Re: [ccp4bb] Off topic: Beryllium chloride
Beryllium chloride is very toxic. More care is needed when preparing it. 在 2011年10月4日 上午7:35，Peter Hsu hsuu...@u.washington.edu 写道： Sorry for the very off topic and dumb question, but does anyone know if BeCl2 needs to be prepared fresh for use (making BeF3) or can it be stored as a solution stock at room temperature/frozen? Thanks, Peter -- Cheng Chen, Ph.D. Candidate Laboratory of Structural Biology Life Science Building,Tsinghua University Beijing 100084 China Tel:+86-10-62772291 Fax:+86-10-62773145 E-mail:che...@xtal.tsinghua.edu.cn 北京市海淀区清华大学生命科学馆201-212室 邮编：100084
Re: [ccp4bb] Calculate real-space R-factor/corr coeff for ligand
Dear Brigitte, Looking at the formulae it could be possible to get those results. Take an example below Rho_cal = -0.11, 0.0, 0.05, 0.05 Rho_obs = -0.08, 0.01, 0.04, 0.04 R-fac = 0.02/0.0 = undefined Correl = 0.0032 - (-0.0025*0.0025) -- = 0.99 sqrt(0.0043 * 0.0024) Did the calculations quickly so hope they are OK. However, I designed the data so that the denominator in the R-fac is zero i.e. the sum of Rho_cal = - sum of Rho_obs. It would imply that the ATMMAP from sfall does not cover the correct set of grid points for the ligand. You expect the Fc map to be positive in this region. You need to generate a new ATMMAP for each different ligand conformation. Adam Hi, I am trying to calculate real-space R-factors and correlation coefficients for an array of different ligand conformations to find out which fits best in experimental density. So far, I have been trying to use Overlapmap in CCP4 6.1.2 to do this, by correlating maps by residue and selecting the list a real-space R-factor option. I would like to compare a map with the ligand omitted to maps calculated with each ligand conformer. I am supplying Overlapmap with a refmac mtz file calculated without ligand in the model for map 1 and a pdb file that contains both protein and ligand coordinates to calculate map 2. However, I’m confused about the output. For the protein, which I know is well-defined and modeled correctly in the density, I see mostly reasonable correlation coefficients, ~0.9, but the real-space R-factor values are all over the place and range from zero to hundreds. For example, for one residue the correlation coefficient is 0.8309 with an R-factor of 210.333. I am very confused about how to interpret these values. Has anyone else tried to use Overlap for a similar purpose and could give suggestions as to what I’m doing wrong? Thanks! Brigitte
Re: [ccp4bb] Calculate real-space R-factor/corr coeff for ligand
On Tue, Oct 4, 2011 at 11:21 AM, Adam Ralph adam.ra...@nuim.ie wrote: Dear Brigitte, Looking at the formulae it could be possible to get those results. Take an example below Rho_cal = -0.11, 0.0, 0.05, 0.05 Rho_obs = -0.08, 0.01, 0.04, 0.04 R-fac = 0.02/0.0 = undefined Correl = 0.0032 - (-0.0025*0.0025) -- = 0.99 sqrt(0.0043 * 0.0024) Did the calculations quickly so hope they are OK. However, I designed the data so that the denominator in the R-fac is zero i.e. the sum of Rho_cal = - sum of Rho_obs. It would imply that the ATMMAP from sfall does not cover the correct set of grid points for the ligand. You expect the Fc map to be positive in this region. You need to generate a new ATMMAP for each different ligand conformation. Adam Hi Adam That doesn't look right to me, the formula according to Jones et al is: RSR = sum(| rho_obs - rho_calc |) / sum(| rho_obs + rho_calc |) So for your example we have RSR = (.03 + .01 + .01 + .01) / (.19 + .01 + .09 + .09) = .13 which is obviously quite a reasonable number. If you want some numbers which will cause a zero divide you have to make rho_obs = - rho_calc for every point so each term in the sum in the denominator above is