Re: [ccp4bb] Hydrophobic interactions
LIGPLOT will show this graphically, if the correct parameters are set in ligplot.prm, but not state the interactions explicitly: http://www.ebi.ac.uk/thornton-srv/software/LIGPLOT/ The relevant lines in ligplot.prm: PLOT PARAMETERS --- Y- Include: Hydrophobic interactions - (Y/N)? HTH, Iain On Wednesday,Dec 14 12:34 PM, Luthra,Amit wrote: Hi Everyone I have to calculate hydrophobic interactions in pdb files. Is any server available for this type of calculation? Thanks in advance Amit
Re: [ccp4bb] Coot File Save Coordinates
Hi Raji, Yeah, this can be frustrating. I had a related problem a few years ago. The following thread may be informative: https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0710L=COOTP=R26791=COOT9=AJ=ond=No+Match%3BMatch%3BMatchesz=4 As Antony points out, it's a problem with X11 as implemented under the quartz window manager in MacOSX. I switched to KDE for a while and that solved the problem, but ultimately found that switching between KDE and quartz was a bit of a pain and reverted back to the latter. HTH, Iain On 8/15/2011 6:08 PM, Raji Edayathumangalam wrote: Thanks for pointing that out. -Raji On Mon, Aug 15, 2011 at 4:29 PM, Antony Oliver antony.oli...@sussex.ac.uk mailto:antony.oli...@sussex.ac.uk wrote: If you're running Coot on a Mac - it's also unfortunately a well-documented feature, something to do with Apple's implementation of X11. Sent from my iPhone On 15 Aug 2011, at 21:25, Raji Edayathumangalam r...@brandeis.edu mailto:r...@brandeis.edu wrote: Thanks Mischa and Juergen. That was probably my most ridiculous post to the CCP4BB!! I found the pop-up dialog box hiding behind all my zillion windows. Now why the pop-up window would not pop up actively on top of all other windows is a question for another time. Nevertheless, your replies helped :) Raji On Mon, Aug 15, 2011 at 3:56 PM, Bosch, Juergen jubo...@jhsph.edu mailto:jubo...@jhsph.edu wrote: Have you moved your primary window away ? I mean just in case the pop up window opened behind the actual scene window. Jürgen On Aug 15, 2011, at 3:54 PM, Raji Edayathumangalam wrote: Hi Folks, Apologies for a non-CCP4 question. I am trying to write our coordinates following SSM superposition using the File Save Coordinates option in Coot. But if I click the Select Filename button, nothing happens. I thought I would get an option to pick a filename and specify what I want my output coordinate filename to be called. But that isn't happening. Also, clicking on the molecule on the graphics screen (as someone pointed out in a previous post) doesn't help either. I was able to run this very identical routine several times recently so not sure what just happened now! Haven't upgraded Coot or anything. Am using Coot 0.6.2-pre-1 (revision 3468) [with guile 1.8.7 embedded] [with python 2.7.1 embedded]. Help? Thanks. Raji -- -- Raji Edayathumangalam Instructor in Neurology, Harvard Medical School Research Associate, Brigham and Women's Hospital Visiting Research Scholar, Brandeis University .. Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Phone: +1-410-614-4742 tel:%2B1-410-614-4742 Lab: +1-410-614-4894 tel:%2B1-410-614-4894 Fax: +1-410-955-3655 tel:%2B1-410-955-3655 http://web.mac.com/bosch_lab/ -- -- Raji Edayathumangalam Instructor in Neurology, Harvard Medical School Research Associate, Brigham and Women's Hospital Visiting Research Scholar, Brandeis University -- -- Raji Edayathumangalam Instructor in Neurology, Harvard Medical School Research Associate, Brigham and Women's Hospital Visiting Research Scholar, Brandeis University
Re: [ccp4bb] Off topic question. NACCESS
Hi Armando, The information can be found here: http://www.bioinf.manchester.ac.uk/naccess/ It looks like you'll need to compile it from source code. I can help you with this, if you're unsure. It also plugs in nicely to the excellent LIGPLOT, which I have found incredibly useful (and, by extension, HBPLUS). best, Iain Iain Kerr Senior Scientist Dept. of Cellular Molecular Pharmacology and The Sandler Center for Drug Discovery Phone: 415-502-8219 Fax: 415-502-8193 E-mail: ik...@cmp.ucsf.edu QB3/Byers Hall Rm. 509 1700 4th Street University of California San Francisco, CA 94158 http://sandler.cgl.ucsf.edu/ On 6/19/2011 2:09 PM, VAN RAAIJ , MARK JOHAN wrote: Dear Armando, don't know about NACCESS, but I guess it is superseded by AREAIMOL in CCP4 (also in CCP4i); it outputs the accessible volume per atom in the pdb file and per residue and per chain and some other statistics in the log-file. Mark Quoting Armando Albert: Does anyone has got some information about how to get a mac version (intel), of the old unix program naccess?. It was meant to calculate the solvent accessibility per residue from a pdb file. Armando Mark J van Raaij Laboratorio M-4 Dpto de Estructura de Macromoléculas Centro Nacional de Biotecnología - CSIC c/Darwin 3, Campus Cantoblanco 28049 Madrid tel. 91 585 4616 email: mjvanra...@cnb.csic.es
Re: [ccp4bb] bruker smart and mosflm
Hi Ed, Bruker used to supply a utility called FRM2FRM that would unwarp their images so that they were readable by Mosflm. You may want to consult them directly; Matt Benning (I believe he's still there) was most helpful when I was having problems with Bruker images a few years ago. HTH, Iain On 11/8/2010 12:01 PM, Ed Pozharski wrote: I am trying to read Bruker's Smart 6000 images with mosflm and it fails. Based on some limited googlearch I feel that NPIXELB:1 is a relevant information and when these files were processed in HKL (not by me), the relevant detector line says format ccd bruker smart6000 binned. I see from mosflm website that I might be in trouble here although it says that in recent version handling of bruker smart has been improved. In the mosflm crash file I get this From information in the image file, the detector has been recognized as: Bruker SMART If this is incorrect you must supply a DETECTOR keyword So my question is how do I figure out if this particular format is supported or not? Cheers, Ed.
