Re: [ccp4bb] different Rfactors in different Refmac versions
Garib Murshudov schrieb: What is the version of refmac you arre using. There was a bug and I think we have fixed it. If you take the version from www.ysbl.york.ac.uk/refmac/latest_refmac.html it may give consistent results. Only mac and linux versions are available. For windows version you will need to take from the latest ccp4 version (6.1.2 should have the newer version of refmac also) regards Garib On 20 Oct 2009, at 15:34, Gesa Volkers wrote: Dear Ccp4 Users, I have refined a 2.3 A structure with Refmac in space group I4(1)22. Lately I had to switch from refmac version 5.2.0019 running on a Linux computer to refmac version 6.0.2 on a Windows Vista system. Refmac works fine but I’m a little concerned about the fact that R/Rfree/FOM became really worse from 19.5/25.7/80.0 (older version) to 21.5/27.3/77.1 (newer version) just by changing the refmac version. Also the correlation coefficients became worse. The overall temperature factor was significantly lower. I observed this also with another newer version on a Linux system. I strictly used the same protocol with TLS restrained refinement using Babinet scaling without changing anything in the structure. Are there other restraints for bonds etc. in the different versions leading to such differences? I would like to know what is going on. I would appreciate your help or any hints! Thank you in advance, Gesa -- Thank you, Garib. The old version of refmac which gave good results, was 5.2.0019. The vista version with worst results of the same data was 5.5.0088. Another linux version, which gave worse results than the older linux version was 5.5.0047. Then I will install ccp4 6.1.2 on the vista system and see what happens. Regards, Gesa -- Gesa Volkers Institut für Biochemie, Molekulare Strukturbiologie Felix-Hausdorff-Straße 4 17489 Greifswald 03834/864392
[ccp4bb] AW: [ccp4bb] Colored proteins :)
Cytochrome c Best CSt -Ursprüngliche Nachricht- Von: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] Im Auftrag von Artem Evdokimov Gesendet: Wednesday, October 21, 2009 2:25 AM An: CCP4BB@JISCMAIL.AC.UK Betreff: [ccp4bb] Colored proteins :) Hello CCP4 folks! I have a quick question - could you suggest a few naturally intensely colored proteins? Colors based on small molecule co-factors (i.e. metal ions, flavonoids, etc.) are perfectly fine for my needs :) I already looked into GFP and its relatives, (bacterio)rodopsin, azurins/pseudoazurins, and hemoglobins - but I would appreciate more examples. I am sure there's a nice review out there somewhere but so far I've not found it. Thank you, Artem
Re: [ccp4bb] Colored proteins :)
Have a look at the phycobiliproteins. Best, Tim
Re: [ccp4bb] Two Equally Good MR Solutions Found by Phaser
From the Pattersn peak it seems very likely that you have two molecules in the asymmetric unit seperated by the very vector that seperates your two MR solutions, and both MR solutions are correct? Or is that not possible? Is there no room for 2 molecules in the asymmetric unit, and the Patterson peak isa function of the highly repetitive dimer Eleanor If that is so you need to set the occupancy of any differences in the solution to 0.00 and check from the maps after refinement if you can see which copy of the molecule fits the difference density best - it would nice if you had a TRP/ALA pair of residues or something very distinctive.. Eleanor X Xiong, Cellular Molecular Medicine wrote: Dear Crystallographers, We got a highly repetitive dimeric protein solved by SeMet-SAD in P21 crystal form, and I am now trying to solve a dataset collected from a non-reproducible orthorhombic crystal of the same protein using the structure refined from P21 data. From the Scala statistics, the orthorhombic crystal diffracted to 2.2Å with an I/sigma of 3.1 at outmost shell; 98% complete overall, 89% complete 43.4-7.0Å, 99% complete 2.32-2.2Å, no twinning was detected. Due to the incompleteness at low resolution, it was hard to determine which orthorhombic space group it is in so data was scaled in P222. Very strong pseudo-translational symmetry has been detected by self-Patterson, as shown for reindexed data P21212 (space group later found by Phaser): Order No. Site Height/RmsGrid Fractional coordinates Orthogonal coordinates 111 128.24 0 0 0 0. 0. 0. 0.00 0.00 0.00 2 13 13 57.5160 44 38 0.5000 0.2741 0.5000 44.37 31.88 27.55 322 33.75 0 7 0 0. 0.0414 0. 0.00 4.82 0.00 4 14 14 16.0960 50 38 0.5000 0.3150 0.5000 44.37 36.63 27.55 5 12 12 15.7560 37 38 0.5000 0.2324 0.5000 44.37 27.03 27.55 633 12.28 0 13 0 0. 0.0836 0. 0.00 9.72 0.00 7 1507.0660 57 38 0.5000 0.3574 0.5000 44.37 41.56 27.55 8446.18 0 72 0 0. 0.4503 0. 0.00 52.36 0.00 9995.68 5 0 5 0.0410 0. 0.0683 3.64 0.00 3.76 10555.36 2 20 2 0.0142 0.1254 0.0206 1.26 14.59 1.14 11 11 115.3358 31 38 0.4852 0.1909 0.5000 43.06 22.20 27.55 12663.98 5 0 2 0.0435 0. 0.0286 3.86 0.00 1.58 13773.82 2 27 3 0.0168 0.1659 0.0334 1.49 19.30 1.84 14883.68 0 0 5 0. 0. 