arsenal of programs. Nevertheless: Putting the hinge axis along Z was a trick told to me by Steven Sheriff back in the days when we worked on Fab structures - which after all are classical examples of hinged molecules. One would search with separate domain fragments - split either side of the hinge - and the Z-orientation trick makes it easier to spot pairs of peaks from each search model that are related to each other. In the Fab world we searched with Fv models (VH:VL heterodimer) and CH1:CL constant region heterodimeric models. Peaks related solely by hinge motion would have similar alpha and beta angles and potentially different gamma (Crowther convention Eulerian angles). Historical note: this was back in the days when it was possible to remember the names of all the Fab fragments that were in PDB and their respective IDs. This ploy was more important in the days before Phaser or Molrep, which will now gleefully try a long list of rotation function peaks for you quite quickly, so manually parsing the list of rotation function peaks is rather unnecessary. And perhaps counter-productive. Split your molecule apart at the hinge, giving fragment1 and fragment2. Attempt to find both fragments independently. Choose the one that gives the best results: TFZ score or LLG score or discrimination between possible space groupr or whatever you like. Then, attempt to find the *other* fragment in the context of that first solution. Phil Jeffrey Princeton On 10/5/14 3:34 AM, Luzuokun wrote: Dear all, I’m doing molecular replacement using Phaser. My protein is predicted to have two domain with a “hinge” linking them. The model sequence identity is 0.27. But the MR result is poor. I’ve tried other programme (Molrep, MrBump, Balbes,,,_.) But no improvement was observed. I think that this is due to the “open” or “closed” conformation around the hinge. I was told that I could place the Z axis along the hinge (http://xray0.princeton.edu/~phil/Facility/Guides/MolecularReplacement.html), could anyone tell me more details about how to do next? Thanks! Lu Zuokun
[ccp4bb] Traveling Salesman with Simulated Annealing
Hi Everyone, I thought this was a good basic introduction (help those that click it 'on' or 'off' cause they've been told to do it) / visualization of simulated annealing using a map as the basis. http://toddwschneider.com/posts/traveling-salesman-with-simulated-annealing-r-and-shiny/ Take Care, Sean Seaver, PhD P212121 http://store.p212121.com/
Re: [ccp4bb] Molecular Replacement model preparation
Hi Phil, Thank you for the input. I would like to get CCP4ers input. I deal with multiple domain cytokine receptors in a manner very similar to antibody molecules. Have people have more correct solutions searching for 1 domain sequentially and then other domains OR searching for multiple domains all at once? I am curious to hear peoples’ experiences on this topic? Cheers, Scott Scott T. R. Walsh, PhD Assistant Professor University of Maryland IBBR/CBMG 3127E CARB-2 9600 Gudelsky Drive Rockville, MD 20850 USA phone: (240) 314-6478 fax: (240) 314-6225 email: swals...@umd.edu On Oct 6, 2014, at 2:11 PM, Phil Jeffrey pjeff...@princeton.edu wrote: That document is fairly old and is in dire need of revision to reflect the modern arsenal of programs. Nevertheless: Putting the hinge axis along Z was a trick told to me by Steven Sheriff back in the days when we worked on Fab structures - which after all are classical examples of hinged molecules. One would search with separate domain fragments - split either side of the hinge - and the Z-orientation trick makes it easier to spot pairs of peaks from each search model that are related to each other. In the Fab world we searched with Fv models (VH:VL heterodimer) and CH1:CL constant region heterodimeric models. Peaks related solely by hinge motion would have similar alpha and beta angles and potentially different gamma (Crowther convention Eulerian angles). Historical note: this was back in the days when it was possible to remember the names of all the Fab fragments that were in PDB and their respective IDs. This ploy was more important in the days before Phaser or Molrep, which will now gleefully try a long list of rotation function peaks for you quite quickly, so manually parsing the list of rotation function peaks is rather unnecessary. And perhaps counter-productive. Split your molecule apart at the hinge, giving fragment1 and fragment2. Attempt to find both fragments independently. Choose the one that gives the best results: TFZ score or LLG score or discrimination between possible space groupr or whatever you like. Then, attempt to find the *other* fragment in the context of that first solution. Phil Jeffrey Princeton On 10/5/14 3:34 AM, Luzuokun wrote: Dear all, I’m doing molecular replacement using Phaser. My protein is predicted to have two domain with a “hinge” linking them. The model sequence identity is 0.27. But the MR result is poor. I’ve tried other programme (Molrep, MrBump, Balbes,,,_.) But no improvement was observed. I think that this is due to the “open” or “closed” conformation around the hinge. I was told that I could place the Z axis along the hinge (http://xray0.princeton.edu/~phil/Facility/Guides/MolecularReplacement.html), could anyone tell me more details about how to do next? Thanks! Lu Zuokun
[ccp4bb] How to rename nucleic acid residues in PDB files
Hello All, I would like to know how to change the nomenclature of bases (for example from Ad to DA for adenosine triphosphate) in PDB file.
Re: [ccp4bb] How to rename nucleic acid residues in PDB files
On Oct 6, 2014, at 12:04 PM, Sasha Pausch sashapau...@gmail.com wrote: Hello All, I would like to know how to change the nomenclature of bases (for example from Ad to DA for adenosine triphosphate) in PDB file. perl -pi -e ‘s|Ad|DA|g’ your.pdb
