Re: [ccp4bb] pymol help
Is there an option to include a small inset in the corner with a structure diagram? CPK colors do not always work well when obscured by e.d. mesh. Artem -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Yanming Zhang Sent: Monday, October 29, 2007 1:36 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] pymol help Hi, all, I want to make a pymol figure wich can show the pretty density of a ligand. But we don't want to show the detailed chemical info of the ligand. If I use a large enough sphere_scale for the ligand, the chemical info will be hidden but the density map will be disrupted. If I use a smaller sphere_scale, the density looks great but the chemical info of the ligand will be visible. How should I overcome this dilemma? Thank you very much for your help. Yanming
Re: [ccp4bb] Is phophorylation possible in E. coli expression system?
Hi, Elongation factor Tu was one of the first E. coli proteins that was identified as being phosphorylated given certain conditions (early 90s). What I find interesting is the fact that EF-Tu becomes hyperphosphorylated if the cells grow at 20 degrees. Maybe this is also true for other proteins that are abundantly expressed Did you reduce the _expression_ temperature from 37 to 20 degrees? J. El-Fahmawi B, Owttrim GW. Related Articles, Links Cold-stress-altered phosphorylation of EF-Tu in the cyanobacterium Anabaena sp. strain PCC 7120. Can J Microbiol. 2007 May;53(5):551-8. Lippmann C, Lindschau C, Vijgenboom E, Schroder W, Bosch L, Erdmann VA. Related Articles, Links Prokaryotic elongation factor Tu is phosphorylated in vivo. J Biol Chem. 1993 Jan 5;268(1):601-7. Alexander C, Bilgin N, Lindschau C, Mesters JR, Kraal B, Hilgenfeld R, Erdmann VA, Lippmann C. Related Articles, Links Phosphorylation of elongation factor Tu prevents ternary complex formation. J Biol Chem. 1995 Jun 16;270(24):14541-7. -- Jeroen Raymundus Mesters, Ph.D. Institut fuer Biochemie, Universitaet zu Luebeck Zentrum fuer Medizinische Struktur und Zellbiologie Ratzeburger Allee 160, D-23538 Luebeck Tel: +49-451-5004070, Fax: +49-451-5004068 E-mail: [EMAIL PROTECTED] Http://www.biochem.uni-luebeck.de Http://www.iobcr.org Http://www.opticryst.org -- If you can look into the seeds of time and say which grain will grow and which will not - speak then to me (Macbeth) --
Re: [ccp4bb] pymol help
Hi Yangming, If you change the HETATM records of the ligand to ATOM records in the PDB file, you can replace the spheres for a surface representation, for which you can set the transparancy to make it less visible, that might help. Flip -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Yanming Zhang Sent: Monday, October 29, 2007 6:36 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] pymol help Hi, all, I want to make a pymol figure wich can show the pretty density of a ligand. But we don't want to show the detailed chemical info of the ligand. If I use a large enough sphere_scale for the ligand, the chemical info will be hidden but the density map will be disrupted. If I use a smaller sphere_scale, the density looks great but the chemical info of the ligand will be visible. How should I overcome this dilemma? Thank you very much for your help. Yanming
[ccp4bb] Workshop Announcement - X-ray Radiation Damage to Biological Crystalline Samples
The Fifth International Workshop on X-ray Radiation Damage to Biological Crystalline Samples will be held at the Swiss Light Source from 13:00 March 3rd to 13:00 March 5th 2008. This series of workshops was originally concerned with the effects of radiation damage during investigation of protein structures by X-ray crystallography. Other techniques of structural biology are now being included to ensure greater information exchange. The workshop will therefore be of interest to all those using ionising radiation to examine biological structures at the molecular and cellular level. Topics under discussion will include: 1. Progress in the understanding of radiation damage in PX 2. Reducing or mitigating radiation damage 3. Correcting for the effects of radiation damage 4. Spectroscopies for studying radiation damage processes 5. Radiation damage in EM and EC 6. Radiation damage in XAS, SAXS and X-ray microscopy 7. Radiation chemistry and radiolysis of biological molecules The organizers are Clemens Schulze-Briese, Elspeth Garman, Colin Nave, Sean McSweeney, Raimond Ravelli, Gerd Rosenbaum and Soichi Wakatsuki. Anyone who would like to participate should e-mail Elspeth Garman ([EMAIL PROTECTED]) who will forward further information to interested parties once it is available. - Dr. Elspeth F. Garman, Reader in Molecular Biophysics, Department of Biochemistry, Rex Richards Building, University of Oxford, Tel: (44)-1865-275398 South Parks Road, FAX: (44)-1865-275182 OXFORD, OX1 3QU, U.K. E-mail: [EMAIL PROTECTED] - DIVFONT size=1 color=grayThis e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom /FONT/DIV
Re: [ccp4bb] pymol help
Dear Yanming, To show pretty density of a model you have to import a ccp4 density map and display it around your ligand. The simplest solution is using ccp4 and tick the box Generate weighted difference maps files in CCP4 format when running Refmac5 (one or two cycles are enough). Specify names for FWT and DelFwt maps and rename the maps afterwards to *.ccp4. This renamed map (e.g. fwt.ccp4) can be opened in pymol. To show density around our ligand you can use the following command: isomesh map, name_of_fwtmap, 1.0, ligand, carve=1.8 (map = greats an object name map, name_of_fwtmap = name of your map, 1.0 = Sigma level, carve=1.8 = width map is displayed around your ligand This will allow you to show a pretty electron density map around your ligand without any chemical info of the ligand. Stefan Schmelz Yanming Zhang wrote: Hi, all, I want to make a pymol figure wich can show the pretty density of a ligand. But we don't want to show the detailed chemical info of the ligand. If I use a large enough sphere_scale for the ligand, the chemical info will be hidden but the density map will be disrupted. If I use a smaller sphere_scale, the density looks great but the chemical info of the ligand will be visible. How should I overcome this dilemma? Thank you very much for your help. Yanming
[ccp4bb] carving up maps (was re: pymol help)