0.0722 0.00 0.00 3.98 15 10 103.4160 64 37 0.5000 0.4007 0.4872 44.37 46.59 26.84 Phaser was used to test all possible alternative space groups to find MR solution using the structure from P21 data: # Phaser_P222_MosFLM_all_spacegroup SPACegroup HALL P 2bc 2 #P 2 21 21 SOLU SET RFZ=9.1 TFZ=24.3 PAK=0 LLG=2545 LLG=3718 SOLU 6DIM ENSE ensemble1 EULER 273.0971.162 88.144 FRAC -0.03394 0.50659 -0.22125 SOLU SET RFZ=9.1 TFZ=25.0 PAK=0 LLG=2496 LLG=3622 SOLU 6DIM ENSE ensemble1 EULER 91.4910.850 89.812 FRAC 0.03435 -0.00618 0.00352 and it found 2 solutions with very similar Z-scores and LLG gains, If I am right they are not crystallographic equivalent, and Phaser checks that as well. I reindexed the data to P21212 and Phaser found the same solutions: # Phaser_Reindexed_P21212_2_solutions SPACegroup HALL P 2 2ab #P 21 21 2 SOLU SET RFZ=10.0 TFZ=23.0 PAK=0 LLG=3266 LLG=3718 SOLU 6DIM ENSE ensemble1 EULER 88.843 90.0631.249 FRAC -0.00661 -0.22126 -0.46598 SOLU SET RFZ=9.9 TFZ=23.2 PAK=0 LLG=3178 LLG=3624 SOLU 6DIM ENSE ensemble1 EULER 270.841 89.977 181.339 FRAC -0.50634 -0.00350 0.46533 The difference between the two solutions seems to be that the second solution translated along the longer 21 axis by about ~32Å, I chose the first solution to re-build and refine, and final R/Rfree I got was 21.6%/26.5%. After that, I hope to solve the ambiguity of which MR solution is right by running Phaser again with the complete model (including H2O): # Phaser_Reindexed_P21212_2_solutions SPACegroup HALL P 2 2ab #P 21 21 2 SOLU SET RFZ=12.8 TFZ=28.4 PAK=0 LLG=6542 LLG=7649 SOLU 6DIM ENSE ensemble1 EULER 180.1560.0000.000 FRAC -0.50060 -0.00065 0.49998 SOLU SET RFZ=12.8 TFZ=32.3 PAK=0 LLG=6036 LLG=7059 SOLU 6DIM ENSE ensemble1 EULER 179.201 180.0000.000 FRAC 0.00227 0.22262 -0.50054 It seems that the previous first solution has become the second solution, while the previous second solution became the first. Refmac refinement was performed on both solutions (H2O removed) came out from Phaser, solution 1 R/Rfree = 24.1/28.9 solution 2 R/Rfree = 24.8/28.7 the previous first solution got slightly worse
[ccp4bb] New loop building program: sloop
People keep asking me if buccaneer can build loops. In response to which I usually point them to 'loopy' and 'rapper', both of which do an excellent job. However, I seem to have written a loop building program by accident, and since people have been asking I guess I may as well release it. The origins of this are a library I'm writing for Coot to implement 'O'-style lego-build tools using the Richardson's Top500 protein library as a basis. The same library can also be used for C-alpha-mainchain and possibly chain growing; I also hope to use it for several new jobs in buccaneer. Using the same code for loop fitting (basically incomplete fragment matching) is trivial, and since that is a bit different from the normal approaches it seemed worth a try. It is also blisteringly fast. Is it useful? I don't know, but if you want to give it a try it is pretty simple. Please tell me how you get on. Get it here: http://www.ysbl.york.ac.uk/~cowtan/sloop/sloop.html On a related note, has anyone found sequins (the sequence validation program) to be useful? I know it works on my synthetic problems, but I don't if those cases are actually relevant to the real world. I've had no feedback about it and am looking for ways to reduce my maintenance workload.
Re: [ccp4bb] Colored proteins :)
- E. coli cytochrome b562: the entire culture turns red upon overexpression. - The bilin-binding protein of Pieris brassicae is a blue protein, although its chromophore biliverdin IXgamma only occurs in insects. - The neutrophil gelatinase-associated lipocalin (NGAL) is wine-red if produced in the periplasm of E. coli where it takes up the endogenous siderophore Fe-enterobactin. If you need references, just let me know. Arne Skerra At 5:38 Uhr -0500 21.10.2009, Artem Evdokimov wrote: Hello CCP4 folks! I have a quick question - could you suggest a few naturally intensely colored proteins? Colors based on small molecule co-factors (i.e. metal ions, flavonoids, etc.) are perfectly fine for my needs :) I already looked into GFP and its relatives, (bacterio)rodopsin, azurins/pseudoazurins, and hemoglobins - but I would appreciate more examples. I am sure there's a nice review out there somewhere but so far I've not found it. Thank you, Artem -- Prof. Dr. Arne Skerra ske...@wzw.tum.de Lehrstuhl f. Biologische Chemie Phone: +49 (0)8161 71-4351 Technische Universitaet MuenchenFax: -4352 85350 Freising-Weihenstephan Germany http://www.wzw.tum.de/bc
[ccp4bb] Moving copies to be close to one unit cell.
Dear crystallographers, After solving a structure by molecular replacement I have 16 copies of my protein in the asymetric unit. However in the PDB file they are scattered over several unit cells. I would like to know if there is an easy way or software to move all of the 16 copies close to one unit cell on my PDB file, so that the packing is compact in the PDB file. Thank you very much in advance Regards FX CHAUVIAC -- Mr Francois-Xavier CHAUVIAC PhD Student School of Crystallography, Birkbeck, University of London, Malet Street, Bloomsbury LONDON WC1E 7HX Email: f.chauv...@mail.cryst.bbk.ac.uk Telephone: Office: (0)20-7631-6835 Room B55 Lab:(0)20-7631-6868 Rosalind Franklin Lab
Re: [ccp4bb] Moving copies to be close to one unit cell.
