[ccp4bb] How to show density map in pymol?
Hi All, If I want to show the density map in pymol--like coot open mtz file--, what format should I use? It seems pymol doesnot recognise the mtz format . Thanks!
Re: [ccp4bb] Crystal Screens
Dear Ray: The Crystal Screen I is based on a screen that was developed over a period of years in Sung-Hou Kim's lab, and is heavily weighted with conditions that were successful for obtaining the protein crystals that were particular to his lab at that time (which was when I was a graduate student and before, so Ronald Reagan was still President and my rent in Berkeley was $250/mo). The Natrix screen is based on one I made for screening RNA crystals using primarily PEGs in 1993, with no particular insight. The screens are convenient, but they aren't magical. Don't be shy about making your own up. Bill Scott On Tue, 30 Oct 2007 14:22:40 -0400 Ray Changrui Lu [EMAIL PROTECTED] wrote: Hello all, I am forwarding this email as requested by a lab member due to technical difficulties in school mail accounts. Ray Hello, I usually try out Hampton crystal screen I II, and PEG/ion screens on my proteins, sometimes varying protein concentrations and incubation temperature. If no hints are obtained, I will go back to test alternative constructs and purification protocols. With more and more companies selling crystal screens, and the accumulation of knowledge from structural genomics projects, I worry that my practice might have been outdated. I wonder if people could share with me: 1) What is your favorite set of crystal screens that maximize the chance of getting the crystals while minimize the sample usage, and perhaps more importantly, when do you decide to stop for better constructs? 2) Are there any other screens targeting nucleic acid and NA-protein complexes other than the Natrix and the Nucleic Acid Mini Screen sold by Hampton Research? Here I mean real different conditions, not just a re-label. I'd appreciate your thoughts. Best
[ccp4bb] Sliding window net charge program?
Hello all, does anybody know of a program which calculates net charge within a sliding window of user-defined size? Hydropathy programs are almost this, but not quite--they use absolute values rather than the signed ones (what is the opposite of an absolute value called? the relative value?). Jacob ps I sent a version of this email earlier, but did not see it show up on the BB. *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program Dallos Laboratory F. Searle 1-240 2240 Campus Drive Evanston IL 60208 lab: 847.467.4049 cel: 773.608.9185 email: [EMAIL PROTECTED] ***
Re: [ccp4bb] Pseudo-merohedral twinning and Molecular replacement
Yes, as the twinning fraction increases from 0 to 0.5, the cumulative intensity distribution curve changes in a continuous way from untwinned to perfectly twinned. The exact way in which it does this was calculated by Rees (Acta A 36, 578 (1980)). Note that the variation is markedly non-linear - if the plot is 'a little off' the untwinned plot the twinning fraction may be rather more than you think, whereas if the plot is 'a little off' the perfectly twinned plot, the twinning fraction will still be very close to 0.5. The usual caveats apply - for example the shape of the cumulative intensity distribution can be affected by pseudosymmetry as well as twinning, so while the cumulative intensity distribution can indeed be used to detect partial as well as perfect twinning, it is important to consider other measures (e.g. moments) as well. Norman -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Bryan W. Lepore Sent: 30 October 2007 17:29 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Pseudo-merohedral twinning and Molecular replacement On Mon, 29 Oct 2007, Iain Kerr wrote: The cumulative intensity distribution plot from crystal A did suggest partial twinning (attached, doesn't look too bad though..) notwithstanding other plots/statistics, does the cum. intens. dist. plot (e.g. from truncate) really show a continuum from untwinned to twinned? i.e, if the plots are 'overlapped in the middle', no question - twinned. but, if the plots are 'a little off, but not in the middle' can this result (alone) really mean the data is - as we want to say - partially twinned? i.e. is the plot robust only for the detection of perfect twinning? -bryan
Re: [ccp4bb] How to show density map in pymol?
Dear Yang Li, to quote from Stefan Schmelz's post on this topic: Date: Mon, 29 Oct 2007 08:40:42 + From: Stefan Schmelz [EMAIL PROTECTED] To: CCP4BB@JISCMAIL.AC.UK Subject: 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. [...] -- Daniel Schlieper email: [EMAIL PROTECTED] Molecular Motors Group phone: +44 1883 722306 (x 305) Marie Curie Research Institute fax : +44 1883 714375 The Chart, Oxted RH8 0TL, UK web : http://mc11.mcri.ac.uk On Wed, 31 Oct 2007, yang li wrote: Hi All, If I want to show the density map in pymol--like coot open mtz file--, what format should I use? It seems pymol doesnot recognise the mtz format . Thanks!