I'd be curious to know if there is any consensus in the community with using the carve command for showing maps. I have never felt comfortable showing density within a cutoff radius of a particular residue or--even worse--a ligand, and felt the figures should display the extraneous bits as well. The burden was on the crystallographer to find an appropriate view (slab, sigma, etc...) to display the map. The Bobscript manual appears to agree with me on this one as it states: http://www.strubi.ox.ac.uk/bobscript/doc24.html If your density is good then you will just have density over residue 999, but if things are not so hot then you may want to cheat and just draw the bits of density near to the selected atoms. Just curious, Andy -- Andrew M. Gulick, Ph.D. --- (716) 898-8619 Hauptman-Woodward Institute 700 Ellicott St Buffalo, NY 14203 --- Senior Research Scientist Hauptman-Woodward Institute Assistant Professor Dept. of Structural Biology, SUNY at Buffalo http://www.hwi.buffalo.edu/Faculty/Gulick/Gulick.html http://labs.hwi.buffalo.edu/gulick On 10/29/07 4:40 AM, Stefan Schmelz [EMAIL PROTECTED] wrote: Dear Yanming, To show pretty density of a model you have to import a ccp4 density map and display it around your ligand. The simplest solution is using ccp4 and tick the box Generate weighted difference maps files in CCP4 format when running Refmac5 (one or two cycles are enough). Specify names for FWT and DelFwt maps and rename the maps afterwards to *.ccp4. This renamed map (e.g. fwt.ccp4) can be opened in pymol. To show density around our ligand you can use the following command: isomesh map, name_of_fwtmap, 1.0, ligand, carve=1.8 (map = greats an object name map, name_of_fwtmap = name of your map, 1.0 = Sigma level, carve=1.8 = width map is displayed around your ligand This will allow you to show a pretty electron density map around your ligand without any chemical info of the ligand. Stefan Schmelz Yanming Zhang wrote: Hi, all, I want to make a pymol figure wich can show the pretty density of a ligand. But we don't want to show the detailed chemical info of the ligand. If I use a large enough sphere_scale for the ligand, the chemical info will be hidden but the density map will be disrupted. If I use a smaller sphere_scale, the density looks great but the chemical info of the ligand will be visible. How should I overcome this dilemma? Thank you very much for your help. Yanming
Re: [ccp4bb] pymol help
Dear all, Sorry I did not make it clear in my first email. Now my question can boil down to: IS IT POSSIBLE TO ONLY ZOOM ONE OBJECT AND KEEP ALL THE OTHER OBJECTS UN-ZOOMED IN PYMOL? thanks Yanming On Mon, 29 Oct 2007, Yanming Zhang wrote: Hi, all, I want to make a pymol figure wich can show the pretty density of a ligand. But we don't want to show the detailed chemical info of the ligand. If I use a large enough sphere_scale for the ligand, the chemical info will be hidden but the density map will be disrupted. If I use a smaller sphere_scale, the density looks great but the chemical info of the ligand will be visible. How should I overcome this dilemma? Thank you very much for your help. Yanming
Re: [ccp4bb] Cost-effective imaging systems: recommendations and opinions requested
Dear Rebecca, a good microscope is very difficult to beat. The reason for this is the larger numerical aperture (= the maximum cone of light that can enter the lens) when compared to long and small-diameter tubes with a camera on top. The resolution of the camera is less important here and it does not compensate for poor optics. What is most important is a proper illumination of the sample! To the best of my knowledge and I am sure I have forgotten a few, a listing of all more or less simple, medium throughput (without plate-hotel), not so expensive, imagers: Crystal Pro Minstrel 1 Rockimager 1 Crystal Monitor CrysCam The best thing is to go and test these yourself with your favorite plate and a difficult protein a specifically selected 96-well plate with lysozyme crystals always look great in almost any imager. Nevertheless, the crystal pictures in brochures of some companies already reveal problems with the illumination as a clear dark ring is visible at the rim of the image... Good luck. J. *R. Page wrote: * * From:* CCP4 bulletin board [mailto:[EMAIL PROTECTED] *On Behalf Of *Page, Rebecca *Sent:* Friday, October 26, 2007 6:10 PM *To:* CCP4BB@JISCMAIL.AC.UK *Subject:* [ccp4bb] Cost-effective imaging systems: recommendations and opinions requested Dear CCP4 community, I know this question has been posted before, but imaging systems are updated so often that I’d like to post it again. I am considering purchasing *a crystal imaging system*. I am looking for a system that is 1) cost-effective 2) straightforward to use 3) suitable for a low-medium throughput (2-4 academic laboratories; with primary use by graduate students) 4) nice clear crystals images I am interested in all systems, but I’d be especially interested to know how people feel about the ArtRobbins CrysCam, including its pros and cons and if there are any other comparable systems available for a similar price. If you have an imaging system you are especially fond of (or regret buying), any information that you can provide about that system is very welcome as well, as is any information about the associated software. I’ll compile and re-post all comments and opinions for everyone else who might find this information useful. Thanks very much in advance, Rebecca Rebecca Page Brown University -- Jeroen Raymundus Mesters, Ph.D. Institut fuer Biochemie, Universitaet zu Luebeck Zentrum fuer Medizinische Struktur und Zellbiologie Ratzeburger Allee 160, D-23538 Luebeck Tel: +49-451-5004070, Fax: +49-451-5004068 E-mail: [EMAIL PROTECTED] Http://www.biochem.uni-luebeck.de Http://www.iobcr.org Http://www.opticryst.org -- If you can look into the seeds of time and say which grain will grow and which will not - speak then to me (Macbeth) --
Re: [ccp4bb] Cost-effective imaging systems: recommendations and opinions requested
