[ccp4bb] Is there a gold standard binding-site hydrophobicity score?
Dear list, Is there a way that for a binding site (defined as the protein surface atoms N Angstroms around a ligand molecule) we can assign a (preferably normalized) hydrophobicity score to the binding site? - I would prefer something that I can run offline rather than a webserver (but a webserver would be better than nothing). - it should be a published, sound method The use-case is that I would like to rank some binding sites in terms of hydrophobicity. Like in binding site A is more hydrophobic than binding site B (with the required score backing the claim). Thanks a lot, Francois.
Re: [ccp4bb] Data mining interactions in the PDB
On 10/29/2013 03:23 AM, Katherine Sippel wrote: Hi all, I was wondering if anyone knew of a software or server to mine the PDB for a specific class of interactions? I've tried PDBeMotif without much luck and I thought I'd check to see if there was an alternative before I go re-inventing the wheel. Maybe this one (SuMo): http://sumo-pbil.ibcp.fr/cgi-bin/sumo-welcome paper: http://bioinformatics.oxfordjournals.org/content/21/20/3929.full Or this one (Drugsite): https://drugsite.msi.umn.edu. paper: http://pubs.acs.org/doi/abs/10.1021/ci4002537 Cheers, Katherine -- Nil illegitimo carborundum/- /Didactylos -- Best regards, Francois Berenger. https://www.linkedin.com/in/fberenger
Re: [ccp4bb] Advise on setting up/ maintaining a Ubuntu cluster
Be careful that running data intensive jobs over NFS is super slow (at least an order of magnitude compared to writing things on a local disk). Not only the computation is slow, but you may be slowing down all other users of the cluster too... F. On 07/30/2013 11:28 PM, Adam Ralph wrote: Dear Sergei, Second point is probably easier to do. An alternative to NFS is sshfs. The advantage is that it uses SSH which is installed by default and configured the same way. If you generate key pairs you can use ssh or sshfs without a password. Check this page below; http://www.howtoforge.com/mounting-remote-directories-with-sshfs-on-ubuntu-11.10 Typically LDAP is being used for centralised authentication but NIS is probably just as good. Page below is about the client setup. https://help.ubuntu.com/community/LDAPClientAuthentication Both of the above are more likely to survive upgrades. Adam
Re: [ccp4bb] CCP4 6.3.0 PBS/qsub configuration
You need to source the CCP4 config file.
At my site:
# for Bash
source /usr/local/src/ccp4/ccp4-6.3.0/setup-scripts/ccp4.setup-sh
I guess that would be the first command in the script
you send to your cluster via qsub.
Regards,
F.
On 07/02/2013 11:55 PM, AFL wrote:
Dear Group Members,
I'm attempting to configure CCP4 installation for the batch job
submission and have encountered numbers of problems.
The one that is currently haunting me is the error message:
can't read CCP4I_TCLTK: no such variable
while executing
exec $CCP4I_TCLTK/tclsh $0 -- ${1+$@}
(file /share/apps/software/ccp4/share/ccp4i/bin/ccp4ish line 9)
The variable in question is defined when the CCP4 is running in
interactive shell.
I have also added an 'echo $CCP4I_TCLTK' statement to the 'Command to
set up CCP4' which outputs (correct location for tclsh):
/share/apps/software/ccp4/bin
However, the same statement added to the 'Command to run CCP4i' outputs:
/share/apps/software/ccp4/bin -r /tmp/software/1_import.def
Our system is build on Rocks 6.1(Emerald Boa, CentOS 6.3).
The qsub is currently run with the following command:
qsub -V -q little -l nodes=1:ppn=1
I would highly appreciate suggestion on how to solve this
configuration problem.
Best regards, Andrzej Lyskowski
Re: [ccp4bb] AW: [ccp4bb] insertion code problem
I think pdbset from CCP4 can renumber a PDB and hence get rid of the uggly insertion codes. On 06/26/2013 03:33 PM, herman.schreu...@sanofi.com wrote: Dear Rain, Insertion codes are still a sore point for many CCP4 programs and one of the reasons I prefer Buster over Refmac. Refmac5 does not remove insertion codes so I suspect the problem was with autoMR. The easiest is to superimpose your search model with insertion codes onto the pdb file which came out of the autoMR procedure. You could use lsqkab, but I think you can also do it in Coot. Then you continue refinement with this superimposed model. However, when I refined some structure with insertion codes in Refmac last week, Refmac created LINKR gap records for the inserted residues, cutting all peptide links. With an editor I had to change the gap to TRANS and then it worked. Good luck! Herman *Von:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *Im Auftrag von *MAGGIE *Gesendet:* Mittwoch, 26. Juni 2013 04:07 *An:* CCP4BB@JISCMAIL.AC.UK *Betreff:* [ccp4bb] insertion code problem Dear group, I have a insertion code question. I used molecular replacement (CCP4, autoMR) to solve two structures: one is monomer, and another one is tetramer. The model I used is one chain of a dimer and the model has insertion code. After molecular replacement and refinement using refmac5 in CCP4, the new structures lost the insertion code, and the residues were numbered consecutively. Can anyone tell me how to keep the insertion code in the new structures? Thank you, Rain
Re: [ccp4bb] Gnuplot: how to plot with resolution values as labels on x-axis?
On 06/25/2013 12:36 AM, Tim Gruene wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hello Kay, the rotation can be achieved with 'set xtics rotate by 30' I did not know about xticlabels, suggested by Abhinav - very useful! My preferred gnuplot reference: http://security.riit.tsinghua.edu.cn/~bhyang/ref/gnuplot/index-e.html The original site seems down unfortunately (http://t16web.lanl.gov/Kawano/gnuplot/). Best, Tim On 06/24/2013 04:54 PM, Kay Diederichs wrote: Dear Gnuplot users, you all know the crystallographic tables which have a column of resolution values, and columns of crystallographic indicators (R, I/sigma, ... whatever). Assuming that I want to plot the indicator in column 2 as a function of resolution, I can simply say plot 'table.dat' us 2 but the problem is now that I would like to have the resolution values as labels, so instead of 0 1 2 3 4 5 ... I would like to have 30.6 5.72 3.90 3.17 2.64 ... or so. Furthermore these labels might be fairly wide, so I would like to rotate them, by (say) 30° or even 90°. In the past, I seem to remember that I have manually positioned the labels, as individual text strings. This can be done for a single plot ... but then again, we live in the 3rd millenium and there must be a better way. Can Gnuplot take the labels from the file and put them into the right place? Could anyone please share the Gnuplot magic for doing so? thanks, Kay - -- - -- 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/ iD8DBQFRyGeKUxlJ7aRr7hoRAvDzAKDsFX8Hj8FiQlulx8LEW9i9IDR//QCg7Fl5 JMcIJYnPpl/3dQNyGQfKhX0= =vgxc -END PGP SIGNATURE-
Re: [ccp4bb] Active site volume calculator
On 06/06/2013 08:47 AM, Bosch, Juergen wrote: Hi Yuri, http://fpocket.sourceforge.net http://sts-fw.bioengr.uic.edu/castp/calculation.php I think GHECOM also compute this. GHECOM uses morpho maths operators in 3D. Quite beautiful. http://strcomp.protein.osaka-u.ac.jp/ghecom/ Just to name 2 Jürgen On Jun 5, 2013, at 7:12 PM, Yuri Pompeu wrote: Dear BB, I am sorry for posting off-topic but it is hard not to ask when you know you can get a good answer ;-) I need to calculate the volume of several active sites. Nothing fancy, just a number for comparison sake. I understand there are probably 10 different ways/programs and I would appreciate some feedback. cheers .. Jürgen Bosch Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Office: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-2926 http://lupo.jhsph.edu
Re: [ccp4bb] Windows 8?
On 06/07/2013 06:10 AM, Ho Leung Ng wrote: Hello, Are there any issues with crystallography related software on Windows 8, especially with PyMol or Coot? The operating system you are mentioning is unobservable, non causal and has a response time far greater than one second. To me, as an engineer, these are all very serious problems. Here we run CentOS on the xtal-related workstations and graphical software like pymol (even in 3D stereo) work fine. Best regards, Francois. Thank you, Ho Ho Leung Ng University of Hawaii at Manoa Assistant Professor, Department of Chemistry h...@hawaii.edu
Re: [ccp4bb] Screening a protein surface for interaction sites
On 05/29/2013 04:30 PM, Gang Dong wrote: Try FTsite: http://ftsite.bu.edu/. I have seen people using metapocket: http://projects.biotec.tu-dresden.de/metapocket/ Gang On Wed, May 29, 2013 09:17, Karsten Niefind wrote: Dear colleagues, please allow me to ask crystallography experts for advice in a bioinformatics issue: Which methods (programs, servers) would you use and recommend to search computationally on the surface of a protein/protein complex ( 1100 aa) for concave and convex interaction sites with potential ligands of any kind (preferentially other proteins and peptides, but also nucleic acids or small metabolites and with emphasis on potential, i.e. if no concrete ligand is known)? Thanks for any help from Karsten Niefind --- Karsten Niefind University of Cologne Department of Chemistry Institute of Biochemistry Otto-Fischer-Str. 12-14 D-50674 Cologne Tel.: +49 221 470 6444 Fax: +49 221 470 3244
Re: [ccp4bb] PISA interface question
On 05/13/2013 06:34 PM, Evgeny Osipov wrote: Hello everybody, I am trying to evaluate solvatation energy of my protein and. Unfortunately the protein highly glycosilated and it seems that PISA does not take into account hydrogen bonds between mannose from one molecule and symmetry related molecule. Is there any way to tell PISA to use ligands in calculations of the assembly solvatation energy. Isn't it a job for APBS? http://www.poissonboltzmann.org/apbs
[ccp4bb] new phaser and threads
Hello, Is there a way to tell the new phaser to not use more than N threads when running? I have a problem with it overloading some cluster nodes. Thanks a lot, F.
Re: [ccp4bb] Child Killed error in SCALA
You can try to run your program under strace in order to get more info about what went wrong. Look at the end of the trace to have an idea. strace your program and parameters On 03/08/2013 02:47 AM, Roger Rowlett wrote: OK, here is a strange one: I have 4 client machines (3 absolutely identical hardware) all running ccp4i from a central server and 2 of the 4 machines (always the same 2) will fail when running a certain scala job with a child killed error. I can run the same job on the 2 good machines. All the machines call the same ccp4 source file in .tcshrc. I'm stumped. It's probably some sort of cryptic permissions error or something like that. Anyone seen anything like this and have some clue as to the origin of the crash? AFAIK, it only happens running scala in 6.3.0. The home directories for users are served via NFS, but that should be the same for all machines. Log file follows: !-- CCP4 HTML LOGFILE -- pre#CCP4I VERSION CCP4Interface 2.2.0 #CCP4I SCRIPT LOG scala #CCP4I DATE 05 Mar 2013 14:28:22 #CCP4I USER xrdcamp4 #CCP4I PROJECT chem385 #CCP4I JOB_ID 4 #CCP4I SCRATCH /tmp/xrdcamp4 #CCP4I HOSTNAME malagueta #CCP4I PID 18904 /pre *** * Information from CCP4Interface script *** The program run with command: /usr/local/xtal/ccp4-6.3.0/bin/scala HKLIN /home/xrdcamp4/chem385/Chem385-2013Srefinaloutput.mtz HKLOUT /tmp/xrdcamp4/chem385_4_1_mtz.tmp SCALES /home/xrdcamp4/chem385/chem385_4.scala ROGUES /home/xrdcamp4/chem385/chem385_4_rogues.log NORMPLOT /home/xrdcamp4/chem385/chem385_4_normplot.xmgr ANOMPLOT /home/xrdcamp4/chem385/chem385_4_anomplot.xmgr PLOT /home/xrdcamp4/chem385/chem385_4_surface_plot.plt CORRELPLOT /home/xrdcamp4/chem385/chem385_4_correlplot.xmgr ROGUEPLOT /home/xrdcamp4/chem385/chem385_4_rogueplot.xmgr has failed with error message child killed: kill signal *** #CCP4I TERMINATION STATUS 0 child killed: kill signal #CCP4I TERMINATION TIME 05 Mar 2013 14:28:22 #CCP4I MESSAGE Task failed
Re: [ccp4bb] compiling Fortran 77 code on a Linux box (using gfortran ?)