Re: [ccp4bb] Crystals grown from high ammonium sulphate
Hi Sabine, I had a similar problem years ago. Have you tried oils ? (mineral oil, paraffin oil, 50:50 mixtures of either with N-paratone) You can either 1. add a small amount (1ul or less) to the drop containing the crystals and mount from there or 2. if you are quick enough, transfer the crystal to a small drop of oil and mount it in the cryostream straight from the oil. HTH, Iain Sabine Schneider wrote: Hi everyone, We got crystals that grew in ~3.2M ammonium sulphate and some tris-buffer at 18dgC. Unfortunately the crystals take a while to grow (~4-5 weeks) and so far we only have 4-5 xtals. I tried to freeze the crystals, but as soon as I broke though the skin of the drop the ammonium sulphate started to crystallise. I got the crystals out, froze them using sort of an artifical mother liquor with sodium malonate as cryo and tested the diffraction. The freezing seems to be OK and it is definitely a protein crystal. The crystal suffered when the ammonium sulphate in the drop started to crystallise, but didn't seem to deteriorate anymore in the cryo. Well the corners had already more or less disappeared by the time I got them out of the drop... Since we only have a few xtals at the moment and I can't try out a lot of things, I was wondering if anyone has experienced and solved a similar problem? My freezing attempt so far was in an airconditioned room with 18dgC. I thought about higher humidity and temperature in the room, and/or adding the cryo directly to the drop Any ideas are very much appreciated! Sabine -- Dr. Sabine Schneider Ludwig-Maximilians-University Department of Chemistry and Pharmacy Butenandtstrasse 5-13, Building F 81377 Munich Germany Phone: +49 (0)89 2180 77846 Fax: +49 (0)89 2180 77756 http://www.carellgroup.de/
Re: [ccp4bb] ccp4 install on Leopard
Patrick, I've not used fink to install ccp4 so can't comment on that, but if you want a quickie working suite: I downloaded the pre-compiled binaries from the CCP4 ftp site and they work fine. ftp://ftp.ccp4.ac.uk/ccp4/6.0.2/binaries/ Use the Tcl/tk and Blt distributions on the CCP4 website (from the automated download page) and not the one that comes with Leopard...for me, ccp4i crashed with the latter when browsing for files... HTH, Iain Patrick Loll wrote: Accck! 1. I tried to install Bill Scott's precompiled ccp4 on an intel mac running OS X 10.5. When attempting launch ccp4i, I receive this error message: /sw/share/xtal/ccp4-6.0.2/ccp4i/bin/ccp4i: line 4 /bltwish: no such file or directory Typing which bltwish returns /sw/bin/bltwish, which jibes with the definition of $CCP4I_TCLTK, so I'm not sure where the problem is... 2. Pfui. So next I tried jettisoning the apt-get installation, and instead used the installer downloaded from the ccp4 site (ccp4-6.0.2-osx-i386.dmg.gz). This goes swimmingly, until I actually try to do something. Commands like ccp4i or mtzdump aren't recognized, so I go looking for the ccp4.setup file; but it's not there. Huh? Also, there's no folder named ccp4i, even though this install is supposed to include it... It's Friday, and I'm at the nadir of my weekly brain function, so perhaps some kind soul will tell me where I'm going astray. Thanks, Pat --- Patrick J. Loll, Ph. D. Professor of Biochemistry Molecular Biology Director, Biochemistry Graduate Program Drexel University College of Medicine Room 10-102 New College Building 245 N. 15th St., Mailstop 497 Philadelphia, PA 19102-1192 USA (215) 762-7706 [EMAIL PROTECTED] mailto:[EMAIL PROTECTED]
Re: [ccp4bb] Vista
Deena, A lot of this comes down to personal preference at the end of the day..you just have to find what works for you. I primarily use MacOSX and Linux. I also have a Vista partition on my laptop to share Microsoft office files with others in the department that use Windows or Macs..no comment on crystallography applications, but I think Vista is a regression from XP and I do not particularly enjoy using it. Linux has, obviously, been very well supported by software developers for many years...pre-compiled binaries for the popular flavours are mostly available and, with the odd afternoon bashing (no pun intended) your head off the monitor excluded, is fairly logical once you get to grips with it. Fedora/RedHat and Ubuntu are both excellent distributions...I'm currently using Fedora 8 on a (fairly new) Dell XPS M1330 and it mostly worked out-the-box. In my opinion MacOSX falls short in package managers..fink, in my humble opinion, is vastly inferior to yum and apt..although this may be partly down to my inability to dedicate the time required to truly get to grips with the program. Also, I much prefer GNOME (got to