Just my two cents with a bit of a delay ... 1. I have tried the 'cheap' solution and simply lost not so much money since it was damped to the junk yard at the end. We now have an 'expensive' solution (Crystal Farm) but - guess what - it works. Our cheap solution was the BioTom robot, from a company that - not shockingly - is bankrupt. Some of the machines they built had better fates. I have not checked current 'cheap' solutions for a while though and this is by no means a critique of any existing systems. But, still, as far as I know capitalism won and you get what you pay for. 2. The best thing about an automated imager is that, unlike me or my group members, it is as happy to take pictures at 03:00 in the morning as at 11:00 or 15:30. The thing that makes that possible is the hotel. As said below a good microscope is difficult to beat. The automated imager beats it for the reason it can take pictures at various times. You see in day 2 a thing that could be dust or crystal ? You look at 'time 0' and 'day 0.5' and see if it was there or not. yes, the images are not as good as your old Leica/Olympus and your eyes and hands scanning, but the *hotel* attached to it that makes it possible to take many images, beats that. For an imager I would choose one that: 1. Takes good images for my usual trays 2. Has a hotel that allows my plates to stay there for a month or so and good scheduling (we use 0, 6 hrs, 12 hrs, 24, hrs, 2 days 7 days, 2 weeks I think) 3. Comes with a good DB and software for viewing, or even better it is supported in PiMS ;-) (coming soon!) 4. Make sure the hotel is either thermostated or that my crystallization room will not suffer from the extra machine(s) inside. There are quite a few solutions that meet these criteria out there and I would not be shocked if some cheaper ones work fine. A. On Oct 29, 2007, at 9:52, mesters wrote: Dear Rebecca, a good microscope is very difficult to beat. The reason for this is the larger numerical aperture (= the maximum cone of light that can enter the lens) when compared to long and small-diameter tubes with a camera on top. The resolution of the camera is less important here and it does not compensate for poor optics. What is most important is a proper illumination of the sample! To the best of my knowledge and I am sure I have forgotten a few, a listing of all more or less simple, medium throughput (without plate-hotel), not so expensive, imagers: Crystal Pro Minstrel 1 Rockimager 1 Crystal Monitor CrysCam The best thing is to go and test these yourself with your favorite plate and a difficult protein a specifically selected 96-well plate with lysozyme crystals always look great in almost any imager. Nevertheless, the crystal pictures in brochures of some companies already reveal problems with the illumination as a clear dark ring is visible at the rim of the image... Good luck. J. *R. Page wrote: * * From:* CCP4 bulletin board [mailto:[EMAIL PROTECTED] *On Behalf Of *Page, Rebecca *Sent:* Friday, October 26, 2007 6:10 PM *To:* CCP4BB@JISCMAIL.AC.UK *Subject:* [ccp4bb] Cost-effective imaging systems: recommendations and opinions requested Dear CCP4 community, I know this question has been posted before, but imaging systems are updated so often that I’d like to post it again. I am considering purchasing *a crystal imaging system*. I am looking for a system that is 1) cost-effective 2) straightforward to use 3) suitable for a low-medium throughput (2-4 academic laboratories; with primary use by graduate students) 4) nice clear crystals images I am interested in all systems, but I’d be especially interested to know how people feel about the ArtRobbins CrysCam, including its pros and cons and if there are any other comparable systems available for a similar price. If you have an imaging system you are especially fond of (or regret buying), any information that you can provide about that system is very welcome as well, as is any information about the associated software. I’ll compile and re-post all comments and opinions for everyone else who might find this information useful. Thanks very much in advance, Rebecca Rebecca Page Brown University -- Jeroen Raymundus Mesters, Ph.D. Institut fuer Biochemie, Universitaet zu Luebeck Zentrum fuer Medizinische Struktur und Zellbiologie Ratzeburger Allee 160, D-23538 Luebeck Tel: +49-451-5004070, Fax: +49-451-5004068 E-mail: [EMAIL PROTECTED] Http://www.biochem.uni-luebeck.de Http://www.iobcr.org Http://www.opticryst.org -- If you can look into the seeds of time and say which grain will grow and which will not - speak then to me (Macbeth) --
Re: [ccp4bb] carving up maps (was re: pymol help)
Dear Andrew, Thank you for that posting; I would like to simply agree with the Bobscript manual and your suggested practice. I think the 'carve' commands should not be there; if you wonder why, take a ligand, put it wherever you want in space, set the map sigma to -0.5, display a map with carve=1.2 and think if this picture is informative, especially in the context of your favorite competitor publishing it in Nature. A. PS Yanming, if you really want to do that what you ask for, ADOBE ILLUSTRATOR IS THE BEST WAY TO GO From: [EMAIL PROTECTED] Subject:Re: [ccp4bb] pymol help Date: October 29, 2007 8:44:46 GMT+01:00 To: CCP4BB@JISCMAIL.AC.UK Reply-To: [EMAIL PROTECTED] Dear all, Sorry I did not make it clear in my first email. Now my question can boil down to: IS IT POSSIBLE TO ONLY ZOOM ONE OBJECT AND KEEP ALL THE OTHER OBJECTS UN-ZOOMED IN PYMOL? thanks Yanming On Oct 29, 2007, at 13:43, Andrew Gulick wrote: I'd be curious to know if there is any consensus in the community with using the carve command for showing maps. I have never felt comfortable showing density within a cutoff radius of a particular residue or--even worse--a ligand, and felt the figures should display the extraneous bits as well. The burden was on the crystallographer to find an appropriate view (slab, sigma, etc...) to display the map. The Bobscript manual appears to agree with me on this one as it states: http://www.strubi.ox.ac.uk/bobscript/doc24.html If your density is good then you will just have density over residue 999, but if things are not so hot then you may want to cheat and just draw the bits of density near to the selected atoms. Just curious, Andy -- Andrew M. Gulick, Ph.D. --- (716) 898-8619 Hauptman-Woodward Institute 700 Ellicott St Buffalo, NY 14203 --- Senior Research Scientist Hauptman-Woodward Institute Assistant Professor Dept. of Structural Biology, SUNY at Buffalo http://www.hwi.buffalo.edu/Faculty/Gulick/Gulick.html http://labs.hwi.buffalo.edu/gulick On 10/29/07 4:40 