Hi, The command: $ aptitude install fort77 would install an f77 command on Ubuntu/Debian Linux. In fact that's a wrapper for f2c, but maybe it behaves like a real f77 compiler, I would give it a try personnally. On 03/06/2013 06:48 PM, vellieux wrote: Hello, For those who still know the Fortran language and its Fortran 77 variant, I used to have a g77 compiler here (Linux box), and now on the new box it's no longer g77 but gfortran. When compiling Fortran77 code (these are the flags used for compilation: -o ../bin/$1 -std=legacy -Wno-globals -w -O3 -malign-double -funroll-loops -ffast-math -fno-second-underscore $1.f , followed by the libraries on that same compile line) I get errors (at run time) of the type: At line 138 of file program.f (unit = 6, file = 'stdout') Fortran runtime error: Missing initial left parenthesis in format When looking at this code (which compiled perfectly well using g77 - I removed the flag -fno-globals which doesn't seem to exist any more in gfortran) the Fortran code that I see appears to have all parentheses in the correct places. Any idea of what must be done with existing Fortran 77 code in order to get it to compile and run with gfortran ? Otherwise any idea which compiler should be used to compile Fortran 77 code ? Thanks in advance, Fred.
[ccp4bb] Thanks for the new graphical CCP4 installer
It is easy to use and even nice looking. Regards, F.
Re: [ccp4bb] Any tool to calculate surface accessible by ... another protein?
On 02/13/2013 04:51 AM, Emmanuel Levy wrote: Hello, I have been looking for a tool to measure the Protein accessible surface area, which could be defined exactly as the solvent ASA except with a probe of larger radius. Most tools that calculate ASA however do not work with a probe radius of a size equal to 10 or 50 Angstroms. Plus, ideally one would like to know the largest probe size that can access each atom or residue. So using classic ASA programs means one would have to run it ~30 times, each time with different probe radius for each protein. So my question is, do you know of a tool that could help us in obtaining this type of information? Without any guarantee, you may try Voroprot: http://code.google.com/p/baltymus/wiki/Tutorial I think it would never crash, whatever the probe size. Thanks in advance for any hint, All the best, Emmanuel
[ccp4bb] pdbset: filtering out ANISOU lines
Hello, Would it be possible to have pdbset take care of only the ATOM lines in a given PDB? I managed to make it do what I want but in case there are ANISOU lines, I want to ignore them. Currently, I'm using grep before pdbset, but I would prefer to avoid it as I am doing some computational experiment which is quite data intensive. If there is a way to filter out ANISOU lines or to work only on ATOM lines with pdbset, then I would be very happy. Thanks a lot, Francois.
[ccp4bb] thanks god for pdbset
Especially the renumber command that changes residue insertion codes into an increment of the impacted residue numbers. Regards, F.
Re: [ccp4bb] adding some user-defined graphical objects in a PDB file (and displaying them)
On 10/27/2012 05:32 AM, Pete Meyer wrote: Just out of curiosity, why use PDB format instead of converting PDB into a format readable by a more general 3d graphics program and combining with your cube/sphere/line segment there? I want to interact with the scene. Rotate, view, zoom, change protein representation, etc. So, if I go for some pymol-supported format, I will do all my visual inspection in pymol. Pete Francois Berenger wrote: Hello, For some new project, I'd like to be able to generate things and store them in PDB format. For example, a triangle, a line segment, a square, a cube, a sphere, an arrow, etc. Being able to change the color and line width would be nice. Is there some official recommended way of doing this? Is there some software able to read and display such graphical annotations of PDB files? I'll also need the format description in that case. I want to be able to process a PDB file and store the result of my processing in the same PDB file as some kind of annotation. My current way of doing this is to discretize my objects as H atoms in some other output PDB file, but that's just a temporary workaround. My current search got me this: http://www.cgl.ucsf.edu/eccc1/ So, maybe there is some support for what I am looking for into Chimera. Thanks a lot for your suggestions, Francois.
Re: [ccp4bb] adding some user-defined graphical objects in a PDB file (and displaying them)
For those interested, I think I'll go for Chimera and its support for .bild files. And that will be the end of this not so much xtal-related topic. ;) Sorry for the noise. Regards, F. On 10/29/2012 09:47 AM, Francois Berenger wrote: On 10/27/2012 05:32 AM, Pete Meyer wrote: Just out of curiosity, why use PDB format instead of converting PDB into a format readable by a more general 3d graphics program and combining with your cube/sphere/line segment there? I want to interact with the scene. Rotate, view, zoom, change protein representation, etc. So, if I go for some pymol-supported format, I will do all my visual inspection in pymol. Pete Francois Berenger wrote: Hello, For some new project, I'd like to be able to generate things and store them in PDB format. For example, a triangle, a line segment, a square, a cube, a sphere, an arrow, etc. Being able to change the color and line width would be nice. Is there some official recommended way of doing this? Is there some software able to read and display such graphical annotations of PDB files? I'll also need the format description in that case. I want to be able to process a PDB file and store the result of my processing in the same PDB file as some kind of annotation. My current way of doing this is to discretize my objects as H atoms in some other output PDB file, but that's just a temporary workaround. My current search got me this: http://www.cgl.ucsf.edu/eccc1/ So, maybe there is some support for what I am looking for into Chimera. Thanks a lot for your suggestions, Francois. .color white .dot 0 0 0 .color red .vector 0 0 0 20 0 0 .dot 20 0 0 .color green .vector 0 0 0 0 20 0 .dot 0 20 0 .color blue .vector 0 0 0 0 0 20 .dot 0 0 20 .color 44 .arrow 1 1 1 5 5 5 .arrow 1 1 2 8 6 9 .arrow 1 2 1 10 10 4 .arrow 2 1 1 -2 7 10 .color 22 .polygon 20 0 0 0 20 0 0 0 20 .color 5 .marker 20 20 20 .dr -20 0 0 .v 20 20 20 20 0 20 .dr 0 20 -20 .v 20 20 20 20 20 0 .dr -20 0 20 .dr 20 -20 0 .color 12 .sphere 10 10 10 3 .color 10 .arrow 19 19 19 12 12 12 0.2 1.0 .color 53 .cylinder 14 -5 14 14 0 14 2 open .sphere 14 -5 14 2 .sphere 14 0 14 2
[ccp4bb] adding some user-defined graphical objects in a PDB file (and displaying them)
Hello, For some new project, I'd like to be able to generate things and store them in PDB format. For example, a triangle, a line segment, a square, a cube, a sphere, an arrow, etc. Being able to change the color and line width would be nice. Is there some official recommended way of doing this? Is there some software able to read and display such graphical annotations of PDB files? I'll also need the format description in that case. I want to be able to process a PDB file and store the result of my processing in the same PDB file as some kind of annotation. My current way of doing this is to discretize my objects as H atoms in some other output PDB file, but that's just a temporary workaround. My current search got me this: http://www.cgl.ucsf.edu/eccc1/ So, maybe there is some support for what I am looking for into Chimera. Thanks a lot for your suggestions, Francois.
Re: [ccp4bb] adding some user-defined graphical objects in a PDB file (and displaying them)
On 10/26/2012 12:16 PM, James Stroud wrote: This sounds like something that a PDB file is not intended to do. I think everyone has universally agreed to the PDB specification at the RCSB, which makes no provisions for arbitrary objects, as cool as they would be. But you could put your information into REMARK records, which are free-form. Maybe you could then find some people to honor your specification or build an implementation yourself... 21st century solution The simplest way, would be to write a converter that embeds a pymol script into REMARK records and a preprocessor for pymol that extracts them and feeds them into the pymol stream. That's an idea. I may have a look at Pymol's support for user-defined object indeed (specification and rendering). If you write the implementation then you have a de facto standard. It would take a handful of lines of code. Write it in python and claim the mantle of coolness and the disdain of python detractors everywhere! I was looking for something already existing, as I guess I'm not the first person to need this (for productivity reasons also). You could set up a home page using wikispaces or even the pymol wiki, pointing to your implementation that you keep on github. I do have a github page, and do open source what's worth it. ;) Thanks, F. James On Oct 25, 2012, at 7:25 PM, Francois Berenger wrote: Hello, For some new project, I'd like to be able to generate things and store them in PDB format. For example, a triangle, a line segment, a square, a cube, a sphere, an arrow, etc. Being able to change the color and line width would be nice. Is there some official recommended way of doing this? Is there some software able to read and display such graphical annotations of PDB files? I'll also need the format description in that case. I want to be able to process a PDB file and store the result of my processing in the same PDB file as some kind of annotation. My current way of doing this is to discretize my objects as H atoms in some other output PDB file, but that's just a temporary workaround. My current search got me this: http://www.cgl.ucsf.edu/eccc1/ So, maybe there is some support for what I am looking for into Chimera. Thanks a lot for your suggestions, Francois.
Re: [ccp4bb] adding some user-defined graphical objects in a PDB file (and displaying them)
On 10/26/2012 12:16 PM, James Stroud wrote: This sounds like something that a PDB file is not intended to do. I think everyone has universally agreed to the PDB specification at the RCSB, which makes no provisions for arbitrary objects, as cool as they would be. I see that there was a proposal for extension in order to support kind of what I need: Annotating PDB files with scene information Gregory S. Couch, Eric F. Pettersen, Conrad C. Huang, Thomas E. Ferrin http://www.sciencedirect.com/science/article/pii/02637855953O# doi = 10.1016/0263-7855(95)3-O, An interesting citation from the paper: We propose that the extensions to the PDB presented here be adopted by the molecular modeling community for in- corporation into visualization programs. But you could put your information into REMARK records, which are free-form. Maybe you could then find some people to honor your specification or build an implementation yourself... 21st century solution The simplest way, would be to write a converter that embeds a pymol script into REMARK records and a preprocessor for pymol that extracts them and feeds them into the pymol stream. If you write the implementation then you have a de facto standard. It would take a handful of lines of code. Write it in python and claim the mantle of coolness and the disdain of python detractors everywhere! You could set up a home page using wikispaces or even the pymol wiki, pointing to your implementation that you keep on github. James On Oct 25, 2012, at 7:25 PM, Francois Berenger wrote: Hello, For some new project, I'd like to be able to generate things and store them in PDB format. For example, a triangle, a line segment, a square, a cube, a sphere, an arrow, etc. Being able to change the color and line width would be nice. Is there some official recommended way of doing this? Is there some software able to read and display such graphical annotations of PDB files? I'll also need the format description in that case. I want to be able to process a PDB file and store the result of my processing in the same PDB file as some kind of annotation. My current way of doing this is to discretize my objects as H atoms in some other output PDB file, but that's just a temporary workaround. My current search got me this: http://www.cgl.ucsf.edu/eccc1/ So, maybe there is some support for what I am looking for into Chimera. Thanks a lot for your suggestions, Francois.
Re: [ccp4bb] calculating dialectric properties of enzyme active site
On 10/07/2012 12:02 AM, Boaz Shaanan wrote: Hi If you want to calculate the electrostatic properties of your protein/mutants you can use Delphi or APBS. Calculation of the dielectric constants is most challenging. I think that these two programs use some approximations to estimate the variation of dielectric constants between the outside (water with epsilon = 80 and inside with epsilon = 4 or whatever values you use as input) but I'm not sure they output those values. For, APBS, the epsilon values used can be found in the .in file generated by pdb2pqr if you use it to generate the file driving APBS. However, the variation is taken into account when reporting the electrostatic potential which you can display using PyMol or UCSF-chimera. As for the hydrophobicity - there are hydrophobicity scales around (whether you believe them or not is a different matter) which you can use to display on the surface, again by Pymol or Chimera (and probably many other programs). My 2p/2c thoughts. Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaa...@bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Yarrow Madrona [amadr...@uci.edu] Sent: Saturday, October 06, 2012 4:48 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] calculating dialectric properties of enzyme active site Hello CCP4 list readers, Does anyone know how to calculate the dielectric properties of an enzyme active site? I would like to compare the polarity/hydrophobicity of similar proteins and different mutants. Thank you. -- Yarrow Madrona Graduate Student Molecular Biology and Biochemistry Dept. University of California, Irvine Natural Sciences I, Rm 2403 Irvine, CA 92697
Re: [ccp4bb] residues forming the surface of a cavity
On 10/04/2012 04:09 PM, sreetama das wrote: Dear all, Is there any CCP4 module/ other software/ web server which can determine which particular residues form the surface of a pocket/ binding-site in a protein? Do you mean residues not far from any ligand atom? And you know where is the ligand. Or do you mean residues surfacing a pocket or cavity? Regards, F.
Re: [ccp4bb] Overlapping transparent surface representations in Pymol
On 10/03/2012 12:09 AM, Christopher Browning wrote: Dear All, I was wondering if anybody knows how one can have two transparent surfaces overlapping but then being able to see how the 2 intersect using PYMOL. At the moment, if I have two transparent surfaces overlapping I don't see how they overlap internally, only externally. I can see how they overlap internally if one surface is transparent and the other is solid, but that is not quite what I'm after. If Pymol Map_set proposed by Dan is not what you want, maybe you should try the show as mesh mode of Pymol. Regards, F.