You can do it easily in coot: display your objects. Then display the symmetry (draw, cell symmetry) with a large enough radius. Then File: save symmetry coordinates, click on one atom of one of the equivalent copies you're interested in. You have to repeat the process several times. It can help to draw the cell. HTH, Fred. FRANCOIS XAVIER CHAUVIAC wrote: Dear crystallographers, After solving a structure by molecular replacement I have 16 copies of my protein in the asymetric unit. However in the PDB file they are scattered over several unit cells. I would like to know if there is an easy way or software to move all of the 16 copies close to one unit cell on my PDB file, so that the packing is compact in the PDB file. Thank you very much in advance Regards FX CHAUVIAC
Re: [ccp4bb] Two Equally Good MR Solutions Found by Phaser
Hi All, Thanks for all the replies, I would like to add more information, after reindex it to P21212, the cell parameter is a=88.71, b=116.26, c=55.12, the molecule is a long rod like head to head dimer with a length of 110Å (55Å long for each monomer) and we used the dimer to search the orthorhombic data, two solutions were found as shown in the original thread which can be both refined to almost the same very good R/Rfree, coot was used to generated the symmetry related molecules from both solutions and the two solutions had the same packing but translated along the b axis by 31.9Å, thus clashed into each other and made a mess in the overlap region, so I think they are not crystallographically the same solutions, unless the origin of the cell in P21212 can be placed on b-axis arbitrarily, and I think Phaser will also prune the crystallographically same solutions. Interestingly, the most prominent pseudo-translational peak (1/3 of the origin peak), has a fractional vector 0.5000 0.2741 0.5000, and the fraction on b axis = 0.2741*116.26 = 31.8755Å, and that is exactly how long the two solutions translated along the b-axis, I don't know what that means, does these information verify this is the second case Eleanor suggested? if so should I keep the messy overlapped region and set the rest 0 occupancy to check the density? Thanks for all the suggestions so far! Xiaoli From the Pattersn peak it seems very likely that you have two molecules in the asymmetric unit seperated by the very vector that seperates your two MR solutions, and both MR solutions are correct? Or is that not possible? Is there no room for 2 molecules in the asymmetric unit, and the Patterson peak isa function of the highly repetitive dimer Eleanor If that is so you need to set the occupancy of any differences in the solution to 0.00 and check from the maps after refinement if you can see which copy of the molecule fits the difference density best - it would nice if you had a TRP/ALA pair of residues or something very distinctive.. Eleanor X Xiong, Cellular Molecular Medicine wrote: Dear Crystallographers, We got a highly repetitive dimeric protein solved by SeMet-SAD in P21 crystal form, and I am now trying to solve a dataset collected from a non-reproducible orthorhombic crystal of the same protein using the structure refined from P21 data. From the Scala statistics, the orthorhombic crystal diffracted to 2.2Å with an I/sigma of 3.1 at outmost shell; 98% complete overall, 89% complete 43.4-7.0Å, 99% complete 2.32-2.2Å, no twinning was detected. Due to the incompleteness at low resolution, it was hard to determine which orthorhombic space group it is in so data was scaled in P222. Very strong pseudo-translational symmetry has been detected by self-Patterson, as shown for reindexed data P21212 (space group later found by Phaser): Order No. Site Height/RmsGrid Fractional coordinates Orthogonal coordinates 111 128.24 0 0 0 0. 0. 0. 0.00 0.00 0.00 2 13 13 57.5160 44 38 0.5000 0.2741 0.5000 44.37 31.88 27.55 322 33.75 0 7 0 0. 0.0414 0. 0.00 4.82 0.00 4 14 14 16.0960 50 38 0.5000 0.3150 0.5000 44.37 36.63 27.55 5 12 12 15.7560 37 38 0.5000 0.2324 0.5000 44.37 27.03 27.55 633 12.28 0 13 0 0. 0.0836 0. 0.00 9.72 0.00 7 1507.0660 57 38 0.5000 0.3574 0.5000 44.37 41.56 27.55 8446.18 0 72 0 0. 0.4503 0. 0.00 52.36 0.00 9995.68 5 0 5 0.0410 0. 0.0683 3.64 0.00 3.76 10555.36 2 20 2 0.0142 0.1254 0.0206 1.26 14.59 1.14 11 11 115.3358 31 38 0.4852 0.1909 0.5000 43.06 22.20 27.55 12663.98 5 0 2 0.0435 0. 0.0286 3.86 0.00 1.58 13773.82 2 27 3 0.0168 0.1659 0.0334 1.49 19.30 1.84 14883.68 0 0 5 0. 0. 0.0722 0.00 0.00 3.98 15 10 103.4160 64 37 0.5000 0.4007 0.4872 44.37 46.59 26.84 Phaser was used to test all possible alternative space groups to find MR solution using the structure from P21 data: # Phaser_P222_MosFLM_all_spacegroup SPACegroup HALL P 2bc 2 #P 2 21 21 SOLU SET RFZ=9.1 TFZ=24.3 PAK=0 LLG=2545 LLG=3718 SOLU 6DIM ENSE ensemble1 EULER 273.0971.162 88.144 FRAC -0.03394 0.50659 -0.22125 SOLU SET RFZ=9.1 TFZ=25.0 PAK=0 LLG=2496 LLG=3622 SOLU 6DIM ENSE ensemble1 EULER 91.4910.850 89.812 FRAC 0.03435 -0.00618 0.00352 and it found 2 solutions with very similar Z-scores and LLG gains, If I am right they are not crystallographic equivalent, and Phaser checks that as well. I reindexed the data to P21212 and Phaser found the same solutions: # Phaser_Reindexed_P21212_2_solutions SPACegroup HALL P 2 2ab #P 21 21 2 SOLU SET RFZ=10.0 TFZ=23.0 PAK=0
[ccp4bb] structure validation tools
Hi everybody, I solved my first crystalstructure and now want to publish it. But how do I know the structure is ready for publication and deposition in the pdb. We can explain our theory with the structure but which factors I have to regard to publish nothing wrong or bad. Can anybody tell how many outliers are allowed as long as they are in a well defined density? I found several validation tools in coot, but I would like to be sure on what I have to emphasize. Thank you very much in advance, Katja __ Do You Yahoo!? Sie sind Spam leid? Yahoo! Mail verfügt über einen herausragenden Schutz gegen Massenmails. http://mail.yahoo.com
[ccp4bb] Postdoctoral position available