AM, Stefan Schmelz [EMAIL PROTECTED] wrote: Dear Yanming, To show pretty density of a model you have to import a ccp4 density map and display it around your ligand. The simplest solution is using ccp4 and tick the box Generate weighted difference maps files in CCP4 format when running Refmac5 (one or two cycles are enough). Specify names for FWT and DelFwt maps and rename the maps afterwards to *.ccp4. This renamed map (e.g. fwt.ccp4) can be opened in pymol. To show density around our ligand you can use the following command: isomesh map, name_of_fwtmap, 1.0, ligand, carve=1.8 (map = greats an object name map, name_of_fwtmap = name of your map, 1.0 = Sigma level, carve=1.8 = width map is displayed around your ligand This will allow you to show a pretty electron density map around your ligand without any chemical info of the ligand. Stefan Schmelz Yanming Zhang wrote: Hi, all, I want to make a pymol figure wich can show the pretty density of a ligand. But we don't want to show the detailed chemical info of the ligand. If I use a large enough sphere_scale for the ligand, the chemical info will be hidden but the density map will be disrupted. If I use a smaller sphere_scale, the density looks great but the chemical info of the ligand will be visible. How should I overcome this dilemma? Thank you very much for your help. Yanming
Re: [ccp4bb] carving up maps (was re: pymol help)
Anastassis Perrakis wrote: Dear Andrew, Thank you for that posting; I would like to simply agree with the Bobscript manual and your suggested practice. I think the 'carve' commands should not be there; if you wonder why, take a ligand, put it wherever you want in space, set the map sigma to -0.5, display a map with carve=1.2 and think if this picture is informative, especially in the context of your favorite competitor publishing it in Nature. A. The fact that a tool can be misused does not necessarily mean that there is something wrong with the tool, just with some users. I agree that with current ray-traced images there is less need for this tool than in the old blackwhite line diagrams where a lack of 3D perception easily led to cluttered images. However, if showing the density of interest really benefits from this trick then it's fine with me as long as you indicate in the legend what map and carve settings were used. Bart -- == Bart Hazes (Assistant Professor) Dept. of Medical Microbiology Immunology University of Alberta 1-15 Medical Sciences Building Edmonton, Alberta Canada, T6G 2H7 phone: 1-780-492-0042 fax:1-780-492-7521 ==
Re: [ccp4bb] Pseudo-merohedral twinning and Molecular replacement
Thanks very much for all the suggestions so far. While I am pursuing all the checks and balances for twinning here are the Wilson plots I forgot to attach before..I am not sure what is going on, especially in B ! best, Iain On Oct 25 2007, Iain Kerr wrote: Dear all, I find myself posed with a rather interesting if somewhat confusing problem. Two crystals grown from the same conditions, let's call them A and B.. A: Resolution 2.1A SpacegroupP4? Rmerge0.137 (0.324) Mean((I)/sd(I)) 41.0 (17.8) Completeness 100 (100) Multiplicity53.6 (56.3) 4/mmm is clear from indexing...systematic absences show a clear 4 fold screw-axis..Pointless gives the most likely as P4_1 22 (I'm not clear on how it distinguishes P4_1 22 and P4_3 22..) Molecular replacement in Phaser, checking all the possible spacegroups, gives two outstanding solutions LLG Z-score P4_3 22 1972 41 (1mol/asu) P4_3 3801 54 (2mols/asu, ASU too full warning !) Solutions in other spacegroups had negative LLGs and/or were rejected for poor packing...the P1 solutions have LLGs of around -22000 I rebuilt both solutions in ARP/wARP both giving Rfree ~32% and Rfac ~23%...rebuilding (most residues accounted for), adding ligands and water makes no difference. Different iterations of refinement/rebuilding eg. cutting resolution make no difference...the maps are really well defined and packing is very reasonable with no clashes in either spacegroup. B: Resolution 2.3A Spacegroup C222? Rmerge0.187 (0.402) Mean((I)/sd(I)) 11.8 (4.8) Completeness 99.4 (98.8) Multiplicity 6.8 (6.6) Mosflm: 11 144 mC 255.6164.3263.9790.0 90.3 76.1 C2 10 7 oC 90.69 90.74 124.09 90.3 90.7 89.7 C222,C2221 9 7tP63.9764.32 124.0990.7 90.3 90.0 P4,P41,P42,P43,P422,P4212,P4122,P41212,P4222,P42212,P4322,P43212 8 5 oP63.9764.32 124.0990.7 90.3 90.0 P222,P2221,P21212,P212121 7 5 mP63.97 124.0964.3290.7 90.0 90.3 P2,P21 6 4 mC90.6990.74 124.0989.7 90.7 90.3 C2 5 4 mC90.6990.74 124.0990.3 90.7 89.7 C2 4 3 mP64.3263.97 124.0990.3 90.7 90.0 P2,P21 3 1 mP64.3263.97 124.0990.3 90.7 90.0 P2,P21 2 0 aP63.9764.32 124.0989.3 89.7 90.0 P1 1 0 aP63.9764.32 124.0990.7 90.3 90.0 P1 This suggests pseudo-merohedral twinning to me...in C222/C222_1 ...a and b are almost equivalent, so the 4/mmm symmetry would be apparent ? The Rmerge in 422 (19.6%) is only slightly higher than C222/C222_1 systematic absences again suggest a 4 fold...the curves calculated from the cumulative intensity distribution suggest partial twinning (when inputting C222_1 into the 'old' server to calculate a twin fraction from the partial twin test it says there are no twin laws for that spacegroup...) _ The outstanding solutions in Phaser this time are: LLG Z-score P4_3 22 131735 (1mol/asu) C222_1 223746 (2mols/asu, ASU too full warning !) Rigid body refinement of the solutions give (C222_1 ) Rfree 43%, Rfac 42% and ( P4_3 22 ) Rfree 44%, Rfac 43%I'm thinking this is high and the maps from Phaser although fitting the placed molecules have poor connectivity (high Rmerge anything to do with this ?) Going back to crystal A it turns out the same C222/C222_1 is found but lower down in the list amongst the other solutions... I have attached the Wilson plots for both crystals...A has a large spike at high resolution (which is why I cut the data to 2.4A to try and improve refinement, to no avail) and B looks horrid ! OK, I think that is all the information I have at the moment...have I completely missed the correct symmetry..the Rmerge does seem high.. I have not yet tried to detwin the data (if it truly is twinned) and perhaps that is impeding refinement ?? Any suggestions would be greatly appreciated. Thank you, Iain _ inline: A.tiffinline: B.tiff
Re: [ccp4bb] Electron density function for ligands in real space?