Re: [ccp4bb] off topic: pdf to word conversion
On 09/01/2012 07:48 PM, Rex Palmer wrote: Dear CCP4BB Does anyone know how to convert a .pdf file into a meaningful Word file. Maybe through Google doc you can do something for free (if you are OK with Google looking into your PDF file). On Linux, there are the pdftohtml and pdftotext commands that may be useful too (package poppler-utils under Ubuntu). Any suggestions will be greatly appreciated. The pdf file has numerous figures and tables. Rex Palmer http://www.bbk.ac.uk/biology/our-staff/emeritus-staff http://rexpalmer2010.homestead.com
Re: [ccp4bb] Does anyone have used DelPhi to calculate the Electrostatic potentials of DNA ？
On 07/11/2012 11:36 AM, dengzq1987 wrote: Hi all, recently，I want to use DelPhi to calculate the Electrostatic potentials of DNA.but in the manual,i can not find the method to create the inputfile fort.11 、fort.12 and fort.13.Does anyone have experience on this? Please suggest Why not using pymol and it's apbs plugin (if it handles DNA)? Thank you in advance Sincerely dengzq
Re: [ccp4bb] sequence format conversion
Hello, The tool is called awk. There is also another tool called Perl, but I won't recommend it. Regards, F. On 05/08/2012 04:02 PM, K Singh wrote: Dear All I was looking for a script or an informatics tool enabling me to change the sequence from FASTA format to something like following: FASTA FORMAT abcdefghijklmnopqrstuvwxyz to 1 abcde fghij 11 klmno pqrst 21 uvwxy z Many thanks in advance Regards Kris
Re: [ccp4bb] Off-topic: Supplying PDB file to reviewers
Hi, There is the exact same problem when releasing a software, possibly open source, before the corresponding article is accepted. And I don't know a correct solution to this problem. Regards, F. On 04/19/2012 05:34 PM, Yu Wai Chen wrote: Dear Marc, As a reviewer I find it difficult to “visualise” a structure based on a static 2D figure. I echo Joel's comments. If the (unreleased) coordinates are not supplied by the authors on request, I would simply refuse to review the paper on that ground. I suppose one can trust a reputable journal on the confidentiality issue. Wai -- Yu Wai Chen, PhDLecturer King's College London, Randall Division +44-207-848-8206 New Hunt's House, Guy's Campus, London SE1 1UL, U.K.
[ccp4bb] a question about protein sequences in the PDB
Dear list, If I take all the fasta files for proteins in the PDB, are the sequences complete? I mean, do they have holes sometimes (missing amino acids)? Sorry for the maybe stupid question but I know that sometimes the PDB files have missing residues, I am hoping that it is not the case with the FASTA files. Regards, Francois.
Re: [ccp4bb] a question about protein sequences in the PDB
On 03/27/2012 12:20 PM, Ethan Merritt wrote: On Monday, 26 March 2012, Francois Berenger wrote: Dear list, If I take all the fasta files for proteins in the PDB, are the sequences complete? I mean, do they have holes sometimes (missing amino acids)? In theory the SEQRES records describe the sequence of the entity that was crystallized, whether or not it is all visible in the electron density or present in the deposited model. So normally there should not be any missing internal residues. But if the expression construct was a not the full gene sequence, e.g. an N-terminal truncation, then those N- or C- terminal residues (or whole domains) will not be listed. So goes the theory. There are always corner cases. I remember having a dispute with the PDB long ago about whether a peptide chain that was known to have undergone loop cleavage was properly described with a single chain identifier or with two chain identifiers. And if the cleavage involved excission of one or more residues, would they appear in the SEQRES records anyhow? Sorry for the maybe stupid question but I know that sometimes the PDB files have missing residues, I am hoping that it is not the case with the FASTA files. I was assuming that the FASTA files you refer to are just conversions of the SEQRES records. If not, then all bets are off. If the FASTA files are retrieved by gene ID from Uniprot or some other sequence data base, then they will be complete in one sense but may not perfectly match what was in the deposited crystal structure due to cloning artifacts, strain variation, allelic non-uniformity, etc. OK, thanks for the answers. I'll try to find out more about the FASTA files present in the database then. Regards, F. Ethan Regards, Francois.
Re: [ccp4bb] Disulfide bonds
I wonder if it's not in the output of pisa from ccp4mg. On 03/05/2012 12:30 AM, Bart Hazes wrote: Hi Fred, The SSBOND server has indeed been moved as we have relocated to a new building. SSBOND is still available at the new server address: http://hazeslab.med.ualberta.ca/forms/ssbond.html This was my first ever program,with help from Bauke Dijkstra, and I was pleasantly surprised how many messages I got after the server relocation. SSBOND will soon get some competition for most used service as I am about to release some bioinformatics services. Bart On 12-03-04 02:36 AM, Frederic VELLIEUX wrote: I'd google for Bart Hazes and SSBOND myself. There is (or was) a server, and the publication is Prot. Eng. 1988, 119, 25 (PMID 3244694). The server seems to be down or has moved. HTH, Fred. Message du 04/03/12 05:07 De : Naveed A Nadvi A : CCP4BB@JISCMAIL.AC.UK Copie à : Objet : [ccp4bb] Disulfide bonds Hello everyone, I was wondering if there is any information available regarding the range of Ca-to-Ca distances between two cysteine residues forming disulfide bonds. Is there any software available for analysing the PDB for this kind of information? Some old textbooks suggest a distance of 4.4-6.8 A. I would very much appreciate any comments or suggestions you may have. Regards, Naveed Faculty of Pharmacy, The University of Sydney
[ccp4bb] shape complementarity
Hello, After following the discussion on [ccp4bb] shape complementarity between protein and DNA surface, is there someone here able to explain simply what the SC software of CCP4 is calculating? I mean, is there some intuitive/easy to understand explanation of what SC is calculating? I know I should read the corresponding paper, but I'd like someone to enlighten me before so I have better chances of understanding the article. Thanks, Francois.
Re: [ccp4bb] shape complementarity
On 02/08/2012 12:47 PM, Mike Lawrence wrote: Hi Francois Here's a one-liner. The major concept behind the Sc coefficient is that it measures the extent to which, on average, the normal vectors between closest-neighbour opposing points within the molecular interface are antiparallel. Sc=1 implies that the surfaces fit exactly, all such vectors are perfectly antiparallel. Heuristically, Sc values of 0.86 are about as good as protein-protein interfaces get (see Nature. 2005 435, pp773-8). Values below 0.65 indicate relatively poor shape complementarity. Use of a normal vector -based metric is considered superior to a distance-based metric, though Sc does have a distance-based weight applied to the normal dot products. Critical to this calculation is that the boundary of the buried molecular interface has to be discarded from the measure, as this region is intrinsically geometrically divergent. Sc is thus computed across only that part of the buried surface that might be expected to be shape complementarity, which makes it somewhat ill-suited to smaller interfaces. All these details are in the JMB paper, which, unfortunately, there is no substitute for reading :-) Thanks a lot for this very nice answer. I will definitely read your JMB article. Best regards, Francois.
Re: [ccp4bb] off-topic:schematic representations for secondary structure
On 02/04/2012 08:11 PM, Vellieux Frederic wrote: I believe Procheck generates drawings such as those. It generates PostScript files, and if you need to have (eg) jpg files, a PostScript interpreter, screen capture and there you are (Gimp to select only the areas you're interested in) The convert command from the ImageMagick package on Linux can usually deal with any image format conversion. Regards, F. HTH, Fred. WENHE ZHONG wrote: Dear memebers, Thank you all firsit for the helps on my previous post about sequence alignment. They are really useful! Apologize for the off-topic question again. I usually use DSSP method to calculate the secondary structures on my sovled structures. I saw a nice schematic representation for secondary structure from PDB database website (please see the attached figure). Does anyone know whether there is a program to draw these schematics? Thank you. King regards, Wenhe
Re: [ccp4bb] Iphone app to display protein models
On 01/27/2012 04:00 PM, Shiva Bhowmik wrote: Dear All, I was wondering if there is any IOS5 based app to display protein models, which are not in public database, on Iphone. Better than this: Jolecule from Dr. Bosco Ho. Jolecule works in HTML5 browsers such as Chrome and Safari, mostly in Firefox, and even on the iPad http://jolecule.appspot.com/ However, if you intend to keep your PDB secret, I'm not sure it is wise to use any webservice. Regards, Francois. There is an app called Molecules for displaying models but that utilizes coordinates from RCSB and pubchem. Thanks, Shiva
Re: [ccp4bb] linux upgrade preferences for CCP4
On 12/22/2011 06:56 AM, David Schuller wrote: Fedora releases are supported for about a year from initial release. Red Hat Enterprise, Centos and Scientific Linux are all supported for about 5 years. Ubuntu has long term support distributions as well: Starting with Ubuntu 12.04 LTS [...] versions will receive 5 years support Previous versions were 3 years for desktop and 5 years for server. cf. https://wiki.ubuntu.com/LTS Regards, F.
Re: [ccp4bb] Efficient way of showing residue conservation
On 12/08/2011 05:11 PM, Petr Leiman wrote: Dear Bostjan, There is Chimera for almost anything you can think of. Not coot, you are sure? Because (i) Chimera is not part of CCP4 and (ii) usually coot does everything on this mailing list. :) Search for Structure-Based Sequence Alignment on this page: http://www.cgl.ucsf.edu/chimera/features.html Petr On Dec 8, 2011, at 6:39 AM, Bostjan Kobe wrote: Consurf will do this for you. Bostjan --- Bostjan Kobe NHMRC Research Fellow Professor of Structural Biology School of Chemistry and Molecular Biosciences and Institute for Molecular Bioscience (Division of Chemistry and Structural Biology) and Centre for Infectious Disease Research Cooper Road University of Queensland Brisbane, Queensland 4072 Australia Phone: +61 7 3365 2132 Fax: +61 7 3365 4699 E-mail: b.k...@uq.edu.au URL: http://www.scmb.uq.edu.au/staff/bostjan-kobe Office: Building 76 Room 329 Notice: If you receive this e-mail by mistake, please notify me, and do not make any use of its contents. I do not waive any privilege, confidentiality or copyright associated with it. Unless stated otherwise, this e-mail represents only the views of the Sender and not the views of The University of Queensland. On 8/12/11 3:26 PM, Yuri Pompeuyuri.pom...@ufl.edu wrote: I once saw a figure showing the protein as surface, but instead of having it coloured by atom type or potential, it was shown by percent conservation in the family. Something like red highly conserved, all the way to white, not conserved at all... Now, I assume the figure was done by uploading aligned sequnces of several members of a family, and the colouring the generated surface accordingly. Does anyone know a way to do this more elegantly than what I tried doing? ps. I quit colouring them manually after I remebered my protein was 407 aa long...
Re: [ccp4bb] phaser openmp
On 11/09/2011 07:21 PM, Pascal wrote: Le Tue, 8 Nov 2011 16:25:22 -0800, Nat Echolsnathaniel.ech...@gmail.com a écrit : On Tue, Nov 8, 2011 at 4:22 PM, Francois Berengerberen...@riken.jp wrote: In the past I have been quite badly surprised by the no-acceleration I gained when using OpenMP with some of my programs... :( You need big parallel jobs and avoid synchronisations, barriers or this kind of things. Using data reduction is much more efficient. It's working very well for structure factors calculations for exemple. Amdahl's law is cruel: http://en.wikipedia.org/wiki/Amdahl's_law You can have much less than 5% of serial code. I have more problems with L2 misse cache events and memory bandwidth. A quad cores means 4 times the bandwidth necessary for a single process... If your code is already a bit greedy, the scale up is not good. I never went down to this level of optimization. Are you using valgrind to detect cache miss events? After gprof, usually I am done with optimization. I would prefer to change my algorithm and would be afraid of introducing optimizations that are architecture-dependent into my software. Regards, F.