Re: [ccp4bb] Crystal Screens
There are some screens for sale based on experiences of large Structural Genomics consortia, the JCSG (+) screen is an example. Screens like these are often biased towards the type of organism targeted by the consortium (e.g. eukaryotic/prokaryotic) Flip -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of William Scott Sent: Tuesday, October 30, 2007 8:09 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Crystal Screens Dear Ray: The Crystal Screen I is based on a screen that was developed over a period of years in Sung-Hou Kim's lab, and is heavily weighted with conditions that were successful for obtaining the protein crystals that were particular to his lab at that time (which was when I was a graduate student and before, so Ronald Reagan was still President and my rent in Berkeley was $250/mo). The Natrix screen is based on one I made for screening RNA crystals using primarily PEGs in 1993, with no particular insight. The screens are convenient, but they aren't magical. Don't be shy about making your own up. Bill Scott On Tue, 30 Oct 2007 14:22:40 -0400 Ray Changrui Lu [EMAIL PROTECTED] wrote: Hello all, I am forwarding this email as requested by a lab member due to technical difficulties in school mail accounts. Ray Hello, I usually try out Hampton crystal screen I II, and PEG/ion screens on my proteins, sometimes varying protein concentrations and incubation temperature. If no hints are obtained, I will go back to test alternative constructs and purification protocols. With more and more companies selling crystal screens, and the accumulation of knowledge from structural genomics projects, I worry that my practice might have been outdated. I wonder if people could share with me: 1) What is your favorite set of crystal screens that maximize the chance of getting the crystals while minimize the sample usage, and perhaps more importantly, when do you decide to stop for better constructs? 2) Are there any other screens targeting nucleic acid and NA-protein complexes other than the Natrix and the Nucleic Acid Mini Screen sold by Hampton Research? Here I mean real different conditions, not just a re-label. I'd appreciate your thoughts. Best
[ccp4bb] your favorite crystallization screens
Hello, I usually try out Hampton crystal screen I II, and PEG/ion screens on my proteins, sometimes varying protein concentrations and incubation temperature. If no hints are obtained, I will go back to test alternative constructs and purification protocols. With more and more companies selling crystal screens, and the accumulation of knowledge from structural genomics projects, I worry that my practice might have been outdated. I wonder if people could share with me: 1) What is your favorite set of crystal screens that maximize the chance of getting the crystals while minimize the sample usage, and perhaps more importantly, when do you decide to stop for better constructs? 2) Are there any other screens targeting nucleic acid and NA-protein complexes other than the Natrix and the Nucleic Acid Mini Screen sold by Hampton Research? Here I mean real different conditions, not just a re-label. I'd appreciate your thoughts. Best Ailong --
[ccp4bb] Programs for analysing the drugability of a small-molecule binding pocket
Dear colleagues, I am looking for a computational method to assess reliably the drugability of a small- molecule binding pocket (volume, surface, interaction potential etc.) on a protein surface. Any recommandations and experiences are welcome! Many thanks in advance! Karsten Niefind Institute of Biochemistry University of Cologne Zuelpicher Str. 47 D-50674 Cologne Germany
[ccp4bb] converting structure factor files to mtz files
Hi, Could anyone give a quick hint for the Fortran format for the following structure factor mmCIF file? or Is there any easy program or better way to convert it? I think I need to skip first 3 columns. Thanks in advance. Joe loop_ _refln.crystal_id _refln.wavelength_id _refln.scale_group_code _refln.index_h _refln.index_k _refln.index_l _refln.F_meas_au _refln.F_meas_sigma_au _refln.status 1 1 1200 617.50 5.41 o 1 1 1400 773.50 6.92 o 1 1 1600 62.30 3.19 o I am trying to view the electron density of a published structure. I downloaded the file from pdb and used cif2mtz in ccp4. I think the following output mtz is wrong. * Column Labels : H K L FREE FP SIGFP F(+) SIGF(+) F(-) SIGF(-) DP SIGDP I(+) SIGI(+) I(-) SIGI(-) * Column Types : H H H I F Q G L G L D Q K M K M * Associated datasets : 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 * Cell Dimensions : (obsolete - refer to dataset cell dimensions above) 88.0800 86.3600 80.7700 90. 95.7100 90. * Resolution Range : 0.000450.29217 ( 47.298 - 1.850 A ) * Sort Order : 1 2 3 0 0 * Space group = 'C 1 2 1' (number 5) OVERALL FILE STATISTICS for resolution range 0.000 - 0.292 === Col SortMinMaxNum % Mean Mean Resolution Type Column num order Missing complete abs. LowHigh label 1 ASC-47 47 0 100.00 -1.4 17.9 47.28 1.85 H H 2 NONE 0 46 0 100.00 17.2 17.2 47.28 1.85 H K 3 NONE 0 43 0 100.00 16.4 16.4 47.28 1.85 H L 4 NONE0.019.0 0 100.00 9.52 9.52 47.28 1.85 I FREE 5 NONE0.0 1566.050 99.90 162.85 162.85 47.28 1.85 F FP 6 NONE0.082.150 99.90 9.49 9.49 47.28 1.85 Q SIGFP 7 BOTH ? ? 513730.00 ?? -999.00 0.00 G F(+) 8 BOTH ? ? 513730.00 ?? -999.00 0.00 L SIGF(+) 9 BOTH ? ? 513730.00 ?? -999.00 0.00 G F(-) 10 BOTH ? ? 513730.00 ?? -999.00 0.00 L SIGF(-) 11 BOTH ? ? 513730.00 ?? -999.00 0.00 D DP 12 BOTH ? ? 513730.00 ?? -999.00 0.00 Q SIGDP 13 BOTH ? ? 513730.00 ?? -999.00 0.00 K I(+) 14 BOTH ? ? 513730.00 ?? -999.00 0.00 M SIGI(+) 15 BOTH ? ? 513730.00 ?? -999.00 0.00 K I(-) 16 BOTH ? ? 513730.00 ?? -999.00 0.00 M SIGI(-) No. of reflections used in FILE STATISTICS51373 LIST OF REFLECTIONS === -47 1 10.00 0.00 0.00 ? ? ? ? ? ? ? ? ? ? -47 1 20.00 0.00 0.00 ? ? ? ? ? ? ? ? ? ? -47 1 3 17.00 0.00 0.00 ? ? ? ? ? ? ? ? ?