A post-doctoral position to study cystoskeletal macromolecular assemblies using cryo-electron microscopy is available in the Sosa lab. For this position the ideal candidate will be interested in solving problems related to the structure and function of proteins and will be willing to learn or develop new experimental techniques as needed for the project. Experience in any one of these areas is desirable: Electron Microscopy, Image Analysis, Cellular Light Microscopy, Protein Expression and Purification. In our lab we employ a variety of approaches such as site-directed mutagenesis, cryo-electron microscopy and single molecule fluorescence microscopy to investigate cystoskeletal motors at the molecular level (e. g. see: Tan et al., Structure 16: 1732-9, 2008; Asenjo Sosa PNAS 106: 5657-62, 2009). We have access to state of the art facilities for cryo-em work located at the Albert Einstein College of Medicine and at the New York Structural Biology Center that include several cryo-em microscopes (Tecnai 200, Tecnai G2 F20, JEOL 1230, JEOL 2100F, JEOL 3200FSC). Our laboratory is located in the Albert Einstein College of medicine in New York City, which offers excellent opportunities for scientific interaction within the college and with many other scientific institutions in the New York area. Interested candidates please send a letter (or email), CV and reference names to: Hernando Sosa Dept. of Physiology and Biophysics Albert Einstein College of Medicine 1300 Morris Park Av. Bronx NY 10461 Office: 718-430-3456 Lab: 718-430-3451 FAX: 718-430-8819 Email: hernando.s...@einstein.yu.edu The Albert Einstein College of Medicine is an equal opportunity employer. -- --- Hernando Sosa Dept. of Physiology and Biophysics Albert Einstein College of Medicine 1300 Morris Park Av. Bronx NY 10461 phone (718) 430-3456 FAX (718) 430-8819 email hernando.s...@einstein.yu.edu ---
Re: [ccp4bb] structure validation tools
Dear Katja, I find the Molprobity server very useful. It analyses key factors of your structure like Ramachandran plot, rotamer outliers or clashes and tells you where improvements are necessary. It also ranks your model in respect to other structures in the pdb of similar resolution which gives you some idea how much you still have to work on it. Of course it will stay a bit of a subjective decision when to stop refinement but this may help you make this decision. Good luck, Joerg http://molprobity.biochem.duke.edu/ On 21 Oct 2009, at 14:20, Katja Schleider wrote: Hi everybody, I solved my first crystalstructure and now want to publish it. But how do I know the structure is ready for publication and deposition in the pdb. We can explain our theory with the structure but which factors I have to regard to publish nothing wrong or bad. Can anybody tell how many outliers are allowed as long as they are in a well defined density? I found several validation tools in coot, but I would like to be sure on what I have to emphasize. Thank you very much in advance, Katja __ Do You Yahoo!? Sie sind Spam leid? Yahoo! Mail verfügt über einen herausragenden Schutz gegen Massenmails. http://mail.yahoo.com *** Dr Jörg Standfuss Medical Research Council Laboratory of Molecular Biology Hills Road Cambridge CB2 0QH
Re: [ccp4bb] Colored proteins :)
Some redox proteins from sulfate reducing bacteria are expressed at high levels: Yellow-brownish APS reductase (FAD FeS) Brown Hydrogenase Ferredoxin rubredoxin ... (FeS) Green Sulfite reductase (Siroheme, FeS) Red c-type cytochromes (1 heme, 4 heme, 9 heme or even 16 heme) lots of colours! best guenter Hello CCP4 folks! I have a quick question - could you suggest a few naturally intensely colored proteins? Colors based on small molecule co-factors (i.e. metal ions, flavonoids, etc.) are perfectly fine for my needs :) I already looked into GFP and its relatives, (bacterio)rodopsin, azurins/pseudoazurins, and hemoglobins - but I would appreciate more examples. I am sure there's a nice review out there somewhere but so far I've not found it. Thank you, Artem
[ccp4bb] X-ray diffraction image -- .jpg
Hi everyone, Is there a free utility that can convert an x-ray diffraction image collected with an ADSC detector to a standard image file format e.g. .jpg, png, etc.? I'm looking for something more elegant than a screen-capture that will yield a higher (graphics) resolution image. I'm sure someone must have done this, but I haven't been able to find one. Thanks, Andy Torelli
Re: [ccp4bb] X-ray diffraction image -- .jpg
Hi Andy, If you have a recent CCP4 installation (i.e. 6.something I think) there's diff2jpeg, which does exactly what you want. Otherwise there are also spells to use Mosflm for this which allows a little more control over the greyscale settings. Cheers, Graeme 2009/10/21 Andy Torelli at...@cornell.edu: Hi everyone, Is there a free utility that can convert an x-ray diffraction image collected with an ADSC detector to a standard image file format e.g. .jpg, png, etc.? I'm looking for something more elegant than a screen-capture that will yield a higher (graphics) resolution image. I'm sure someone must have done this, but I haven't been able to find one. Thanks, Andy Torelli
Re: [ccp4bb] Moving copies to be close to one unit cell.
Hello FX, As already mentioned there a number of programs that can perform this task. If you end up deciding to go with Coot, I put together a play by play that should help. http://bit.ly/oHqDW Hope that helps. Sean
Re: [ccp4bb] X-ray diffraction image -- .jpg
Hi Mosflm has done this for years - there's a recipe on the Mosflm FAQ pages (well, the questions were asked frequently when I originally wrote them about 7 or 8 year ago!). Someone called Graeme Winter (now at Diamond) wrote this code originally...) On 21 Oct 2009, at 15:53, Andy Torelli wrote: Hi everyone, Is there a free utility that can convert an x-ray diffraction image collected with an ADSC detector to a standard image file format e.g. .jpg, png, etc.? I'm looking for something more elegant than a screen-capture that will yield a higher (graphics) resolution image. I'm sure someone must have done this, but I haven't been able to find one. Thanks, Andy Torelli Harry -- Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road, Cambridge, CB2 0QH
[ccp4bb] align DNA structures
Hi all, I will highly appreciate your help regarding following: How to align two DNA structures in Pymol or Coot or any other softwares? ( I tried regular align in Pymol, but it doesn't work for DNA; it works great for protein structures.) Thanks a lot in advance ! Mike
Re: [ccp4bb] align DNA structures
Hi Mike, By 'align', if you mean superimposition, lsqman will do the job. Raji --- Raji Edayathumangalam Joint Research Fellow Brigham and Women's Hospital/ Harvard Medical School Brandeis University On Oct 21, 2009, at 11:06 AM, Mike England wrote: Hi all, I will highly appreciate your help regarding following: How to align two DNA structures in Pymol or Coot or any other softwares? ( I tried regular align in Pymol, but it doesn't work for DNA; it works great for protein structures.) Thanks a lot in advance ! Mike
Re: [ccp4bb] Moving copies to be close to one unit cell.