Re: [ccp4bb] Insufficient virtual memory
On 10/14/2011 06:31 PM, Ian Tickle wrote: Hello all, some Fortran developer out there must know the answer to this one. I'm getting a forrtl: severe (41): insufficient virtual memory error when allocating dynamic memory from a F95 program compiled with Intel Fortran v11.1.059. The program was compiled on an old ia-32 Linux box with 1Gb RAM + 2Gb swap (I only have one Intel license to compile on this machine), but I'm running it on a brand new x86-64 box with 12Gb RAM + 8Gb swap. This should be ample: the program's maximum total memory requirement (code + static data + dynamic data) should be no more than 3Gb. My question is: what do I have to do to make it work? According to the ifort man page I need to specify -mcmodel=medium -shared-intel. It says: If your program has COMMON blocks and local data with a total size smaller than 2GB -mcmodel=small is sufficient. COMMONs larger than 2GB require mcmodel=medium or -mcmodel=large. Allocation of memory larger than 2GB can be done with any setting of -mcmodel. I'm a bit confused about the difference here between COMMONS 2Gb (which I don't have) and allocation of memory 2Gb (which I assume I do). When I try setting -mcmodel=medium (and -shared-intel) I get ifort: command line warning #10148: option '-mcmodel' not supported. Is this telling me that I have to compile on the 64-bit machine? Whatever happened to cross-compilation? All suggestions greatly appreciated! Try the GNU (compiler) and see what it says. ;)
Re: [ccp4bb] change of origin for reflections or map
Hello, The more I read this mailing list, the more I feel the crystallographer is a very special human being: - he lives in the Fourier space - when he goes to the Cartesian space, he restricts himself to a small box that is replicated to the infinity using symmetry operators and origin shifts That being said, some live in a world made of zero and ones... Regards, F.
Re: [ccp4bb] software for surface curvature
On 10/05/2011 07:25 AM, Jun Liao wrote: Dear All, These days, I want to calculate the surface curvature for my proteins in a quantitative way and show the results in a graphics software such as Pymol. Does someone have a good idea of which program will do a nice job? If you are a C++ expert and have some strong computational geometry knowledge: http://www.cgal.org/Manual/latest/doc_html/cgal_manual/Jet_fitting_3/Chapter_main.html Maybe by post-processing the output of MSMS (which gives surface normals) you can get something working, more easily. Regards, F. Thanks in advance, Best, Jun Liao Dept. of Physiology UTSW medical center at Dallas
Re: [ccp4bb] Linux vs MacOS for crystallographic software
On 09/29/2011 09:46 AM, William G. Scott wrote: On Sep 28, 2011, at 5:26 PM, Jacqueline Vitali wrote: Dear colleagues, I need some advice for a new computer. (1) I have the option of an HP Z210 8 GB with a low end Quadro Nvidia 400 512 MB. --How does Coot run with this card? OK --I am happy with any Linux. However, the system needs updates for security purposes (the University requires it). Do I have to remake the NVidia driver every time there is a kernel update or is there a way around it for this NVidia card? Do you suggest another NVidia card (inexpensive) that is good for coot and automatically updates when the kernel is updated? Try Ubuntu (or Kubuntu or Xubuntu, etc). You can have Linux and proprietary drivers. By the way, how about some Debian packages for CCP4? That would make it installable painlessly on both Ubuntu and Debian systems for academic users, which would be quite cool. Regards, F.
[ccp4bb] renaming an holo PDB after the alo one
Hello, I have one bound complexe (a ligand + a protein in holo conformation). I also have the apo structure for a very similar protein. Is there a tool to create a new PDB, whose coordinates are taken from the holo structure but residue names and numbers are taken from the alo structure (by looking at the corresponding residues in the output of a sequence alignment program)? I thought about doing a script using clustalw for the alignment part, but the task seems not trivial. Thanks a lot, Francois.
Re: [ccp4bb] renaming an holo PDB after the alo one
On 09/27/2011 09:55 AM, David Veesler wrote: Hi François, Chainsaw should do the job for you if you input a clustal alignment. Cheers David Thanks! I'm happy I asked. I'll give a try at chainsaw. Hope to not cut one of my fingers during the process... Le 26 sept. 2011 à 17:44, Francois Berenger a écrit : Hello, I have one bound complexe (a ligand + a protein in holo conformation). I also have the apo structure for a very similar protein. Is there a tool to create a new PDB, whose coordinates are taken from the holo structure but residue names and numbers are taken from the alo structure (by looking at the corresponding residues in the output of a sequence alignment program)? I thought about doing a script using clustalw for the alignment part, but the task seems not trivial. Thanks a lot, Francois.
Re: [ccp4bb] more Computer encryption matters
On 08/18/2011 09:34 PM, Andreas Förster wrote: Since we're on the subject... I've been tempted on and off to encrypt my hard drive, but after getting burned once a hundred years ago when encrypted data turned into garbled bytes all of a sudden I've been hesitant. I've gone so far as to install TrueCrypt (on a MacBook), but I haven't put it into action. Before I do, the big question: What software do people on the bb use for encryption? What can be recommended without hesitation? For Linux: checking the encrypted disk option of the installer (if I remember well I did this with a Ubuntu Linux once). Regards, F. Thanks. Andreas On 18/08/2011 1:19, Eric Bennett wrote: John, Since so many people have said it's flawless, I'd like to point out this is not always the case. The particular version of the particular package that we have installs some system libraries that caused a program I use on a moderately frequent basis to crash every time I tried to open a file on a network drive. It took me about 9 months to figure out what the cause was, during which time I had to manually copy things to the local drive before I could open them in that particular program. The vendor of the encryption software has a newer version but our IT department is using an older version. There is another workaround but it's kind of a hack. So I'd say problems are very rare, but if you run into strange behavior, don't rule out encryption as a possible cause. -Eric
Re: [ccp4bb] Computer encryption matters
On 08/18/2011 04:13 AM, Jrh wrote: Dear Colleagues, My institution is introducing concerted measures for improved security via encryption of files. A laudable plan in case of loss or theft of a computer with official files eg exams or student records type of information stored on it. Files, folders or a whole disk drive can be encrypted. Whilst I can target specific files, this could get messy and time consuming to target them and keep track of new to-be-encrypted files. It is tempting therefore to agree to complete encryption. However, as my laptop is my calculations' workbench, as well as office tasks, I am concerned that unexpected runtime errors may occur from encryption and there may be difficulties of transferability of data files to colleagues and students, and to eg PDB. Hello, Whole disk encryption is wise in case the machine is stolen. On Linux and Macs (I don't know other platforms) this is transparent and I don't see how it could trigger some runtime errors (once the computer is booted: the files are seen unencrypted by the operating system). The only concern may be that for some really I/O demanding applications (like video editing), this may slow down the video processing task. However, with decent hardware and file system, this may be just an old concern which crystallographers really don't need to care about. Another minor drawback is that you will possibly need a password to boot your machine (on Linux at least). Regards, F. Does anyone have experience of encryption? Are my anxieties misplaced? If not, will I need to plan to separate office files, which could then all be encrypted, from crystallographic data files/calculations, which could be left unencrypted. If separate treatment is the best plan does one need two computers once more, rather than the one laptop? A different solution would be to try to insist on an institutional repository keeping such files. In anticipation, Thankyou, John Prof John R Helliwell DSc
[ccp4bb] adding side-chains to a backbone model (without introducing clashes in the process)
Hello, Recently I was advised PULCHRA on phenixbb for such task (http://www.pirx.com/pulchra/index.shtml). I wonder if there is another tool in the CCP4 treasure chest for the same kind of task (preferably open source). Regards, F.
Re: [ccp4bb] research paper
On 07/29/2011 06:30 PM, Robbie Joosten wrote: Jung-Hoon, This is a so-called WaReZ request, which could get you banned a lot of webfora. Of course, we are all guilty of it at some occasions. The best way to get an article is to ask the authors, they are allowed give away free copies (depending on the journal I guess). Hooray, for authors who pay open access fees. Open Access fees are bad. Read this and you will understand: (HTML) http://cacm.acm.org/magazines/2010/2/69353-open-access-to-scientific-publications/fulltext (PDF) http://www.lri.fr/~mbl/pdf/cacm-openaccess-feb10.pdf Regards, F. Cheers, Robbie Date: Thu, 28 Jul 2011 12:23:10 -0400 From: f...@bernstein-plus-sons.com Subject: Re: [ccp4bb] research paper To: CCP4BB@JISCMAIL.AC.UK The article is available for purchase for $40. Journals cannot survive without funding which can come from many sources - subscriptions, author payment to make the article open-access, etc. But asking someone to provide a 'free' copy without Acta's permission is tantamount to theft. Frances Bernstein = 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 Thu, 28 Jul 2011, Ed Pozharski wrote: On Thu, 2011-07-28 at 14:35 +, Jung-Hoon Lee wrote: Acta Cryst D63 (2007), 550-554. I can't believe Cornell has no access to Acta D. -- Hurry up before we all come back to our senses! Julian, King of Lemurs
Re: [ccp4bb] Phaser and Molrep gave different solutions
On 07/21/2011 01:45 PM, Hubing Lou wrote: Dear all, I am stuck in a molecular replacement case and looking for advices. I have been working on a protein-DNA complex structure. Data was processed by HKL2000 to 2.6Ang and some of the data statistics are shown below: Space group: P21, Unit Cell: 54.73, 104.91, 78.40, 90, 100.2, 90 Redundancy: 2.8 (2.7) Completeness: 94.8 (93.1) Linear R-fac: 0.051 (0.442) Data quality was checked by Phenix.xtriage and there's no problem. I then prepared a model by Chainsaw. Our protein shares only 30% of sequence similarity with the model, but structurally they are in the same group and almost identical in apo form. Matthrews Coeff indaced two monomers in AU. I then ran Phaser in automated search mode and there's a solution with RFZ score 4.8, TFZ score 3.8. Hi, Isn't this a bad sign usually when the TFZ score is lower than the RFZ score? Regards, F. The electron density map was not bad with DNA double helix clearly seen. However Refmac5 couldn't get Rfree lower than 50%. I then changed to MolRep, ran self rotation function first then used the first 10 peaks for translation search. Again there's a solution but it is different from that from Phaser. I attached a picture here. Checking in coot, the packing is the same. But, the refinement couldn't get Rfree lower than 50%. I have tried to include NCS, TLS refinement in Refmac, both not working. Hope someone out there can help. Thanks very much for your time. Hubing
Re: [ccp4bb] Off Topic: How to delete loops from a protein
Hi Obayed, If I understood your question well, you are looking for something called secondary structure prediction. I googled these keywords and found this server: http://bioinf.cs.ucl.ac.uk/psipred/ You may find other interesting servers on the web and some literature comparing them. I think such methods need only the sequence of your protein to predict its secondary structures. Hope this helps, Francois. On 07/19/2011 02:14 PM, Eric Larson wrote: Hi Obayed, you could give in situ protolysis a try. This is where you add a bit of protease along with you target protein to the crystallization drop. It has been quite successful for the folks at the SGC. Here are the relevant references: Dong A, et al. In situ proteolysis for protein crystallization and structure determination. Nat Methods. 2007 Dec;4(12):1019-21.PMID: 17982461. (http://www.ncbi.nlm.nih.gov/pubmed/17982461) Wernimont A, Edwards A. In situ proteolysis to generate crystals for structure determination: an update. PLoS One. 2009;4(4):e5094. PMID: 19352432. (http://www.ncbi.nlm.nih.gov/pubmed/19352432) good luck, Eric Eric T. Larson, PhD Biomolecular Structure Center Department of Biochemistry Box 357742 University of Washington Seattle, WA 98195 email: larso...@u.washington.edu On Mon, 18 Jul 2011, Obayed Ullah wrote: Hi all I wrote last time but got only one feedback. I know some of you guys must have this experience that how to delete loops from the protein. Please help me with suggestions. I am working with a human protein which have around 20% sequence identity with the other proteins of the same family. Structure of some of the proteins from this family have been solved. All the solved structures have around 20% identity with my protein. I am trying to crystallize the protein but it looks like very hard to get crystal. I have tried different N and C terminally truncated constructs for crystallization but no crystal. My feeling is that probably there is some flexible loops with in the protein which limiting the crystallization. So I want to delete the loops with in the protein (not to truncate in the terminal, I already have done this). I am not asking suggestion about how to delete the loop rather how to decide where the loop is. I am not sure how much it will be helpful to get a homology model of such a protein having low sequence identity. Is there any strategy to decide where the loop could be? Does anybody know any established/ rational method to do that. Waiting for your suggestions Obayed Ullah
Re: [ccp4bb] Off topic question. NACCESS
On 06/17/2011 05:25 PM, Armando Albert wrote: Does anyone has got some information about how to get a mac version (intel), of the old unix program naccess?. It was meant to calculate the solvent accessibility per residue from a pdb file. Armando Maybe this server can do the job: http://cgal.inria.fr/abs/Vorlume/ And many other servers will be proposed maybe. Regards, F.