have those multiple desktops) over QUARTZ (MacOSX), although with some work you can get GNOME running on a Mac.. Bill Scott provides excellent support for crystallography applications on MacOSX and, I believe, debian-based distros like Ubuntu so you should refer to him on those. Gentoo is also well supported, I think..apologies for not remembering who labors on this and if any of this is repetitious.. Gently fanning the embers, Iain Anastassis Perrakis wrote: flames on Vista or XP, I shamelessly admit that I personally totally fail to see why - ideology left aside - I would ever buy a *laptop* which is not a Mac. Even for the fact that when a Mac is asleep you open the cover and it actually comes up in 1 sec, exactly where it was last evening, its worth it ! I run MS Office (I actually do like Word), iWork (Keynote is what PP might some day be ... Pages is great for eg posters), iLife for home, Coot, O, CCP4, Phenix, ARP/wARP, Solve/Resolve, Phaser, Pymol, Papers (!!! a dream that will not come true for Windows-based scientists - http://mekentosj.com/), R, Adobe and all work. And you also have Xcode, the GUI builder, management tools, and others for development. For the last 4 years I use a G4 as my laptop which is also my desktop with external monitor and keyboard/mouse - I have dropped it a couple of times, have been around the world, still works. I only switched to Macs in 2001 and I am still happy. And I did not even mention that it LOOKS better ;-)) flames off Apologies for not answering the original question, but the discussion was drifting this way. I am now waiting to see what Vista can do that Windows cannot. I am aware of one application I want and does not run on a Mac, and that is the Polar Fitness software for my bike. Argh. Most spyware and virus detection software also do not run in a Mac btw! For a reason: you do not need them dudes ! A. PS And no, I don't work for Apple, I don't get free gifts from Apple, but if Steve is reading and he wants to send me a Mac Air for my kind words, please, go ahead ! ;-)))
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
[ccp4bb] Pseudo-merohedral twinning and Molecular replacement
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 oC90.6990.74 124.0990.3 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] Pseudo-merohedral twinning and Molecular replacement
Apologies, I think I neglected to attach the wilson plots...I'll do so on Friday. best, Iain 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 oC90.6990.74 124.0990.3 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 _ No virus found in this incoming message. Checked by AVG Free Edition. Version: 7.5.503 / Virus Database: 269.15.8/1089 - Release Date: 10/23/2007 7:39 PM
Re: [ccp4bb] Bad sidechain geometry
Setting the atoms to 0.01 occ seems to have solved the problem. Thanks to everyone for their help. best, Iain Eleanor Dodson wrote: If the occupancy is 0.00 there will be no refinement - the output cds are the same as the input, and I guess that will make for horrible geometry - COOT will correct the geometry of all atoms though so you can make a prettier picture - but with no more information content re the model if the occupancies stay 0.00 .. Eleanor Iain Kerr wrote: Dear all, I'm refining a structure (with TLS, Hs in riding positions) to 2.9A - Rfree ~29.9%/Rfac 26.5% in Refmac5 v5.2.0019. Rmsd bonds 0.008A/1.1deg angles. In COOT (0.31) many of the residues whose side chains are (fully or partially) set to 0.00 occupancy have really bad geometry...for want of a better description, the side-chains literally look like they have exploded...a few are intact but have distorted planarity. This occurs in 25 residues out of 480 in the ASU. I have tried: 1. refining without TLS - no change 2. no hydrogens - no change 3. refining OVERall B-factors instead of ISOtropic - overall geometry much worse (rmsd 0.088 bonds) 4. DAMP 0.5 0.5 - no change 5. BABINET scaling instead of SIMPLE - no change in geometry, Rfree and Rfac increase ~3% 6. relaxing geometry (rmsd 0.019A bonds/1.8deg angles) This occurs with two other structures at higher resolution (~2.5A), although only a few violations..it seems to be much worse at low resolution. Any ideas ? Thanks, Iain
[ccp4bb] GRASP colouring
I have a GRASP session saved which I startup by reading in grasp.state. I have changed some colours in defcol.dat and I would like these changes to take effect in my saved session, but everytime I read in grasp.state it changes the colour palette back to the default set again. Does anyone know how I can use my own defcol.dat palette in such a session ? I'm learning PyMOL in tandem while I figure this out.. Thanks in advance. best, Iain