If using Coot, you can also merge molecules on the original and all symmetry related pdb files that you saved, which will automatically renumber the chains for you. Kendall Nettles
Re: [ccp4bb] X-ray diffraction image -- .jpg
Try MarView: http://www.marresearch.com/download.html#Utilities I use the Linux_glibc-2.3.3 (RedHat9, WS3, etc). Just download it, unpack (gunzip marView.gz) # chmod a+x marView a) to run the program from terminal # ./marView or # kate .bashrc: alias marview=/home/user/Desktop/marview/./marView b) alternativelly, place the program in the Desktop and just double-click to start it up. Mauricio On Wed, Oct 21, 2009 at 12:53 PM, Andy Torelli at...@cornell.edu wrote: Hi everyone, Is there a free utility that can convert an x-ray diffraction image collected with an ADSC detector to a standard image file format e.g. .jpg, png, etc.? I'm looking for something more elegant than a screen-capture that will yield a higher (graphics) resolution image. I'm sure someone must have done this, but I haven't been able to find one. Thanks, Andy Torelli
Re: [ccp4bb] X-ray diffraction image -- .jpg
A JPEG has fixed colors for the pixel values. A diffraction image has to use a viewer to convert the pixel values (counts) to a color. One problem with just using a converter to jpeg is how to convert intensities to color (i.e. computer display values). A demo version of d*TREK is freely available. It contains dtdisplay which can display most known diffraction image formats (including Rigaku and ADSC) and allow you to get what you want to see. Then you can use a screen capture. I guess that one should have an option to output a TIFF or JPEG in full-resolution of the detector for use with pixel peeping photo programs like Photoshop. There has not been much demand for such a program, but maybe times have changed. Jim -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Andy Torelli Sent: Wednesday, October 21, 2009 9:53 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] X-ray diffraction image -- .jpg Hi everyone, Is there a free utility that can convert an x-ray diffraction image collected with an ADSC detector to a standard image file format e.g. .jpg, png, etc.? I'm looking for something more elegant than a screen-capture that will yield a higher (graphics) resolution image. I'm sure someone must have done this, but I haven't been able to find one. Thanks, Andy Torelli
Re: [ccp4bb] X-ray diffraction image -- .jpg
Andy, Why not try labelit.png filename output.png [-large]? Labelit is availale at http://cci.lbl.gov/labelit Nick Sauter On 10/21/2009 7:53 AM, Andy Torelli wrote: Hi everyone, Is there a free utility that can convert an x-ray diffraction image collected with an ADSC detector to a standard image file format e.g. .jpg, png, etc.? I'm looking for something more elegant than a screen-capture that will yield a higher (graphics) resolution image. I'm sure someone must have done this, but I haven't been able to find one. Thanks, Andy Torelli
Re: [ccp4bb] align DNA structures
Both pymol/align and coot/ssm (I presume) do the secondary structure alignment first followed by structural alignment. So it only works for proteins. In Pymol, there is fit command that instead matches atoms with the same names; and super which does sequence alignment first. You can try to play with those instead. And of course, coot has the LSQ option where you can specify which residues/nucleotides you would like to match. Some of these options (or all) will do the trick. On Wed, 2009-10-21 at 11:06 -0400, Mike England wrote: Hi all, I will highly appreciate your help regarding following: How to align two DNA structures in Pymol or Coot or any other softwares? ( I tried regular align in Pymol, but it doesn't work for DNA; it works great for protein structures.) Thanks a lot in advance ! Mike --
Re: [ccp4bb] structure validation tools
Hi Katja, a possible option: from main PHENIX GUI select Comprehensive validation. For example, it will do: - all Molprobity checks; - draw POLYGON picture (Acta Cryst. D65, 297-300 (2009) Crystallographic model quality at a glance.); - show all kinds of stereochenistry rmsds; - real-space correlation coefficient computed per residue or atom, and more. Pavel. On 10/21/09 6:20 AM, Katja Schleider wrote: Hi everybody, I solved my first crystalstructure and now want to publish it. But how do I know the structure is ready for publication and deposition in the pdb. We can explain our theory with the structure but which factors I have to regard to publish nothing wrong or bad. Can anybody tell how many outliers are allowed as long as they are in a well defined density? I found several validation tools in coot, but I would like to be sure on what I have to emphasize. Thank you very much in advance, Katja __ Do You Yahoo!? Sie sind Spam leid? Yahoo! Mail verfügt über einen herausragenden Schutz gegen Massenmails. http://mail.yahoo.com
Re: [ccp4bb] align DNA structures
Anna Pyle's group came out with a powerful idea- a simplified set of torsion angles for nucleic acids (NA). http://nar.oxfordjournals.org/content/vol31/issue16/images/small/gkg682f1.gif http://nar.oxfordjournals.org/cgi/content/abstract/31/16/4755 This is implemented in a Perl program, called PRIMOS ( http://www.pylelab.org/software/index.html ), which you use to generate 'worms' corresponding to all the nucleic acid structures in the database that you're working on. You then search with a worm corresponding to the structure of interest. It works very well for RNA, at least, but you have to download the entire NDB yourself and make worms using the PERL scripts (store the worms carefully, you don't want to do this more than once!). A COOT or web (EBI?!) interface would be very welcome, since this process is quite involved. HTH, Mark 2009/10/21 Mike England england@gmail.com: Hi all, I will highly appreciate your help regarding following: How to align two DNA structures in Pymol or Coot or any other softwares? ( I tried regular align in Pymol, but it doesn't work for DNA; it works great for protein structures.) Thanks a lot in advance ! Mike -- Mark Brooks, IBBMC, UMR8619 - Bâtiment 430, Université de Paris-Sud, 91405 Orsay, France. Tel: (33) 169157968 Fax: (33) 169853715 Skype: markabrooks
Re: [ccp4bb] structure validation tools
On Wed, Oct 21, 2009 at 6:20 AM, Katja Schleider katjaschlei...@yahoo.dewrote: I solved my first crystalstructure and now want to publish it. But how do I know the structure is ready for publication and deposition in the pdb. We can explain our theory with the structure but which factors I have to regard to publish nothing wrong or bad. Can anybody tell how many outliers are allowed as long as they are in a well defined density? The Molprobity server suggests the following: 0.2% Ramachandran outliers 98% Ramachandran favored 1% Rotamer outliers 1% of residues with bad bonds 0.5% of residues with bad angles (and the clashscore should be as low as possible.) -Nat