Re: [ccp4bb] Solvent channel volume measurement [SEC=UNCLASSIFIED]
On 06/13/2011 04:55 PM, DUFF, Anthony wrote: It may require some tricks, such as the creation of walls of CA atoms, but Kleywegt's FLOOD will give an answer in terms of number of water molecules. Some more tools are referenced here: http://hollow.sourceforge.net/ However, I did not tried them. I don't know how they delimit the limits of channels, which may be an interesting question. Regards, F. Anthony Duff -Original Message- From: CCP4 bulletin board on behalf of Matthew BOWLER Sent: Mon 6/13/2011 5:40 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Solvent channel volume measurement Dear All, does anyone know of a program that can measure the volume or largest dimension of the solvent channels in crystals? Cheers, Matt. -- Matthew Bowler Structural Biology Group European Synchrotron Radiation Facility B.P. 220, 6 rue Jules Horowitz F-38043 GRENOBLE CEDEX FRANCE === Tel: +33 (0) 4.76.88.29.28 Fax: +33 (0) 4.76.88.29.04 http://go.esrf.eu/MX ===
Re: [ccp4bb] Comparing two proteins
This tool looks cool also (especially to all the maximum likelihood fans of this list I guess): http://www.theseus3d.org/ --- Theseus is a program that simultaneously superimposes multiple macromolecular structures. Instead of using the conventional least-squares criteria, Theseus finds the optimal solution to the superposition problem using the method of maximum likelihood. --- Tim Gruene wrote: Yes, I forgot about escet. The more up to date wab address is http://webapps.embl-hamburg.de/escet/ even though that page still lists Thomas' address in Italy Tim On Thu, Apr 14, 2011 at 10:05:47AM +0200, Gergely Katona wrote: ESCET is also very useful to reveal small, but significant differences. It also identifies conformationally invariant regions for superposition. http://schneider.group.ifom-ieo-campus.it/escet/index.html Gergely On Thu, Apr 14, 2011 at 9:34 AM, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote: Hello Rex, most programs probably use similar algorithms for superpositions, so you can pick your choice: - O - lsqman - lsqkab - coot - ... are all similarily comfortable to use in my opinion. Tim On Wed, Apr 13, 2011 at 09:18:27PM +0100, REX PALMER wrote: Dear All What is the best program to use for comparing two protein structures which are very similar both structurally and wrt aa sequence? ie to get the rms deviations both generally and in selected regions. Rex Palmer Birkbeck College -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen phone: +49 (0)551 39 22149 GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.10 (GNU/Linux) iD8DBQFNpqOSUxlJ7aRr7hoRAuLIAJ0Tf??? x3TuOjPcJqLZgL1vnANuUV0= =vQE1 -END PGP SIGNATURE- -- Gergely Katona, PhD associate professor, docent Department of Chemistry, University of Gothenburg Box 462, 40530 Göteborg, Sweden Tel: +46-31-786-3959 / M: +46-70-716-7586 / Fax: +46-31-786-3910 Web: http://www.csb.gu.se/katona, Email: gergely.kat...@chem.gu.se
[ccp4bb] Getting the triangulated solvent excluded surface of a protein (PDB) as a .obj file
Hello, What are the good software to do this? I already know of Pymol and Jmol. Both can export the result to a .obj file, which is interesting for later processing. However, Pymol's algorithm is not exactly what Connolly described, cf. http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg00179.html Also, Pymol will save the surface with some translation and rotation which are not present in the PDB read in, which is a real pain. For Jmol, sometimes the surface is not a closed polyhedra, so it is kind of useless for my purpose. I know of MSMS, but I don't think it is that robust (I read some source code where someone was using MSMS, the source code had many dirty things in order to try handling the apparently many cases where MSMS was crashing). Is there something freely usable for research, using beta shapes internally, for example? That should be a robust approach. A robust software would be much appreciated (not crashing, whatever the PDB we give it as input). Open source and not in Fortran would be heaven. ;) Thanks a lot for suggestions, F.
Re: [ccp4bb] Getting the triangulated solvent excluded surface of a protein (PDB) as a .obj file
Sorry, I forgot to mention about what is the .obj file I need. It is a pure ASCII geometric description of a polyhedra. Cf. http://en.wikipedia.org/wiki/Wavefront_.obj_file It looks rather easy to parse compared to some VRML file, for example. Thanks, F. Francois Berenger wrote: Hello, What are the good software to do this? I already know of Pymol and Jmol. Both can export the result to a .obj file, which is interesting for later processing. However, Pymol's algorithm is not exactly what Connolly described, cf. http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg00179.html Also, Pymol will save the surface with some translation and rotation which are not present in the PDB read in, which is a real pain. For Jmol, sometimes the surface is not a closed polyhedra, so it is kind of useless for my purpose. I know of MSMS, but I don't think it is that robust (I read some source code where someone was using MSMS, the source code had many dirty things in order to try handling the apparently many cases where MSMS was crashing). Is there something freely usable for research, using beta shapes internally, for example? That should be a robust approach. A robust software would be much appreciated (not crashing, whatever the PDB we give it as input). Open source and not in Fortran would be heaven. ;) Thanks a lot for suggestions, F.
[ccp4bb] What is the simplest method to analytically compute the Solvent-Accessible Surface Area of a given atom in a protein?
Hello, Does someone know some good articles on this particular topic? I'd like to implement the thing myself, however if there is a good software doing the job (with readable source code), I might use and cite it. Best regards, Francois.
[ccp4bb] [Fwd: Re: [ccp4bb] Graphics for notebook]
---BeginMessage--- Kay Diederichs wrote: Eric Karg harvard...@yahoo.com Datum: Sun, 14 Nov 2010 21:37:10 + Dear all, Thanks for your suggestions. From what I learned new GPUs from NVIDIA are using the Optimus technology which does not support Linux, meaning that only the dedicated graphics on the system will be used in Linux. Does it still make sense to go for NVIDIA instead of ATI? No, the right way is to contact NVIDIA and pressure them to support Linux. Just sending a mail to customer support saying what you just wrote before is enough. Also, Eric suggest a smart way. But even if it works, you should bother NVIDIA so that in the future things will evolve in the right way. Many people did this several years ago, so at some point, NVIDIA started providing quality Linux drivers. In fact, people should bother NVIDIA so much so it is even possible for people outside of NVIDIA to support the Linux driver even when NVIDIA will no more be interested into supporting it. Eric Eric, Optimus is a technology for fast switching between the slow internal graphics unit and a fast, but power-hungry, NVidia chip. Unfortunately, it is currently only supported by Windows7. If the notebook's BIOS offers to permanently disable, or permanently enable, the NVidia graphics then, from the Linux view, this would be equivalent to a conventional notebook with slow/fast graphics. If it just defaults to one of those states then, using Linux, you are at the mercy of the decision of the BIOS developers. So I'd say: before you buy investigate what the BIOS offers. HTH, Kay ---End Message---
Re: [ccp4bb] [RANT] Publication Data Formats
James Stroud wrote: On Nov 16, 2010, at 10:57 PM, Ethan Merritt wrote: Bleah. Virtually none of those are human-readable, no matter what the wikipedia page may choose to put as a heading title. What kind of data are you dealing with? PDF would indeed be an odd format for diffraction images, but it would be miles better than most of the formats on the list you point to. The operative word is dataset, which is a subset of all things data. A dataset should be in a format that 1. can be validated 2. is structured 3. is machine readable Hello, They should allow YAML: http://en.wikipedia.org/wiki/YAML Then they will keep all the above and win an extra: 4. human readable Which makes it way better than the ugly and verbose XML. Regards, F. A pdf file *guarantees* none of the above. It is a presentation format and is not optimized for validating, structuring, or ensuring the machine readability of the data that it might contain. I'm not advocating for any particular serialization format. So this isn't about JSON v. XML religion wars. This is JSON or XML versus a file format that is basically designed to ferry presentation information between printers or computer screens. James
Re: [ccp4bb] SC
Hi, This is the first time I read about shape complementarity statistics. According to: A structural basis for the activity of retro-Diels–Alder catalytic antibodies: Evidence for a catalytic aromatic residue As seen here: http://www.pnas.org/content/99/15/9674.full --- [...] compute the SHAPE COMPLEMENTARITY STATISTICS index (Sc). This statistics index measures the geometric surface complementarity via the use of normal products, and the extent to which the interacting surface elements are brought into proximity via an exponential distance separation term. Sc values usually range from 0.70 to 0.76 for proteinase–protein inhibitor surfaces, from 0.64 to 0.68 for antigen–antibody complexes, and from 0.45 to 0.70 for MHC–peptide complexes (30). --- I am frightened. :( I don't think this is in my book The cartoon guide to statistics. Despite the book is really nice. Regards, F. intekhab alam wrote: I want to calculate the shape comlementarity statitics (SC) of a dimeric protein using CCp4. I am using CCP4 6.1.3 on windows but the SC program is not available in that suite. Which version of CCP4 has that program. Are there any other programs that can calculate that. Thanks -- INTEKHAB ALAM LABORATORY OF STRUCTURAL BIOINFORMATICS KOREA UNIVERSITY, SEOUL
Re: [ccp4bb] what package provides libg2c.so.0 on Ubuntu ?
Edward A. Berry wrote: I'm helping set up crystallography programs on a ubuntu system, and we're stuck because one program (scalepack) needs the library libg2c.so.0 . Maybe compat-libf2c I understand this is absent from modern distributions because gcc discontinued support for g77 and f2c in recent releases. However on fedora there are compatibility packages like compat-libf2c which allow running old executables compiled with g77. Is something like this available for ubuntu? Or is there some other trick to get scalepack running? I understand ubuntu is used by many crystallographers, and while I'm sure most of them use mosflm or XDS, I'm sure someone has tried setting up denzo/scalepack. the system: Linux x 2.6.31-22-generic #65-Ubuntu SMP Thu Sep 16 15:48:58 UTC 2010 i686 GNU/Linux gcc (Ubuntu 4.4.1-4ubuntu9) 4.4.1 Thanks, eab
[ccp4bb] Seeking Postdoctoral Researcher
Laboratory: Zhang Initiative Research Unit, Advanced Science Institute, RIKEN, Japan. (Unit Leader: Dr. Kam Zhang) Job title and Job description: Postdoctoral Researchers Job description: We are seeking a highly motivated and experienced computational structural biologist to join the Zhang Initiative Research Unit at RIKEN. The successful candidate will use computational tools to tackle problems in the area of protein folding, structure prediction, and structure-based drug design. Our ability to predict the structure of proteins from their primary sequences will greatly facilitate our understanding of the important biological functions that proteins play in their host systems. The 3D structure information will also facilitate the rationale design of drugs for the treatment of various diseases with unmet medical needs. Qualifications: This position requires a PhD in areas related to biophysics, biochemistry, computational chemistry, bioinformatics, or structural biology with experience in employing computational tools to solve biological or chemical problems. Experiences in protein folding, protein structure prediction, protein structure analysis, protein crystallography, or structure-based drugs are highly desired. Proficiency in object-oriented programming such as C++, Java, scripting languages such as Python, Perl are also desired. Experiences in high performance computing, network computing, or grid computing would be a plus. The ideal candidate should possess a track record of accomplishments demonstrating technical proficiency, independent thinking, and scientific creativity. The research environment will be international and hence communication in English is encouraged. The complete job ad, as well as how to apply can be viewed here: http://www.riken.jp/engn/r-world/info/recruit/k100817_s_asi.html Best regards, Francois.
[ccp4bb] How to get a seq.data file from a FASTA file?
Hello, First, sorry for this not directly CCP4-related question. I have some software here that requires a seq.data file as one of its inputs: any idea on how to create such a file from a FASTA file? Here is how the expected file looks like for protein 101M (it is named seq.dat): --- 1 MET19 2 VAL19 3 LEU18 4 SER18 5 GLU29 6 GLY29 7 GLU29 8 TRP29 9 GLN29 10 LEU29 [...] 147 TYR29 148 LYS28 149 GLU26 150 LEU12 151 GLY17 152 TYR18 153 GLN19 154 GLY19 --- Thanks a lot, Francois.
Re: [ccp4bb] How to get a seq.data file from a FASTA file?
Reply to myself: The author changed his program so that only the 2 first columns are needed now, and they are obvious enough. Regards, F. Francois Berenger wrote: Hello, First, sorry for this not directly CCP4-related question. I have some software here that requires a seq.data file as one of its inputs: any idea on how to create such a file from a FASTA file? Here is how the expected file looks like for protein 101M (it is named seq.dat): --- 1 MET19 2 VAL19 3 LEU18 4 SER18 5 GLU29 6 GLY29 7 GLU29 8 TRP29 9 GLN29 10 LEU29 [...] 147 TYR29 148 LYS28 149 GLU26 150 LEU12 151 GLY17 152 TYR18 153 GLN19 154 GLY19 --- Thanks a lot, Francois.