If you put the coordinates into COOT it will give you a validation score. If you use the CCP$i map correlation procedures it will also give you a CC for the density match. The input in each case is the reflection file with appropriate amplitude and phase terms. What you use depends on what phases are available. Experimental phases - use FP PHI and FOM Output of REFMAC refinement - maybe FWT and PHWT after you have excluded the ligand from the refinement calculation? Eleanor Ask if you need more detailed ideas.. Qing Zhang wrote: Hello, I'm new in x-ray crystallography and trying to compute real-space electron density for ligands. The goal is to evaluate match of ligands with density peaks (like computing local R values in real space). What would be the best electron density function that considers ligand atomic numbers/radii, density map resolution, and some local protein information (to estimate B values of ligand atoms)? Thank you in advance. Qing Zhang
[ccp4bb] COOT 0.3.3 in OSX leopard does not work!!!
Hi,I just installed the OSX leopard on my Macbook. Tried to run COOT 0.3.3for intel 10.4 which I downloaded from CCP4 webpage. The installation proceeds without any problem. But, once I try to start it, it fails to start and give the following error message: 'Dyld Error Message: Symbol not found: __cg_TIFFClientOpen Referenced from: /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/Versions/A/ImageIO Expected in: /Applications/coot.app/Contents/MacOS/../coot/lib/libtiff.3.dylib' When COOT tries to start, the X11 starts automatically, I guess the X11 is fine in this case. Any help is greatly appreciated! :) Cheers, Azmiri
Re: [ccp4bb] Pseudo-merohedral twinning and Molecular replacement
Wilson plots are not very informative for the detection of twinning. The spikes you see in your Wilson plots, could be due to ise ring issues (both 3.89 and 2.24 A are at ice ring related d scapings.) The very large mean intensity in those resolution shells could be due to the fact that only strong reflections were not rejected during data processing. Since there is only 1 spike per dataset and the completeness in those shells is not shown, one canot be sure I guess. The NZ plots or L-stats could be useful. Cheers Peter 2007/10/29, Iain Kerr [EMAIL PROTECTED]: Thanks very much for all the suggestions so far. While I am pursuing all the checks and balances for twinning here are the Wilson plots I forgot to attach before..I am not sure what is going on, especially in B ! best, Iain On Oct 25 2007, Iain Kerr wrote: Dear all, I find myself posed with a rather interesting if somewhat confusing problem. Two crystals grown from the same conditions, let's call them A and B.. A: Resolution 2.1A SpacegroupP4? Rmerge0.137 (0.324) Mean((I)/sd(I)) 41.0 (17.8) Completeness 100 (100) Multiplicity53.6 (56.3) 4/mmm is clear from indexing...systematic absences show a clear 4 fold screw-axis..Pointless gives the most likely as P4_1 22 (I'm not clear on how it distinguishes P4_1 22 and P4_3 22..) Molecular replacement in Phaser, checking all the possible spacegroups, gives two outstanding solutions LLG Z-score P4_3 22 1972 41 (1mol/asu) P4_3 3801 54 (2mols/asu, ASU too full warning !) Solutions in other spacegroups had negative LLGs and/or were rejected for poor packing...the P1 solutions have LLGs of around -22000 I rebuilt both solutions in ARP/wARP both giving Rfree ~32% and Rfac ~23%...rebuilding (most residues accounted for), adding ligands and water makes no difference. Different iterations of refinement/rebuilding eg. cutting resolution make no difference...the maps are really well defined and packing is very reasonable with no clashes in either spacegroup. B: Resolution 2.3A Spacegroup C222? Rmerge0.187 (0.402) Mean((I)/sd(I)) 11.8 (4.8) Completeness 99.4 (98.8) Multiplicity 6.8 (6.6) Mosflm: 11 144 mC 255.6164.3263.9790.0 90.3 76.1 C2 10 7 oC 90.69 90.74 124.09 90.3 90.7 89.7 C222,C2221 9 7tP63.9764.32 124.0990.7 90.3 90.0 P4,P41,P42,P43,P422,P4212,P4122,P41212,P4222,P42212,P4322,P43212 8 5 oP63.9764.32 124.0990.7 90.3 90.0 P222,P2221,P21212,P212121 7 5 mP63.97 124.0964.3290.7 90.0 90.3 P2,P21 6 4 mC90.6990.74 124.0989.7 90.7 90.3 C2 5 4 mC90.6990.74 124.0990.3 90.7 89.7 C2 4 3 mP64.3263.97 124.0990.3 90.7 90.0 P2,P21 3 1 mP64.3263.97 124.0990.3 90.7 90.0 P2,P21 2 0 aP63.9764.32 124.0989.3 89.7 90.0 P1 1 0 aP63.9764.32 124.0990.7 90.3 90.0 P1 This suggests pseudo-merohedral twinning to me...in C222/C222_1 ...a and b are almost equivalent, so the 4/mmm symmetry would be apparent ? The Rmerge in 422 (19.6%) is only slightly higher than C222/C222_1 systematic absences again suggest a 4 fold...the curves calculated from the cumulative intensity distribution suggest partial twinning (when inputting C222_1 into the 'old' server to calculate a twin fraction from the partial twin test it says there are no twin laws for that spacegroup...) _ The outstanding solutions in Phaser this time are: LLG Z-score P4_3 22 131735 (1mol/asu) C222_1 223746 (2mols/asu, ASU too full warning !) Rigid body refinement of the solutions give (C222_1 ) Rfree 43%, Rfac 42% and ( P4_3 22 ) Rfree 44%, Rfac 43%I'm thinking this is high and the maps from Phaser although fitting the placed molecules have poor connectivity (high Rmerge anything to do with this ?) Going back to crystal A it turns out the same C222/C222_1 is found but lower down in the list amongst the other solutions... I have attached the Wilson plots for both crystals...A has a large spike at high resolution (which is why I cut the data to 2.4A to try and improve refinement, to no avail) and B looks horrid ! OK, I think that is all the information I have at the moment...have I completely missed the correct symmetry..the Rmerge does seem high.. I have not yet tried to detwin the data (if it truly is twinned) and perhaps that is impeding refinement ?? Any suggestions would be greatly appreciated. Thank you, Iain _