Re: [ccp4bb] Colored proteins :)
ThyX (also known as Flavin Dependent Thymidyalte Synthase, FDTS) is yellow due to bound FAD. -Partha On Tue, Oct 20, 2009 at 5:25 PM, Artem Evdokimov ar...@xtals.org wrote: Hello CCP4 folks! I have a quick question - could you suggest a few naturally intensely colored proteins? Colors based on small molecule co-factors (i.e. metal ions, flavonoids, etc.) are perfectly fine for my needs :) I already looked into GFP and its relatives, (bacterio)rodopsin, azurins/pseudoazurins, and hemoglobins - but I would appreciate more examples. I am sure there's a nice review out there somewhere but so far I've not found it. Thank you, Artem
Re: [ccp4bb] X-ray diffraction image -- .jpg
Believe it or not, you can do this with ImageMagick, which is already part of most linux distros: convert -depth 16 -type Grayscale -colorspace GRAY -endian LSB -size 3072x3072+512 \ GRAY:test_0_001.img test_0_001.jpg where this example turns a binned Q315 image (3072x3072 pixels) with a 512-byte header (almost always the case) that has BYTE_ORDER=little_endian into a jpg image. For a big_endian image, you change LSB to HSB in the above command. You may notice that the image above compresses incredibly well (about 300 fold), but if you look at it, you will be very disappointed as it is almost totally black. This is because JPEG only uses the high-order byte of a 16-bit image. One could argue that this is perhaps the right way to look at diffraction patterns since the most important information is in the bright spots and not the noisy background, but if you want to render your *.img file in the ADXV way, then this command is close: convert -depth 16 -type Grayscale -colorspace GRAY -endian LSB -size 3072x3072+512 \ GRAY:test_0_001.img -negate -crop 1024x1024+512+512 -equalize test_0_001.jpg The -negate flag will make the spots black and the background grey, and the -equalize filter will throw out all the outlier pixels (spots) so you can look at the background. You may also want to use the -crop option to focus in on just one part of the image. There are other enhancement flags like -normalize, and -contrast-stretch or -brightness and -contrast, but the exact behavior of these flags will depend on the version of ImageMagick you have. There is probably also a way to colorize the data the way ADXV does with the heat or rainbow options, but I don't know how to do that in ImageMagick. In such cases, I do use screen capture, but again ImageMagick's import program is convenient for this. Coupled with the -autoload flag in ADXV, you can set the environment variable $XFORMSTATUSFILE to something like ./temp.txt and write a script to echo $n $filename into this file (where $n is an ever-increasing number), wait a few seconds (sleep 2), and then run import -w root -crop ... to capture the screen and crop out the part you want. This will work for the formats supported by ADXV, but obviously other formats will need another program. The central problem is that every program (ADXV, MOSFLM, HKL, D*trek, etc.) has different ways of crushing the 16-bit pixels into 8 bits for the display, and we all have our favorite (the one that we think makes weak spots show up better), but almost none of the GUI displays have command-line-with-options equivalents. ImageMagick has enough features that you can usually figure out how to replicate a given display program's algorithm, but some file formats (like the packed Mar files) will never be readable by ImageMagick. It is perhaps worth pointing out that the ADSC format is actually called SMV since this file format was originally created about 30 years ago for a program called Super Marty View, (written by Martin Stanton, now at SomaLogic). It has evolved somewhat since then. The taxonomy of image file formats is something of a hobby of mine. There seems to be no less than a hundred different species of them floating around in the world. Some are rare, some are locally prevalent, but they appear to all be highly territorial and you will almost never find more than one varietal populating a given lab, synchrotron or even a given country. Someday I hope to collect specimens of each and every one of them (perhaps even filling out the fossil record or history of different beamlines and detectors) but documentation and particularly example lysozyme datasets are surprisingly hard to come by. For example, I once had a crinkly old paper document that defined the R-axis format, but recent sitings of files from R-axis detectors seem to be a new species descended from an SMV-like ancestor, and yet nowhere on the Rigaku website is there a document describing this new format, much less an example. Most crystallographers do not have good data sets on hand (it is the bad ones that stay on disk forever), and many beamline scientists do not have any test data sets available either (for some reason). Currently, my meager museum is here: http://bl831.als.lbl.gov/example_data_sets/ If anyone would care to donate, I prefer data sets that are easy to process and that have anomalous differences (to clarify the hand of the spindle), but in cases where I have no examples, any data set will do. -James Holton MAD Scientist Andy Torelli wrote: Hi everyone, Is there a free utility that can convert an x-ray diffraction image collected with an ADSC detector to a standard image file format e.g. .jpg, png, etc.? I'm looking for something more elegant than a screen-capture that will yield a higher (graphics) resolution image. I'm sure someone must have done this, but I haven't been able to find one. Thanks,
[ccp4bb] Forcing same origin on different MR solutions
Dear crystallographers, I try to solve a MR problem in P21 with several different structures (and one EM map) as search models. I would like all solutions to have the same origin so I could compare them and see their relative positions. I think a possible solution is to bring the center of mass of all models (and map) to the same point. Is there another, easier, solution ? is there a way, already after molecular replacement, to bring all solutions to the same origin ? Thank you for your time, Peter
Re: [ccp4bb] Forcing same origin on different MR solutions