Re: [ccp4bb] converting structure factor files to mtz files
If you want to roll your own... If you add the data_xxx line to make this a legal CIF, you should be able to read it with ciftbx if you are working in a Fortran application or CBFlib if you are working in a C application. You will find a variety of CIF tools pointed to from the IUCr web site and from the RCSB web site. At 7:49 PM -0400 10/31/07, Zheng Zhou wrote: Hi, Could anyone give a quick hint for the Fortran format for the following structure factor mmCIF file? or Is there any easy program or better way to convert it? I think I need to skip first 3 columns. Thanks in advance. Joe loop_ _refln.crystal_id _refln.wavelength_id _refln.scale_group_code _refln.index_h _refln.index_k _refln.index_l _refln.F_meas_au _refln.F_meas_sigma_au _refln.status 1 1 1200 617.50 5.41 o 1 1 1400 773.50 6.92 o 1 1 1600 62.30 3.19 o I am trying to view the electron density of a published structure. I downloaded the file from pdb and used cif2mtz in ccp4. I think the following output mtz is wrong. * Column Labels : H K L FREE FP SIGFP F(+) SIGF(+) F(-) SIGF(-) DP SIGDP I(+) SIGI(+) I(-) SIGI(-) * Column Types : H H H I F Q G L G L D Q K M K M * Associated datasets : 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 * Cell Dimensions : (obsolete - refer to dataset cell dimensions above) 88.0800 86.3600 80.7700 90. 95.7100 90. * Resolution Range : 0.000450.29217 ( 47.298 - 1.850 A ) * Sort Order : 1 2 3 0 0 * Space group = 'C 1 2 1' (number 5) OVERALL FILE STATISTICS for resolution range 0.000 - 0.292 === Col SortMinMaxNum % Mean Mean Resolution Type Column num order Missing complete abs. Low High label 1 ASC-47 47 0 100.00 -1.4 17.9 47.28 1.85 H H 2 NONE 0 46 0 100.00 17.2 17.2 47.28 1.85 H K 3 NONE 0 43 0 100.00 16.4 16.4 47.28 1.85 H L 4 NONE0.0 19.0 0 100.00 9.52 9.52 47.28 1.85 I FREE 5 NONE0.0 1566.050 99.90 162.85 162.85 47.28 1.85 F FP 6 NONE0.082.150 99.90 9.49 9.49 47.28 1.85 Q SIGFP 7 BOTH ? ? 513730.00 ?? -999.00 0.00 G F(+) 8 BOTH ? ? 513730.00 ?? -999.00 0.00 L SIGF(+) 9 BOTH ? ? 513730.00 ?? - 999.00 0.00 G F(-) 10 BOTH ? ? 513730.00 ?? -999.00 0.00 L SIGF(-) 11 BOTH ? ? 513730.00 ?? -999.00 0.00 D DP 12 BOTH ? ? 513730.00 ?? -999.00 0.00 Q SIGDP 13 BOTH ? ? 513730.00 ?? -999.00 0.00 K I(+) 14 BOTH ? ? 513730.00 ?? -999.00 0.00 M SIGI(+) 15 BOTH ? ? 513730.00 ?? -999.00 0.00 K I(-) 16 BOTH ? ? 513730.00 ?? -999.00 0.00 M SIGI(-) No. of reflections used in FILE STATISTICS51373 LIST OF REFLECTIONS === -47 1 10.00 0.00 0.00 ? ? ? ? ? ? ? ? ? ? -47 1 20.00 0.00 0.00 ? ? ? ? ? ? ? ? ? ? -47 1 3 17.00 0.00 0.00 ? ? ? ? ? ? ? ? ? -- = Herbert J. Bernstein, Professor of Computer Science Dowling College, Kramer Science Center, KSC 121 Idle Hour Blvd, Oakdale, NY, 11769 +1-631-244-3035 [EMAIL PROTECTED] =