Re: [ccp4bb] Format conversion of Shelx coordinate file
Hi, What is the motto/slogan of coot? I read so often about it on ccp4bb. If there is not one yet, I propose: coot, the crystallographer's swiss knife :'D Regards, F. Tim Gruene wrote: Hello Florian, you can read the .hat-file into coot and save it from there, changing the suggested file-extenstion from .ins to .pdb. In case coot crashes when it reads the .res-file, edit the file and make sure there is only one END-card. Maybe shelxpro would also work. Tim On Mon, Aug 30, 2010 at 05:36:37PM -0400, Florian Schmitzberger wrote: Dear All, What is currently the quickest/easiest way to convert a .hat file with fractional coordinates of heavy atoms generated by ShelxE to PDB format and/or a file format accepted by Sharp? I tried to use coordconv from ccp4, but it failed to make the conversion. Thank you. Regards, Florian --- Florian Schmitzberger Biological Chemistry and Molecular Pharmacology Harvard Medical School 250 Longwood Avenue, SGM 130 Boston, MA 02115, US Tel: 001 617 432 5602
Re: [ccp4bb] ROSETTA for MR model generation
Hello, I know at least the following papers on this topic: --- High resolution protein structure prediction and the crystallographic phase problem http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2504711/ Prospects for de novo phasing with de novo protein models http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2631639/ --- I think it worked on several of their cases, better on small proteins if I remember well. Regards, F. Kornelius Zeth wrote: Dear all, I was wondering if anybody has used the ROSETTA software to generate a MR model that could subsequently being used successfully for a MR solution case. The sequence of the protein we work with is relatively small, ~ 85 residues. Crystallization is not very reproducible. Resolution is 1.9 A. Crystals are extremely rare. I would be grateful for any hints and will send a summary of all personally sent comments to the list. Thank you and have a nice day Kornelius -- Kornelius Zeth Max Planck Institute for Developmental Biology Dept. Protein Evolution Spemannstr. 35 72076 Tuebingen, Germany kornelius.z...@tuebingen.mpg.de Tel -49 7071 601 323 Fax -49 7071 601 349
Re: [ccp4bb] Method to calculate the axis of an alpha helix
Hello, Is there some C or C++ code out there doing what you described in 1). If not, is there a very detailed explanation of this procedure somewhere, detailed enough in order to implement it (just getting the best fit vector and its length, no other parameters)? Thanks a lot, Francois. Tom Oldfield wrote: Yuan SHANG 1) DIY The way that has been used is to calculate the inertia tensor matrix for helix (or any other secondary structure element). You can chose backbone atoms or just the CA atoms. Then calculate the eigen vectors and values from this and the largest eigen vector will be the best fit vector to the helix - and its lambda will define its length. For a strand or sheet you can use this method too. This was the standard way from molecular simulation work to look at simplified dynamics of proteins. 2) The program Squid http://www.ebi.ac.uk/~oldfield/squid/ (1992, 1998) has lots of different analysis methods for proteins including calculating vectors for helices, the angles between helices (torsion/distance/opening) and other things. You only problem is that it is very old (1988) and written in Fortran and requires a little effort to install - sorry - I no longer support it. There is a pre compiled linux-32 bit version and I still do all my structure analysis with it. http://www.ebi.ac.uk/~oldfield/xsquid - though this requires installation data too. Tom Fitting a helix is not trivial. If you have access to windows and mathematica, then you might try helfit. (Otherwise, you could implement the algorithm yourself and then share your code with the rest of us ;-) http://dx.doi.org/10.1016/j.compbiolchem.2008.03.012 James On Aug 15, 2010, at 12:29 AM, 商元 wrote: Dear all, I want to compare the conformational change of two similar structures, using one alpha helix as the reference. Then, how can I get a vector that can represent both the position and direction of the helix? Is there any well-known software can do this？ Or, should I build a cylinder model, with parameters [radius,bottom center(x1,y1,z1),top center(x1,y2,z2)], using the coordinates of C,C(alpha) and N to fit these parameters? Thanks for any suggestions Regards, Yuan SHANG
Re: [ccp4bb] Estimation of coordinate errors
By the way, I used this one recently: http://zhang.bioinformatics.ku.edu/TM-score/ It computes a lot of scores: TM-score, MaxSub-score, GDT-TS-score and GDT-HA-score. All of this with a single Fortran file (so nothing more needed except a Fortran compiler), I was impressed. Regards, F. Pavel Afonine wrote: Hi Joe, do you want to calculate rms deviations between two sets of coordinates that are originating from two PDB files? If my guess is correct, then you can get this number using the command below: phenix.superpose_pdbs file1.pdb file2.pdb which will superpose two sets of coordinates and print RMS deviations before and after superposition, like this: RMSD between fixed and moving atoms (start): 0.575 RMSD between fixed and moving atoms (final): 0.563 Is this is what you want? Good luck! Pavel. On 8/2/10 9:59 PM, Joe Yap wrote: Dear CCP4 users, I have two sets of coordinates that are of similar structure and I would like to know is there a program I can use to calculate the coordinate errors between these two sets of coordinates? I would appreciate it if you can help me with this. Thank you so much. Best regards, Joe Yap
Re: [ccp4bb] Matthews coefficient
Hello, I am not a crystallographer, so I will ask a maybe stupid question. When you say After molecular replacement you should check the result with the model building program of your choice and correct as many errors as possible before running a refinement program. Can this step be automated in some way (without any human intervention)? Are there programs to do this? I am interested even if some program does only one part of the job. Thanks a lot, Francois. Tim Gruene wrote: Dear Xinghua, the solvent content provided by yhe Matthews-program is certainly correct. Whether or not it applies to you protein is a different issue. With only 2 molecules in the asymmetric unit the solvent content rises to 65%, and this is stll perfectly fine for proteins. So carry out molecular replacement with only two molecules and start model building and refinement. Your previous message sounds as though to started refinement directly after molecular replacement. I would strongly discourage you from this practice (which somehow seems to be stuck in the heads of many people). After molecular replacement you should check the result with the model building program of your choice and correct as many errors as possible before running a refinement program. Tim On Fri, Jun 25, 2010 at 01:54:05PM +0800, xinghua qin wrote: Hi everyone: Thanks for all the responses. The Matthaws-cell content analysis programe in CCP4 package gives the results: 47% solvent content and 3 molecules in asu with 87% confidence. the space group is P3121. how to carry out self rotation function? can phaser do that work? If there areTwo moleculars in asu ,no clashes and the TF values are above 10.but if three, the clashes are too much and TF valur is about five. And how to calculate the solvent content? Is the calculated solvent content with the Matthews-cell content analysis programe not always right? Best regards Xinghua Qin On Fri, Jun 25, 2010 at 10:42 AM, Vineet Gaur vineetgaur1...@gmail.comwrote: Hi It would b good if u can mention the solvent content and space group along with the no. of molecules in asu/ u can carry out self rotation function to check the no of mol in asu best vineet On Fri, Jun 25, 2010 at 6:42 AM, xinghua qin xtal...@gmail.com wrote: hi CCPeers The Matthews coefficient of my protein is 3 calculated with matthews-cell content analysis CCP4 programe with 87% confidence , but when doing the refinement the third molecular couldn't get into the unit cell because of too many clashes.Deletion of the clashed AA did not work well, Then I used two molecules in the unit cell, After refining with Refmac, I found that the R factor is 0.29, R free is 0.40.I believe the value can be better with the real space refinement.But the question is that can the calculated Matthews coefficient be wrong? Best regards Xinghua Qin -- Xinghua Qin College of Biological Sciences No.2, Yuan Ming Yuan West Road Haidian District,Beijing,China,100094 Tel: +86-10-62732672 -- Xinghua Qin College of Biological Sciences No.2, Yuan Ming Yuan West Road Haidian District,Beijing,China,100094 Tel: +86-10-62732672
Re: [ccp4bb] Matthews coefficient
Vellieux Frederic wrote: Hi, No such thing as a stupid question. If the resolution is sufficient, arp_warp does a good job. But it is a reconstruction and REFINEMENT program. But checking the proper packing (that there are indeed contacts in the 3 dimensions of space to form the crystal): takes only 10 seconds using a graphics program, so there is no need to automate that. Well, if my colleague sends you his 300,000 computer-generated models to use in MR, I am sure you will like to automate the job. ;) And trying to do everything completely automatically (without any human intervention and checks) can lead to big problems (for example if the space group has been wrongly assigned). You may end up publishing a wrong structure if you rely entirely on totally automated crystallographic software without checking anything. Sure, an expert is always useful to check things at some moment. And, I also agree that things made only in the computer have to be checked using some experimental data in order to be relied on. Francois. Fred. Francois Berenger wrote: Hello, I am not a crystallographer, so I will ask a maybe stupid question. When you say After molecular replacement you should check the result with the model building program of your choice and correct as many errors as possible before running a refinement program. Can this step be automated in some way (without any human intervention)? Are there programs to do this? I am interested even if some program does only one part of the job. Thanks a lot, Francois.
Re: [ccp4bb] error in running Phaser NMA mode
Hello, I used this script once just to have a look at some NMA-moved structures: --- #!/bin/bash if [ $# -ne 1 ] ; then #0 1 echo usage: phaser_nma.sh INPUT.PDB exit 1 fi name=`echo $1 | sed s/\.pdb$//g` phaser EOF TITLE moved by some low frequency normal modes MODE NMA ENSEMBLE 1 PDB $1 IDENTITY 100 EIGEN WRITE ON ROOT $name NMAPDB MODE 7 MODE 8 RMS 0.5 FORWARD MAXRMS 3 EOF --- It produced some PDBs (I did not tried MR on them after, I was just curious about the NMA induced moves). Regards, F. Yong Y Wang wrote: I am getting an error in running Phaser in NMA mode based on the usage in the Phaser document. pre BFONT COLOR=#FF html!-- CCP4 HTML LOGFILE -- !--SUMMARY_BEGIN-- # # # ### CCP4 PROGRAM SUITE: Phaser 2.1.4 ### # User: rx36953 Run time: Thu Jun 24 14:01:32 2010 Version: 2.1.4 OS type: linux Release Date: Thu Nov 13 10:53:32 2008 If you use this software please cite: Phaser Crystallographic Software A.J. McCoy, R.W. Grosse-Kunstleve, P.D. Adams, M.D. Winn, L.C. Storoni R.J. Read J. Appl. Cryst. (2007). 40, 658-674 !--SUMMARY_END-- !--END--/FONT/B !--SUMMARY_BEGIN-- * *** Phaser Module: PREPROCESSOR 2.1.4 *** * !--SUMMARY_END-- ENTER KEYWORD INPUT FROM FILE OR FROM STANDARD INPUT !--SUMMARY_BEGIN-- TITLe beta normal mode analysis pdb file generation MODE NMA ENSEmble test PDB protein_A_CRYST.pdb IDENtity 100 ROOT test_nma_pdb # not the default EIGEn test_nma.mat NMAPdb MODE 7 MODE 10 RMS 0.5 FORWARD !--SUMMARY_END-- EXIT STATUS: SUCCESS CPU Time: 0 days 0 hrs 0 mins 0.00 secs (0.00 secs) Finished: Thu Jun 24 14:01:32 2010 /pre /html pre BFONT COLOR=#FF html!-- CCP4 HTML LOGFILE -- # # # ### CCP4 PROGRAM SUITE: Phaser 2.1.4 ### # User: rx36953 Run time: Thu Jun 24 14:01:32 2010 Version: 2.1.4 OS type: linux Release Date: Thu Nov 13 10:53:32 2008 If you use this software please cite: Phaser Crystallographic Software A.J. McCoy, R.W. Grosse-Kunstleve, P.D. Adams, M.D. Winn, L.C. Storoni R.J. Read J. Appl. Cryst. (2007). 40, 658-674 !--END--/FONT/B !--SUMMARY_BEGIN-- * *** Phaser Module: NORMAL MODE ANALYSIS 2.1.4 *** * TITLe beta normal mode analysis pdb file generation ENSEmble test PDB protein_A_CRYST.pdb IDENtity 100 ROOT test_nma_pdb # not the default EIGEn test_nma.mat BFONT COLOR=#FF8800 SYNTAX ERROR: Use READ or WRITE /FONT/B !--SUMMARY_END-- EXIT STATUS: FAILURE CPU Time: 0 days 0 hrs 0 mins 0.00 secs (0.00 secs) Finished: Thu Jun 24 14:01:32 2010 /pre /html Anyone knows how to use the NMA mode? Is the document not up-to-date? Thanks, Yong
Re: [ccp4bb] different compilers for ccp4 code
Hello, This is not what you asked for, but I think it is good to know: Intel compilers don't seem to like non-Intel CPUs: http://www.agner.org/optimize/blog/read.php?i=49 Regards, F. Terry Lang wrote: Hey Everyone, I am considering switching from gcc to the Intel compiler in the hopes of making some of calculations run a bit faster. Has anyone ever tried compiling the ccp4 code base with the Intel compilers? Is there a difference in speed? What about in the reproducibility of the calculations? Any changes in statistics? Any information would be greatly appreciated! Thanks, Terry
Re: [ccp4bb] a simple query: atom selection for CNS
Hello,
Just for your information, there is a mailing list for CNS:
http://groups.yahoo.com/group/cnsbb/
And there is some activity on it.