There is a program in the CCP4 Suite called reforigin, which might be what you want. Since all origins are equivalent, there is no way a-priori to force an MR program to always use the same origin, all you can do is compare to a reference. However, a trick you can play on such programs (that use RMSD as a score) is to make a reference PDB file with all atom coordinates at 0,0,0, or 0,1.0,2.0 (or perhaps the middle of the unit cell). This will origin-shift your MR solution to be as close as possible to that point. Clearly, there are ways for this to go wrong if your molecule is oriented just so but as long as you are careful you should be okay. The best thing is to have a reference.pdb, and the top-scoring MR solution will often do. Independent of reforigin, I also wrote a jiffy to do this: http://bl831.als.lbl.gov/~jamesh/pickup/origins.com You run it like this: origins.com P21 reference.pdb mr_out.pdb correlate where correlate means to use calculated map correlations instead of rmsd between atoms as the score for alignment. This is slower, but good for files that have no atom names in common (like heavy atom site constellations). If you make a PDB file of grid points in your EM map, then the correlate option above should work for aligning your EM map result to a PDB file. -James Holton MAD Scientist Peter Grey wrote: Dear crystallographers, I try to solve a MR problem in P21 with several different structures (and one EM map) as search models. I would like all solutions to have the same origin so I could compare them and see their relative positions. I think a possible solution is to bring the center of mass of all models (and map) to the same point. Is there another, easier, solution ? is there a way, already after molecular replacement, to bring all solutions to the same origin ? Thank you for your time, Peter
[ccp4bb] Dear friend!
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[ccp4bb] 9 ESR (PhD) and 4 ER (Post-doctoral) positions in cellular and structural biology
Marie Curie Initial Training Network on *Muscle Z-disk Protein Complexes: from atomic structure to physiological function (ITN MUZIC) *offers** 9 ESR (PhD) and 4 ER (Post-doctoral) positions in cellular and structural biology All partners of except for Stockholm offer ESR positions, Leeds, Stockholm, Vienna and Hamburg offer also ER positions. *ITN MUZIC**, *funded by the European Commission is filling 9 Doctoral and 4 Postdoctoral positions at 8 Universities/Research Institutions in 6 European countries (from November 2009 on until all positions are filled). The ITN MUZIC research programme is organised in four work packages (WP): • Atomic structure of filamin, telethonin and alpha–actinin in the Z-disk - WP1 • Z-disk Ultrastructure and Molecular Architecture of Its Complexes - WP2 • Dynamic changes of the Z-disk interactome - WP3 • Signalling pathways regulating Z-disk development and remodelling - WP4 The partners of ITN MUZIC are dedicated to producing the next generation of research scholars working in the interdisciplinary field of cellular structural biology. ESR and ER’s individual projects will be integrated into one comprehensive research and training network. In order to train Cellular Structural Biologists profile they will be offered an innovative training in a unique combination of scientific methods that span from biophysical characterisation of proteins and their complexes, high resolution (X-ray crystallography) and low resolution structural biology methods (SAXS, EM, cryo-EM tomography, atomic force microscopy) to a variety of cell biology oriented techniques, ranging from FRET and live-cell imaging, cellular and animal models to animal physiology. The network is strongly based on the exchange and transfers of knowledge between participating institutions and will provide its fellows with network-wide training activities (workshops, summer schools, scientific symposium) and training-in-collaborations (working visits and secondments). ITN MUZIC partners and their fields of research: 1. *Kristina Djinovic Carugo* (Coordinator, Univ. Vienna, Austria) – Structural Biology of Z-Disk with focus on the a-actinin interactome (WP1, WP2); to apply send application to mu...@univie.ac.at, for more information contact kristina.djino...@univie.ac.at 2. *Dieter Fürst* (Univ. Bonn, Germany) – Cell Biology of Z-Disk with focus on protein localization, dynamics and interactions in living cells (WP3, WP4); to apply send application to zellbiolo...@uni-bonn.de, for more information contact dfue...@uni-bonn.de@univie.ac.at 3. *Stefano Schiaffino and Gerolamo Lanfranchi* (Univ. Padova, Italy) - Cell Biology of Z-Disk with focus on signalling pathways involved in mechanical stimuli and on functional genomic analysis of muscle cell silencing (WP4); to apply send application to stefano.schiaff...@unipd.it or gerolamo.lanfran...@unipd.it, for more information contact stefano.schiaff...@unipd.it or gerolamo.lanfran...@unipd.it 4. *Matthias Wilmanns* (EMBL-Hamburg, Germany) - Structural Biology of Z-Disk with focus on the titin interactome(WP1, WP2); to apply send application wilma...@embl-hamburg.de, for more information contact wilma...@embl-hamburg.de 5. *Jari Ylänne* (Univ. Jyväskylä, Finland) – Structural and Cell Biology of Z-Disk with focus on intra-subunit interactions in filamin (WP1, WP2, WP3); to apply send application contact jyla...@bytl.jyu.fi, for more information contact jyla...@bytl.jyu.fi 6. *John Trinick* (Univ. Leeds, UK) - Structural Biology of Z-Disk with focus on the Z-disk ultrastructure (WP2); to apply send application to j.trin...@leeds.ac.uk, for more information contact j.trin...@leeds.ac.uk 7. * Mathias Gautel* (King’s College London, UK) – Cell Biology of Z-Disk with focus on regulation of Z-disk protein interactions by phosphorylation (WP2, WP3, WP4); to apply send application to mathias.gau...@kcl.ac.uk, for more information contact mathias.gau...@kcl.ac.uk 8. *Matthias Rief* (Technical University Muenchen, Germany) – Structural Biology of Z-Disk with focus on biomechanical properties of filamin (WP1, WP2); to apply send application to mr...@ph.tum.de, for more information contact mr...@ph.tum.de 9. *Evitra AB* (Stockholm, Sweden) – Protein production (WP1, WP2); to apply send application to marina.sa...@ki.se, for more information contact marina.sa...@ki.se or par.nordl...@ki.se *Early Stage Researchers* Must be in the first 4 years (full-time equivalent) of research career since gaining a university diploma giving access to doctoral studies. • The length of individual appointment will be limited to between 3 and 36 months. • The basic gross living allowance for the Early Stage Researcher Fellowships is up to about 33.800 €/year mobility allowance + travel allowance + career exploratory allowance *Experienced Researchers* • Must either be in possession of a doctoral degree or have at least 4 years
[ccp4bb] [off topic] another network
Sorry if this is a bit off topic. But I have found it useful. Members of the ccp4bb might be interested in the biomedexperts network ( www.biomedexperts.com ). Once you join (as professionals of biomed science who have already published) you have a homepage that gives you recent publications of your pairs. They send you a short e-mail message every fortnight or so to inform you of recent publications in your field. Following the links, you can consult the abstracts of the relevant publications. This is all free (they haven't charged me anything). Here, with the disappearance of the libraries, I am finding this very useful. Hope it will be useful to members of the bb too. Fred.