Re: [ccp4bb] carving up maps (was re: pymol help)
This is not such a problem when using the old Map-cover command in O, because the cut-offs are flat planes, you would get cubic density around each atom which would raise the suspicion of even the most gullible reader. But a better solution would be to not contour the carved surface- leave a gaping hole in the net where something else is connected. Another way to describe this- contour the real density, but only display the contours within certain radius of selected atoms. Then in Anastassis's example there would be no density for the atoms because the contour is outside the cutoff. Anastassis Perrakis wrote: Dear Andrew, Thank you for that posting; I would like to simply agree with the Bobscript manual and your suggested practice. I think the 'carve' commands should not be there; if you wonder why, take a ligand, put it wherever you want in space, set the map sigma to -0.5, display a map with carve=1.2 and think if this picture is informative, especially in the context of your favorite competitor publishing it in Nature. A. PS Yanming, if you really want to do that what you ask for, ADOBE ILLUSTRATOR IS THE BEST WAY TO GO *From: * [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] *Subject: * *Re: [ccp4bb] pymol help* *Date: * October 29, 2007 8:44:46 GMT+01:00 *To: * CCP4BB@JISCMAIL.AC.UK mailto:CCP4BB@JISCMAIL.AC.UK *Reply-To: * [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] Dear all, Sorry I did not make it clear in my first email. Now my question can boil down to: IS IT POSSIBLE TO ONLY ZOOM ONE OBJECT AND KEEP ALL THE OTHER OBJECTS UN-ZOOMED IN PYMOL? thanks Yanming On Oct 29, 2007, at 13:43, Andrew Gulick wrote: I'd be curious to know if there is any consensus in the community with using the carve command for showing maps. I have never felt comfortable showing density within a cutoff radius of a particular residue or--even worse--a ligand, and felt the figures should display the extraneous bits as well. The burden was on the crystallographer to find an appropriate view (slab, sigma, etc...) to display the map. The Bobscript manual appears to agree with me on this one as it states: http://www.strubi.ox.ac.uk/bobscript/doc24.html If your density is good then you will just have density over residue 999, but if things are not so hot then you may want to cheat and just draw the bits of density near to the selected atoms. Just curious, Andy -- Andrew M. Gulick, Ph.D. --- (716) 898-8619 Hauptman-Woodward Institute 700 Ellicott St Buffalo, NY 14203 --- Senior Research Scientist Hauptman-Woodward Institute Assistant Professor Dept. of Structural Biology, SUNY at Buffalo http://www.hwi.buffalo.edu/Faculty/Gulick/Gulick.html http://labs.hwi.buffalo.edu/gulick On 10/29/07 4:40 AM, Stefan Schmelz [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] wrote: Dear Yanming, To show pretty density of a model you have to import a ccp4 density map and display it around your ligand. The simplest solution is using ccp4 and tick the box Generate weighted difference maps files in CCP4 format when running Refmac5 (one or two cycles are enough). Specify names for FWT and DelFwt maps and rename the maps afterwards to *.ccp4. This renamed map (e.g. fwt.ccp4) can be opened in pymol. To show density around our ligand you can use the following command: isomesh map, name_of_fwtmap, 1.0, ligand, carve=1.8 (map = greats an object name map, name_of_fwtmap = name of your map, 1.0 = Sigma level, carve=1.8 = width map is displayed around your ligand This will allow you to show a pretty electron density map around your ligand without any chemical info of the ligand. Stefan Schmelz Yanming Zhang wrote: Hi, all, I want to make a pymol figure wich can show the pretty density of a ligand. But we don't want to show the detailed chemical info of the ligand. If I use a large enough sphere_scale for the ligand, the chemical info will be hidden but the density map will be disrupted. If I use a smaller sphere_scale, the density looks great but the chemical info of the ligand will be visible. How should I overcome this dilemma? Thank you very much for your help. Yanming
Re: [ccp4bb] carving up maps (was re: pymol help)
I don't like using 'carve' options but I can see where it may come useful. On the positive side, in the age where deposition of coordinates and structure factors is almost mandatory, there shouldn't be a question of how your map looks because presumably the skeptical reader can go and calculate one for themselves. If someone wanted to fib in an image - they can do it in a million different ways regardless of whether 'carve' is used or not (you can create entire fake maps to show whatever features you want, if you're completely evil-minded). Artem -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Andrew Gulick Sent: Monday, October 29, 2007 8:43 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] carving up maps (was re: pymol help) I'd be curious to know if there is any consensus in the community with using the carve command for showing