Regards,
F.
AMIT wrote:
Just type in CNS refine.inp in the atom select option:
{===} atom_select=(not((chainid A and resid 10:15 ) or (chainid B and
resid 12:17 )));
On 4/28/10, Amit Kumar amitkumar.ii...@gmail.com wrote:
Hi all,
Apologies for non-ccp4 and very simple query.
How one will select and write into CNS input file
For example:
I would like to select following residues for omission to calculate SA-omit
map:
residue 10 to 15 of chain A and 12 to 17 of chain B
Thank you very much.
amit k
[ccp4bb] question about rotation search
Hello, While doing a rotation search with Patterson maps, what is the standard way to find the minimum* and maximum** radius to be used while correlating maps? * to avoid the origin peak ** to avoid inter molecular-vectors Is there a CCP4 tool to give me this if I provide it with a model? If you know a good paper describing a smart way to find these 2 limits automatically, I would be happy to know about it. Thank you, Francois.
[ccp4bb] orthogonal limits of a protein
Hello, Is there a ccp4 tool to find automatically the smallest virtual orthogonal box that contain a given PDB ? Even if your favorite tool is not part of ccp4, I would be happy to know about it. ;) Thanks, Francois.
Re: [ccp4bb] Why Do Phases Dominate?
Hello, I was recently advised to have a look at James Holton's videos to have an idea of the effects of various parameters. http://ucxray.berkeley.edu/~jamesh/movies/ There is a video The importance of Phase: http://ucxray.berkeley.edu/~jamesh/movies/dephase.mpeg This is not an explanation, but a very nice illustration I think. This page has examples in image processing: http://homepages.inf.ed.ac.uk/rbf/HIPR2/fourier.htm The Guidelines for Use section shows an image, and what you get if you do an inverse FFT while ignoring the phases. Regards, Francois. Jacob Keller wrote: Dear Crystallographers, I have seen many demonstrations of the primacy of phase information for determining the outcome of fourier syntheses, but have not been able to understand intuitively why this is so. Amplitudes as numbers presumably carry at least as much information as phases, or perhaps even more, as phases are limited to 360deg, whereas amplitudes can be anything. Does anybody have a good way to understand this? One possible answer is it is the nature of the Fourier Synthesis to emphasize phases. (Which is a pretty unsatisfying answer). But, could there be an alternative summation which emphasizes amplitudes? If so, that might be handy in our field, where we measure amplitudes... Regards, Jacob Keller *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program Dallos Laboratory F. Searle 1-240 2240 Campus Drive Evanston IL 60208 lab: 847.491.2438 cel: 773.608.9185 email: j-kell...@northwestern.edu ***
[ccp4bb] Any simple way to scale 2 MTZ?
Hello, Is there a magic tool doing the job of scaling 2 MTZ to the same scale? For the moment I know with ccp4: rwcontents then wilson then mtzutils with phenix: lsq_scale (in fact I am lying, I was forced to run ccp4's cad before) Is there a simpler way with ccp4? As I am not a crystallographer, I am afraid I can do many different stupid errors when I have to use many tools for just one task. Regards, Francois.
Re: [ccp4bb] Any simple way to scale 2 MTZ?
Graeme Winter wrote: Hi Francois, SCALEIT in CCP4 sounds like the tool you want - this is for scaling e.g. native and derivitive data sets together. You will need to cad together the two files first though. My crystallographer colleague tells me that if we use scaleit there is a risk if there are multiple copies in the ASU. So, we should scale both data sets to absolute scale. This is illustrated in the tutorials here: http://www.ccp4.ac.uk/dist/examples/tutorial/html/heavy-tutorial-mad.html#step_4a Best wishes, Graeme On 12 March 2010 08:17, Francois Berenger beren...@riken.jp wrote: Hello, Is there a magic tool doing the job of scaling 2 MTZ to the same scale? For the moment I know with ccp4: rwcontents then wilson then mtzutils with phenix: lsq_scale (in fact I am lying, I was forced to run ccp4's cad before) Is there a simpler way with ccp4? As I am not a crystallographer, I am afraid I can do many different stupid errors when I have to use many tools for just one task. Regards, Francois.
Re: [ccp4bb] linux question
On 2/27/2010 10:10 PM, David Roberts wrote: I have a quick question about linux for all. Is there anybody running a windows pc with linux on a bootable cd or bootable drive/flash drive/??? that works for crystallography apps? I have a colleague who does molecular dynamics calculations and he needs some conversion programs that are unix based (not pc based - they just haven't been ported and that's not my area). We have linux computers that he can use, but I thought in the end it might be easiest if he could just boot up a linux flash drive to run his conversion, then go back to his pc and windows. Something like damn small linux or ?? Alternatively, he can install some xterm emulator for windows (like putty) then use it to connect to the real linux machines you already have. Any thoughts on this? Thanks Dave
Re: [ccp4bb] status of the UCLA DOE anisoscale server?
James Stroud wrote: This seems to be a temporary condition. The page is back up now. Alternatively, if you put the address in Google (http://www.doe-mbi.ucla.edu/~sawaya/anisoscale/), then you click on the Cached link of the first result, then you will access the page as Google remembers it. In many cases, even if the website is really down you can still access some of its content. Although I'm not part of the IT staff here, I have observed that the UCLA-DOE website is well maintained by several individuals who care deeply and any outages are seldom and short lived. Always check back soon after you notice a problem. Problems with the web infrastructure here are usually fixed minutes after they are discovered or reported. James On Feb 23, 2010, at 9:46 AM, Elizabeth McSweeney wrote: Hello everyone, I am writing to ask if anyone knows what the status us for Dr. Eisenberg's anisotropy server at the DOE? ( http://www.doe-mbi.ucla.edu/~sawaya/anisoscale/ )I have been using this server extensively for weeks, and was surprised to see a page not found messege this morning. Apparently, the website is getting a makeover. Does anyone know if UCLA has moved the server somewhere else? If it will be up and functioning again soon? Any information would be awesome, and I'm sure I am not the only person out there who is affected. Thanks so much! Beth McSweeney
Re: [ccp4bb] Strange problem running cpp4i over nx - job reported as failed even though it succeeds-log file has nx errors
Ethan Merritt wrote: On Thursday 04 February 2010 05:14:24 hari jayaram wrote: [...] The program run with command: /mega/ccp4-6.1.3/ccp4-6.1.3/bin/sortmtz HKLOUT /mega/hj-8-2-1/hjbr5-1/hjbr5-1_sorted_mosflm.mtz has failed with error message ERROR: ld.so: object '/usr/NX/lib/libesddsp.so.0' from LD_PRELOAD cannot be preloaded: ignored. My guess is that your machine configuration includes a file that initializes LD_PRELOAD for NX on login. But it should not do this. The LD_PRELOAD setting applies to all programs, so it should not be set blindly to include program-specific libraries. Unfortunately, some ccp4 configuration files also change PYTHONPATH. And exactly the same could be said: The PYTHONPATH setting applies to all programs, so it should not be set blindly... My personal workaround is to start a new shell, then only in this one source the ccp4 configuration files. But this is just a workaround, I hope it can be solved in future releases of ccp4 (ccp4 could creates a CCP4_PYTHONPATH and use this one instead of using the system-wide one). Regards, Francois.
Re: [ccp4bb] reforigin on 2FKA
Ian Tickle wrote: Francois, the possible non-equivalent alternate origins for F432 are: 1 0. 0. 0. 2 0.2500 0.2500 0.2500 3 0.5000 0.5000 0.5000 4 0.7500 0.7500 0.7500 It correspond to what is found at the end of James Holton's origins.com script http://bl831.als.lbl.gov/~jamesh/pickup/origins.com so I guess it should be correct. He also says how he found them: origins.com snippet # TABLE OF ALLOWED ORIGIN SHIFTS These origin shifts were determined emprirically using 100 randomly-placed atoms that were shifted around with pdbset and checked with SFALL for identical amplitudes to the 0 0 0 origin. They should be correct for the CCP4 convention of symmetry. (I.E. R3 and R32 have hexagonal indexing) /origins.com snippet plus of course the symmetry-equivalent origins generated from these 4 by the space-group centring (F) translations: 0. 0.5000 0.5000 0.5000 0. 0.5000 0.5000 0.5000 0. I can see these in syminfo.lib. However, from what you say, I understand that only 2x3 possible origins with each coordinate being 0 or .5 should be accepted by reforigin. But in my test it accepted all 8 possible combinations of 0 and .5 that I artificially introduced in my translated test PDBs: m...@myps:2fka# grep Frac run.log | sort | uniq Fractional origin shift: 0. 0. 0. Fractional origin shift: 0. 0. 0.5000 Fractional origin shift: 0. 0.5000 0. Fractional origin shift: 0. 0.5000 0.5000 Fractional origin shift: 0.5000 0. 0. Fractional origin shift: 0.5000 0. 0.5000 Fractional origin shift: 0.5000 0.5000 0. Fractional origin shift: 0.5000 0.5000 0.5000 Should I be worried? Thanks, Francois. So there will be 12 in all, which I think include the ones you mentioned. If you're going by http://www.ccp4.ac.uk/dist/html/alternate_origins.html then you should be aware of a very recent BB discussion in which it was pointed out that the entries for F222, F23, F432 and possibly others are incomplete. Eleanor has given me the task of checking correcting this particular documentation, until then don't trust it! Of course you shouldn't trust reforigin either, just as you shouldn't trust any program until you have verified that the results are sensible, but I think in this particular the fault doesn't lie with reforigin. Cheers -- Ian -Original Message- From: owner-ccp...@jiscmail.ac.uk [mailto:owner-ccp...@jiscmail.ac.uk] On Behalf Of Francois Berenger Sent: 27 January 2010 06:50 To: CCP4BB@JISCMAIL.AC.UK Subject: reforigin on 2FKA Hello, I am playing with ccp4's reforigin to verify some MR solutions. If I translate a copy of the pdb.org's PDB 2FKA (from spacegroup F432) by +/-0.5 fractional in any unit cell direction, then reforigin will find back this translation and consider it as valid for this spacegroup. But for this spacegroup I should find only (0,0,0) or (1/2,1/2,1/2) as possible alternate origins. Does this mean that I can't trust reforigin and that I must filter out its results to retain only the valid ones? Thanks, Francois. Disclaimer This communication is confidential and may contain privileged information intended solely for the named addressee(s). It may not be used or disclosed except for the purpose for which it has been sent. If you are not the intended recipient you must not review, use, disclose, copy, distribute or take any action in reliance upon it. If you have received this communication in error, please notify Astex Therapeutics Ltd by emailing i.tic...@astex-therapeutics.com and destroy all copies of the message and any attached documents. Astex Therapeutics Ltd monitors, controls and protects all its messaging traffic in compliance with its corporate email policy. The Company accepts no liability or responsibility for any onward transmission or use of emails and attachments having left the Astex Therapeutics domain. Unless expressly stated, opinions in this message are those of the individual sender and not of Astex Therapeutics Ltd. The recipient should check this email and any attachments for the presence of computer viruses. Astex Therapeutics Ltd accepts no liability for damage caused by any virus transmitted by this email. E-mail is susceptible to data corruption, interception, unauthorized amendment, and tampering, Astex Therapeutics Ltd only send and receive e-mails on the basis that the Company is not liable for any such alteration or any consequences thereof. Astex Therapeutics Ltd., Registered in England at 436 Cambridge Science Park, Cambridge CB4 0QA under number 3751674
[ccp4bb] reforigin on 2FKA
Hello, I am playing with ccp4's reforigin to verify some MR solutions. If I translate a copy of the pdb.org's PDB 2FKA (from spacegroup F432) by +/-0.5 fractional in any unit cell direction, then reforigin will find back this translation and consider it as valid for this spacegroup. But for this spacegroup I should find only (0,0,0) or (1/2,1/2,1/2) as possible alternate origins. Does this mean that I can't trust reforigin and that I must filter out its results to retain only the valid ones? Thanks, Francois.