Re: [ccp4bb] [off topic] another network
Hello Fred, Thanks for sharing! I have also been looking for ways to keep up on literature. This weekend, I combined 17 structural journals into a single RSS feed using yahoo pipes. I did a short post about it here: http://tinyurl.com/yhp2xlm I would be curious if others have any tips or tricks that they have been using, thanks. Sean
[ccp4bb] multi domain protein
hello i have 3.25 A data of multidomain protein with 4 individual domain .one domains structure is already known . and for others domain 40 % simmilar structure is known . when i am running phaser with one known domain i am getting the solution but after getting solution i am serching other domains but clashes are coming . how should i proceed . thanx
[ccp4bb] thank you and a summary
Dear ccp4bb crowd, Thank you for the wealth of useful replies to my request! I've received over 100 messages with suggestions! A crude summary of replies is presented below (I've added PDB ID to most of these). Overwhelmingly, the preferences tended towards iron-loaded proteins (red or brown) and copper-loaded proteins (blue) as well as proteins carrying specialized ligands used to harvest light. An equally abundant group of suggestions concerned enzymes loaded with brightly colored organic cofactors (PLP, flavonoids, etc.) The most popular suggestion was cytochrome(s) closely followed by redox copper proteins. The most memorable (at least to me!) suggestion was ranasmurfin - a blue protein from floating foam nests made by tree frogs. It's good to know that sense of humor is alive and well in the sciences. The smallest brightly colored protein that I could identify so far seems to be rubredoxin (52aa) which also happens to be one of the top 1% highest-resolution protein structures in the PDB (at least by my count). The list below has been pruned for obvious replicates. Again, thank you - this has been extremely useful! Artem B. stearothermophilus Mn Superoxide Dismutase - nice purple brown color ThyX (Flavin Dependent Thymidyalte Synthase, FDTS) is yellow due to bound FAD azurin, plastocyanin, CueO (1kv7), ascorbate oxidase, ceruloplasmin HemS from Y.enterocolitica (2j0p, 2j0r) and Shp from S.pyogenes (2q7a) (whole culture turns reddish) Quinone reductase Nqo2 - flavoenzyme, bright yellow (3fw1) APS reductase (FAD FeS) - yellow/brown (2goy), rubredoxin (FeS) - brown (2v3b), Sulfite reductase (Siroheme, FeS) - green (1aop), cytochromes c - red. D. vulgaris flavodoxin - purple (reduced) yellow (oxidized) (1bu5) rubredoxin - dark red Crustacyanin - blue red (1s44) Ranasmurfin - smurfin' blue (2vh3) Peptide deformylase - red (3e3u), diaminopimelate decarboxylase (2qgh), alanine racemase (2vd8) - yellow E.coli cytochrome b562 - red (256b), Insect bilin-binding protein (1bbp) - blue, gelatinase-associated lipocalin - red (with siderophore from E. coli, 1L6M) MICAL from drosophila (2bry) - yellow Auracyanin (2aan, 1ov8), stellacyanin (1jer), umecyanin (1x9r), plastocyanin (1ag6), cucumber basic protein (2cbp) - blue Phycocyanin (3brp), crystacyanin, rusticyanin (1a3z), insecticyanin (lipocalin, binds biliverdin 1z24) - blue, carotenoid-binding proteins - red, light-harvesting proteins - red, green, or blue Glucose oxidase - yellow (1cf3) dihydroorotate dehydrogenase - yellow (1f76) catalase (1tgu) - brown phycobiliproteins (phycocyanin, allophycocyanin, phycoerythrin)- red or blue or cyan cytochrome c - red/brown (1GWS) light harvesting complexes from purple bacteria - purple (2fkW) myoglobin, haemoglobin - brown/red, hemocyanin (1hc1) - blue FMO protein (3eoj) - green Peridinin-chlorophyll protein (1ppr) - green Methylamine dehydrogenase (2gc7) - yellow 'old yellow' - yellow (1oya) Bacterioferritin (1bfr) or ferritin - brown LHC-II from plants - green Indoleamine 2,3-dioxygenase (2d0t) - red Cytochrome b5 (1cyo) - red Cytochrome bc1 complex () - red/orange Phosphotriesterase-like protein from D. radiodurans (3gtf) - pink or purple Nitrosocyanin (1iby) - red