maps. I have never felt comfortable showing density within a cutoff radius of a particular residue or--even worse--a ligand, and felt the figures should display the extraneous bits as well. The burden was on the crystallographer to find an appropriate view (slab, sigma, etc...) to display the map. The Bobscript manual appears to agree with me on this one as it states: http://www.strubi.ox.ac.uk/bobscript/doc24.html If your density is good then you will just have density over residue 999, but if things are not so hot then you may want to cheat and just draw the bits of density near to the selected atoms. Just curious, Andy -- Andrew M. Gulick, Ph.D. --- (716) 898-8619 Hauptman-Woodward Institute 700 Ellicott St Buffalo, NY 14203 --- Senior Research Scientist Hauptman-Woodward Institute Assistant Professor Dept. of Structural Biology, SUNY at Buffalo http://www.hwi.buffalo.edu/Faculty/Gulick/Gulick.html http://labs.hwi.buffalo.edu/gulick On 10/29/07 4:40 AM, Stefan Schmelz [EMAIL PROTECTED] wrote: Dear Yanming, To show pretty density of a model you have to import a ccp4 density map and display it around your ligand. The simplest solution is using ccp4 and tick the box Generate weighted difference maps files in CCP4 format when running Refmac5 (one or two cycles are enough). Specify names for FWT and DelFwt maps and rename the maps afterwards to *.ccp4. This renamed map (e.g. fwt.ccp4) can be opened in pymol. To show density around our ligand you can use the following command: isomesh map, name_of_fwtmap, 1.0, ligand, carve=1.8 (map = greats an object name map, name_of_fwtmap = name of your map, 1.0 = Sigma level, carve=1.8 = width map is displayed around your ligand This will allow you to show a pretty electron density map around your ligand without any chemical info of the ligand. Stefan Schmelz Yanming Zhang wrote: Hi, all, I want to make a pymol figure wich can show the pretty density of a ligand. But we don't want to show the detailed chemical info of the ligand. If I use a large enough sphere_scale for the ligand, the chemical info will be hidden but the density map will be disrupted. If I use a smaller sphere_scale, the density looks great but the chemical info of the ligand will be visible. How should I overcome this dilemma? Thank you very much for your help. Yanming
Re: [ccp4bb] carving up maps (was re: pymol help)
contour the real density, but only display the contours within certain radius of selected atoms. That is exactly what PyMOL does. -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Edward Berry Sent: Monday, October 29, 2007 4:33 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] carving up maps (was re: pymol help) This is not such a problem when using the old Map-cover command in O, because the cut-offs are flat planes, you would get cubic density around each atom which would raise the suspicion of even the most gullible reader. But a better solution would be to not contour the carved surface- leave a gaping hole in the net where something else is connected. Another way to describe this- contour the real density, but only display the contours within certain radius of selected atoms. Then in Anastassis's example there would be no density for the atoms because the contour is outside the cutoff. Anastassis Perrakis wrote: Dear Andrew, Thank you for that posting; I would like to simply agree with the Bobscript manual and your suggested practice. I think the 'carve' commands should not be there; if you wonder why, take a ligand, put it wherever you want in space, set the map sigma to -0.5, display a map with carve=1.2 and think if this picture is informative, especially in the context of your favorite competitor publishing it in Nature. A. PS Yanming, if you really want to do that what you ask for, ADOBE ILLUSTRATOR IS THE BEST WAY TO GO *From: * [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] *Subject: * *Re: [ccp4bb] pymol help* *Date: * October 29, 2007 8:44:46 GMT+01:00 *To: * CCP4BB@JISCMAIL.AC.UK mailto:CCP4BB@JISCMAIL.AC.UK *Reply-To: * [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] Dear all, Sorry I did not make it clear in my first email. Now my question can boil down to: IS IT POSSIBLE TO ONLY ZOOM ONE OBJECT AND KEEP ALL THE OTHER OBJECTS UN-ZOOMED IN PYMOL? thanks Yanming On Oct 29, 2007, at 13:43, Andrew Gulick wrote: I'd be curious to know if there is any consensus in the community with using the carve command for showing maps. I have never felt comfortable showing density within a cutoff radius of a particular residue or--even worse--a ligand, and felt the figures should display the extraneous bits as well. The burden was on the crystallographer to find an appropriate view (slab, sigma, etc...) to display the map. The Bobscript manual appears to agree with me on this one as it states: http://www.strubi.ox.ac.uk/bobscript/doc24.html If your density is good then you will just have density over residue 999, but if things are not so hot then you may want to cheat and just draw the bits of density near to the selected atoms. Just curious, Andy -- Andrew M. Gulick, Ph.D. --- (716) 898-8619 Hauptman-Woodward Institute 700 Ellicott St Buffalo, NY 14203 --- Senior Research Scientist Hauptman-Woodward Institute Assistant Professor Dept. of Structural Biology, SUNY at Buffalo http://www.hwi.buffalo.edu/Faculty/Gulick/Gulick.html http://labs.hwi.buffalo.edu/gulick On 10/29/07 4:40 AM, Stefan Schmelz [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] wrote: Dear Yanming, To show pretty density of a model you have to import a ccp4 density map and display it around your ligand. The simplest solution is using ccp4 and tick the box Generate weighted difference maps files in CCP4 format when running Refmac5 (one or two cycles are enough). Specify names for FWT and DelFwt maps and rename the maps afterwards to *.ccp4. This renamed map (e.g. fwt.ccp4) can be opened in pymol. To show density around our ligand you can use the following command: isomesh map, name_of_fwtmap, 1.0, ligand, carve=1.8 (map = greats an object name map, name_of_fwtmap = name of your map, 1.0 = Sigma level, carve=1.8 = width map is displayed around your ligand This will allow you to show a pretty electron density map around your ligand without any chemical info of the ligand. Stefan Schmelz Yanming Zhang wrote: Hi, all, I want to make a pymol figure wich can show the pretty density of a ligand. But we don't want to show the detailed chemical info of the ligand. If I use a large enough sphere_scale for the ligand, the chemical info will be hidden but the density map will be disrupted. If I use a smaller sphere_scale, the density looks great but the chemical info of the ligand will be visible. How should I overcome this dilemma? Thank you very much for your help. Yanming
[ccp4bb] Logfile Problem on Dual-Core Intal Mac with Os X Server 10.4 and CCP4 6.0.1
Hello All! I have a problem with the output there from CCP4 into the log files on a dual-Core Intel Mac with Os X Server 10.4 and CCP4 6.0.1. ATREF X ALL Y ALL Z ALL OCC ALL AOCC ALL B ALL ATOM13 Ano 0.147 -0.001 0.7232.055 BFAC 20.000 ATREF X ALL Y ALL Z ALL OCC ALL AOCC ALL B ALL ATOM14 Ano 0.347 0.519 0.8950.939 BFAC 20.000 ATREF X ALL Y ALL Z ALL OCC ALL AOCC ALL B ALL ATOM15 Ano 0.232 0.498 0.9650.546 BFAC 20.000 ATREF X ALL Y ALL Z ALL OCC ALL AOCC ALL B ALL ATOM16 Ano 0.031 0.124 0.022 -2.575 MLPHARE: Normal termination Times: User: 84.9s System:0.3s Elapsed: 1:27 /pre /html !--SUMMARY_END--/FONT/B BFAC 20.000 ATREF X ALL Y ALL Z ALL OCC ALL AOCC ALL B ALL ATOM17 Ano 0.027 -0.001 0.8592.450 BFAC 20.000 ATREF X ALL Y ALL Z ALL OCC ALL AOCC ALL B ALL ATOM18 Ano 0.102 -0.002 0.8703.247 BFAC 20.000 ATREF X ALL Y ALL Z ALL OCC ALL AOCC ALL B ALL ATOM19 Ano 0.025 0.107 0.0245.815 BFAC 20.000 ATREF X ALL Y ALL Z ALL OCC ALL AOCC ALL B ALL ATOM20 Ano 0.024 0.072 0.0695.565 BFAC 20.000 ATREF X ALL Y ALL Z ALL OCC ALL AOCC ALL B ALL Many Programs do this e.g. refmac. The Termination message is passed to the log file before all other data is in it. This breaks of ploting or in case of mlphare of the whole process. Does anybody know how to handle this? Is it related to the OS or to CCP4? Thanks for helping another time justin
[ccp4bb] Logfile Problem on Dual-Core Intal Mac with Os X Server 10.4 and CCP4 6.0.1
Hello All! I have a problem with the output there from CCP4 into the log files on a dual-Core Intel Mac with Os X Server 10.4 and CCP4 6.0.1. ATREF X ALL Y ALL Z ALL OCC ALL AOCC ALL B ALL ATOM13 Ano 0.147 -0.001 0.7232.055 BFAC 20.000 ATREF X ALL Y ALL Z ALL OCC ALL AOCC ALL B ALL ATOM14 Ano 0.347 0.519 0.8950.939 BFAC 20.000 ATREF X ALL Y ALL Z ALL OCC ALL AOCC ALL B ALL ATOM15 Ano 0.232 0.498 0.9650.546 BFAC 20.000 ATREF X ALL Y ALL Z ALL OCC ALL AOCC ALL B ALL ATOM16 Ano 0.031 0.124 0.022 -2.575 MLPHARE: Normal termination Times: User: 84.9s System:0.3s Elapsed: 1:27 /pre /html !--SUMMARY_END--/FONT/B BFAC 20.000 ATREF X ALL Y ALL Z ALL OCC ALL AOCC ALL B ALL ATOM17 Ano 0.027 -0.001 0.8592.450 BFAC 20.000 ATREF X ALL Y ALL Z ALL OCC ALL AOCC ALL B ALL ATOM18 Ano 0.102 -0.002 0.8703.247 BFAC 20.000 ATREF X ALL Y ALL Z ALL OCC ALL AOCC ALL B ALL ATOM19 Ano 0.025 0.107 0.0245.815 BFAC 20.000 ATREF X ALL Y ALL Z ALL OCC ALL AOCC ALL B ALL ATOM20 Ano 0.024 0.072 0.0695.565 BFAC 20.000 ATREF X ALL Y ALL Z ALL OCC ALL AOCC ALL B ALL Many Programs do this e.g. refmac. The Termination message is passed to the log file before all other data is in it. This breaks of ploting or in case of mlphare of the whole process. Does anybody know how to handle this? Is it related to the OS or to CCP4? Thanks for helping another time justin
Re: [ccp4bb] Pseudo-merohedral twinning and Molecular replacement
the Nz test says no twinning and the intensity stats say this as well. but the Britton and H-plots give a twin fraction of 0.46-0.47 ! The britton and H test give an estimate of the twin fraction IF THE DATA IS WOULD BE TWINNED. The fact it gives a non zero value does not indicate the presence of twinning. the patterson analysis suggests weak translational pseudo-symmetry..could this be masking the detection of twinning in the Nz test ? The peak is 5% of the origin. This is noise. My first time using Phenix..am I interpreting these results correctly ?..the high twin fraction would certainly explain why I get a lot of really good MR solutions that don't refine... Of course, the fact that the intensity stats do not indicate twinning doesn't mean data is not twinned, so please go ahead in any lower space group that you/PHASER/MOLREP feels comfortable with. make sure however that the reduction you see in the R values are significant. The RvsR stat can be helpfull as well (Lebedev et al, 2005(?)). It is calculated when you supply an mtz file that contains Fcalc as well as Fobs (use obs_lables=FOBS, calc_label=FMODEL or so). Also, check your NCS operators and CA rmsd values when done with refinement to see if they suggest any higher symmetry. Peter HTH Peter