Re: [ccp4bb] verifying a molecular replacement solution (test case where the true structure is known)
James Holton wrote: Looks like you have already gotten several good suggestions, Many good ones indeed, I tried both csymmatch and origins.com for the moment. This mailing list and all its people is extremely helpful. Thank you very much, Francois. but I also wrote a jiffy program for doing this that does not require the two PDB files to have the same atom names: http://bl831.als.lbl.gov/~jamesh/pickup/origins.com Which you run like this: origins.com right_origin.pdb wrong_origin.pdb P212121 correlate nochains The bottom of the script file contains a list of allowed origin shifts, which are each applied in turn and the resulting symmetry-expanded atom constellations compared. If you use the word correlate on the command line the atoms will be converted to an electron density map using sfall and the correlation coefficient used as the match score. By default, the program breaks up the PDBs into their chains (segids) and searches each one separately. You can turn this off by using the word nochains on the command line. I think emma should give you similar results, but the algorithms are certainly different. -James Holton MAD Scientist Francois Berenger wrote: Hello, 1) In the case I know the true structure (I am verifying I use Phaser correctly), is there a program to do so? Some other questions, if I am to write this program by myself: 2) is there a list somewhere of the translation ambiguities for each spacegroup? For example, in P1 it would say me any translation on any axis is fine. 3) is there a list of permissible origins for each space group? For example, in P212121 it would say me there are 8 possible choices and list them for me. I already know of symop.lib, but I don't think it has some of the information I am looking for. I also know the csymmatch example program of the clipper library, it does part of what I intend to do. Thanks a lot, Francois.
[ccp4bb] verifying a molecular replacement solution (test case where the true structure is known)
Hello, 1) In the case I know the true structure (I am verifying I use Phaser correctly), is there a program to do so? Some other questions, if I am to write this program by myself: 2) is there a list somewhere of the translation ambiguities for each spacegroup? For example, in P1 it would say me any translation on any axis is fine. 3) is there a list of permissible origins for each space group? For example, in P212121 it would say me there are 8 possible choices and list them for me. I already know of symop.lib, but I don't think it has some of the information I am looking for. I also know the csymmatch example program of the clipper library, it does part of what I intend to do. Thanks a lot, Francois.
Re: [ccp4bb] verifying a molecular replacement solution (test case where the true structure is known)
Francois Berenger wrote: Hello, 1) In the case I know the true structure (I am verifying I use Phaser correctly), is there a program to do so? Some other questions, if I am to write this program by myself: 2) is there a list somewhere of the translation ambiguities for each spacegroup? For example, in P1 it would say me any translation on any axis is fine. 3) is there a list of permissible origins for each space group? For example, in P212121 it would say me there are 8 possible choices and list them for me. I already know of symop.lib, but I don't think it has some of the information I am looking for. I also know the csymmatch example program of the clipper library, it does part of what I intend to do. I was advised in a private e-mail to look at phenix.emma: http://www.phenix-online.org/documentation/emma.htm I think it is more powerful than csymmatch, I'll try to use it then. Thanks a lot, Francois.
Re: [ccp4bb] Zalman LCD availability
Hello, By the way, does anyone got this LCD in Japan? My team is interested to know the model's exact reference as well as from where you ordered it. Thanks a lot, Francois.
[ccp4bb] Phaser: removing H in PDB increases the RFZ ?!
Hello, I have 4 molecules. If I use Phaser's AUTO_MR with all default parameters on them, I get the following scores: no_modif remove_H molecule RFZ TFZ RFZ TFZ 16.9 9.6 7.0 9.4 25.2 5.9 5.4 6.2 34.2 4.5 4.7 5.2 44.9 6.8 5.2 6.7 Hence, here are my existential questions, given that I heard many times H is transparent for X-rays: * should I always remove H before running Phaser? * why? Here are a few lines of one of my PDBs containing H, in case it is misinterpreted by Phaser: --- ATOM 6 1H ALA A 1 18.629 -3.443 12.782 1.00 0.00 ATOM 7 2H ALA A 1 18.427 -2.484 13.918 1.00 0.00 ATOM 8 3H ALA A 1 17.496 -2.462 12.742 1.00 0.00 ATOM 9 HA ALA A 1 19.811 -0.866 13.013 1.00 0.00 ATOM 10 1HB ALA A 1 21.071 -1.469 10.982 1.00 0.00 ATOM 11 2HB ALA A 1 21.038 -2.809 12.152 1.00 0.00 ATOM 12 3HB ALA A 1 19.983 -2.852 10.720 1.00 0.00 --- Thanks a lot, Francois.
[ccp4bb] open source project announce: parallel/distributed execution of commands
Hello, In order to process things in parallel I developed a simple tool to run (for the moment) parameter sweep applications. I.e. you want to run many times the same program with only different input parameters. It can be used to parallelize execution on a multi processor machine or even to distribute jobs if you have access to a cluster or at least a few workstations (need to have Python Pyro installed on them then). You can download the project from here: http://savannah.nongnu.org/projects/par/ Here is the help message: --- u...@pc:~# parallel.py -i or -c is mandatory Usage: parallel.py [options] -i | -c ... Execute commands in parallel. [-h | --help] you are currently reading it -c | --client servername read commands from a server instead of a file use -c or -i, not both -i | --input commands_file /dev/stdin for example [-o | --output output_file] log to a file instead of stdout [-p | --post python_module] specify a post processing module (omit the '.py' extension) [-s | --server] accept remote workers [-v | --verbose]enables progress bar [-w | --workers n] number of local worker threads must have n = 0 n == 0 can be useful to only run the server --- I hope it can be useful to other people. Regards, Francois Berenger.
[ccp4bb] combining AutoMR and brute
Hello, Is there any way to search in AutoMR mode but have the translation only being brute forced? Regards, F.
Re: [ccp4bb] combining AutoMR and brute [Phaser]
Sorry, I forgot to mention my previous message concerns using Phaser. Francois Berenger wrote: Hello, Is there any way to search in AutoMR mode but have the translation only being brute forced? Regards, F.
[ccp4bb] regarding coot and loading an MTZ file
Hello, When I run coot in order to read the experimental MTZ corresponding to the PDB I am viewing, I got the following messages (attached is long lines original log): --- command: (refmac-for-phases-and-make-map /home/berenger/usr/xp_1m6t_14122009/1m6t/1m6t-sf-exp.mtz /DERIV_AU/DERIV_AU/FP /DERIV_AU/DERIV_AU/SIGFP) (refmac-for-phases-and-make-map /home/berenger/usr/xp_1m6t_14122009/1m6t/1m6t-sf-exp.mtz /DERIV_AU/DERIV_AU/FP /DERIV_AU/DERIV_AU/SIGFP) (molecule-name0) (calc-phases-generic /home/berenger/usr/xp_1m6t_14122009/1m6t/1m6t-sf-exp.mtz) INFO:: Creating directory coot-refmac (write-pdb-file0 coot-refmac/refmac-for-phases.pdb) got args: pdb-in-filename: coot-refmac/refmac-for-phases.pdb, pdb-out-filename: coot-refmac/refmac-for-phases-tmp.pdb, mtz-in-filename: /home/berenger/usr/xp_1m6t_14122009/1m6t/1m6t-sf-exp.mtz, mtz-out-filename: coot-refmac/refmac-for-phases.mtz, imol-refmac-count: 0, show-diff-map-flag: 1, phase-combine-flag: 0, phib-fom-pair: (), force-n-cycles: 0, f-col: /DERIV_AU/DERIV_AU/FP, sig-f-col: /DERIV_AU/DERIV_AU/SIGFP, r-free-col: () Not Passing LIBIN to refmac LIBIN DEBUG:: refmac-extra-params returns () INFO:: Running refmac with these command line args: (XYZIN coot-refmac/refmac-for-phases.pdb XYZOUT coot-refmac/refmac-for-phases-tmp.pdb HKLIN /home/berenger/usr/xp_1m6t_14122009/1m6t/1m6t-sf-exp.mtz HKLOUT coot-refmac/refmac-for-phases.mtz) INFO:: Running refmac with these data lines: (MAKE HYDROGENS NO NCYCLES 0WEIGHT AUTO LABIN FP=FP SIGFP=SIGFP) environment variable: SYMOP: #f environment variable: ATOMSF: #f environment variable: CLIBD: #f environment variable: CLIB: #f --- I am afraid coot is refining my molecule instead of just displaying the map. Am I right? Thanks a lot, Francois. command: (refmac-for-phases-and-make-map /home/berenger/usr/xp_1m6t_14122009/1m6t/1m6t-sf-exp.mtz /DERIV_AU/DERIV_AU/FP /DERIV_AU/DERIV_AU/SIGFP) (refmac-for-phases-and-make-map /home/berenger/usr/xp_1m6t_14122009/1m6t/1m6t-sf-exp.mtz /DERIV_AU/DERIV_AU/FP /DERIV_AU/DERIV_AU/SIGFP) (molecule-name0) (calc-phases-generic /home/berenger/usr/xp_1m6t_14122009/1m6t/1m6t-sf-exp.mtz) INFO:: Creating directory coot-refmac (write-pdb-file0 coot-refmac/refmac-for-phases.pdb) got args: pdb-in-filename: coot-refmac/refmac-for-phases.pdb, pdb-out-filename: coot-refmac/refmac-for-phases-tmp.pdb, mtz-in-filename: /home/berenger/usr/xp_1m6t_14122009/1m6t/1m6t-sf-exp.mtz, mtz-out-filename: coot-refmac/refmac-for-phases.mtz, imol-refmac-count: 0, show-diff-map-flag: 1, phase-combine-flag: 0, phib-fom-pair: (), force-n-cycles: 0, f-col: /DERIV_AU/DERIV_AU/FP, sig-f-col: /DERIV_AU/DERIV_AU/SIGFP, r-free-col: () Not Passing LIBIN to refmac LIBIN DEBUG:: refmac-extra-params returns () INFO:: Running refmac with these command line args: (XYZIN coot-refmac/refmac-for-phases.pdb XYZOUT coot-refmac/refmac-for-phases-tmp.pdb HKLIN /home/berenger/usr/xp_1m6t_14122009/1m6t/1m6t-sf-exp.mtz HKLOUT coot-refmac/refmac-for-phases.mtz) INFO:: Running refmac with these data lines: (MAKE HYDROGENS NO NCYCLES 0WEIGHT AUTO LABIN FP=FP SIGFP=SIGFP) environment variable: SYMOP: #f environment variable: ATOMSF: #f environment variable: CLIBD: #f environment variable: CLIB: #f
Re: [ccp4bb] regarding coot and loading an MTZ file
Paul Emsley wrote: Francois Berenger wrote: When I run coot in order to read the experimental MTZ corresponding to the PDB I am viewing, [snip] I am afraid coot is refining my molecule instead of just displaying the map. Well, Refmac is - at Coot's request. This usually happens because Coot doesn't detect phases in your MTZ file (i.e. you are using a phasing input file, rather than an output file). Or it could be a bug. Hello Paul, Yes, my MTZ doesn't have phase, it is not supposed to. But, as Bernhard C. Lohkamp just pointed out 3 minutes before on this same mailing list: does the fact that NCYCLES 0 is present means that refmac would just compute a map and not do any refinement of my PDB? From the refmac documentation, and not being a crystallographer (sorry for this fact), it is completely not clear for me. Thanks a lot, Francois.
[ccp4bb] Postdoctoral Position in Computational Structural Biology at RIKEN, Japan
Dear ccp4 users, Postdoctoral Fellow Position in Computational Structural Biology at the Zhang Initiative Research Unit, Advanced Science Institute, RIKEN, Japan We are seeking a highly motivated and experienced computational structural biologist to join the Zhang Initiative Research Unit at RIKEN. The successful candidate will use computational tools to tackle problems in the area of protein folding, structure prediction, crystallographic phasing or drug design. Qualifications: This position requires a PhD in biophysics, biochemistry, chemistry, bioinformatics or structural biology with experience in employing computational tools to solve biological or chemical problems. Experience in protein folding, protein structure prediction, protein structure analysis, protein crystallography or structure-based drug design are highly desired. Proficiency in object-oriented programming and scripting languages are also required. Experience in high performance computing, network computing or grid computing would be a plus. The ideal candidate should possess a track record of accomplishments demonstrating technical proficiency, independent thinking, and scientific creativity. The research environment in the unit is international and English will be used for communication and knowledge of Japanese is not required. Salary and benefits: This is a full-time position with an annual renewable contract. Salary will be commensurate with qualification and experience. Commuting and housing allowance will be provided. Application and required documents: Complete CV (including list of publications) and names and contact information of three references. Contact information: Ms. Hiroko Kani Zhang Initiative Research Unit Advanced Science Institute RIKEN 2-1 Hirosawa, Wako, Saitama 351-0198, Japan E-mail: zhang-unit [at] riken.jp