zero, and therefore obviously the denominator itself would be zero. Here are the relevant code snippets from OVERLAPMAP: iave(j,i)=0 xave(j,i)=0. yave(j,i)=0. iave(jj,ii)=iave(jj,ii)+1 xave(jj,ii)=xave(jj,ii)+xwork yave(jj,ii)=yave(jj,ii)+ywork xave(jj,ii)=xave(jj,ii)/iave(jj,ii) yave(jj,ii)=yave(jj,ii)/iave(jj,ii) rfac(jj,ii) = (abs(xave(jj,ii)- yave(jj,ii))) / (abs(xave(jj,ii)+ yave(jj,ii))) This looks wrong to me since the absolute value is being taken after the summation instead of before, i.e. it should be forming sums of abs(xwork-ywork) and abs(xwork+ywork). The absolute value of a sum is not the same as the sum of absoiute values! Note that the division throughout by the no of points (iave(jj,ii)) has no effect on the result. I didn't check the formula for the correlation coefficient. But your broad conclusion (that the data is garbage) is very probably correct! Cheers -- Ian
Re: [ccp4bb] Calculate real-space R-factor/corr coeff for ligand
Ooops (.03+.01+.01+.01)/(.19+.01+.09+.09) = .16 -- Ian On Tue, Oct 4, 2011 at 12:22 PM, Ian Tickle ianj...@gmail.com wrote: On Tue, Oct 4, 2011 at 11:21 AM, Adam Ralph adam.ra...@nuim.ie wrote: Dear Brigitte, Looking at the formulae it could be possible to get those results. Take an example below Rho_cal = -0.11, 0.0, 0.05, 0.05 Rho_obs = -0.08, 0.01, 0.04, 0.04 R-fac = 0.02/0.0 = undefined Correl = 0.0032 - (-0.0025*0.0025) -- = 0.99 sqrt(0.0043 * 0.0024) Did the calculations quickly so hope they are OK. However, I designed the data so that the denominator in the R-fac is zero i.e. the sum of Rho_cal = - sum of Rho_obs. It would imply that the ATMMAP from sfall does not cover the correct set of grid points for the ligand. You expect the Fc map to be positive in this region. You need to generate a new ATMMAP for each different ligand conformation. Adam Hi Adam That doesn't look right to me, the formula according to Jones et al is: RSR = sum(| rho_obs - rho_calc |) / sum(| rho_obs + rho_calc |) So for your example we have RSR = (.03 + .01 + .01 + .01) / (.19 + .01 + .09 + .09) = .13 which is obviously quite a reasonable number. If you want some numbers which will cause a zero divide you have to make rho_obs = - rho_calc for every point so each term in the sum in the denominator above is zero, and therefore obviously the denominator itself would be zero. Here are the relevant code snippets from OVERLAPMAP: iave(j,i)=0 xave(j,i)=0. yave(j,i)=0. iave(jj,ii)=iave(jj,ii)+1 xave(jj,ii)=xave(jj,ii)+xwork yave(jj,ii)=yave(jj,ii)+ywork xave(jj,ii)=xave(jj,ii)/iave(jj,ii) yave(jj,ii)=yave(jj,ii)/iave(jj,ii) rfac(jj,ii) = (abs(xave(jj,ii)- yave(jj,ii))) / (abs(xave(jj,ii)+ yave(jj,ii))) This looks wrong to me since the absolute value is being taken after the summation instead of before, i.e. it should be forming sums of abs(xwork-ywork) and abs(xwork+ywork). The absolute value of a sum is not the same as the sum of absoiute values! Note that the division throughout by the no of points (iave(jj,ii)) has no effect on the result. I didn't check the formula for the correlation coefficient. But your broad conclusion (that the data is garbage) is very probably correct! Cheers -- Ian
[ccp4bb] How to get formfactor for Zn +2.
Can anyone advise me how to get the Zn+2 formfactor from atomsf.lib The input coordinate is given atom type ZN+2 but the formfactor is that for Zn: I changed the atom name to Zn+2 but that made no difference... ATOM 1893 O UNK A 258 -8.934 52.268 49.467 0.00 66.53 O ATOM 1894 ZN+2 ZN B 1 -10.456 38.580 26.267 1.00 57.36 ZN+2 ATOM 1895 O HOH C 1 -5.932 42.917 25.589 1.00 24.02 O refmac log says: loop_ _atom_type_symbol _atom_type_scat_Cromer_Mann_a1 _atom_type_scat_Cromer_Mann_b1 _atom_type_scat_Cromer_Mann_a2 _atom_type_scat_Cromer_Mann_b2 _atom_type_scat_Cromer_Mann_a3 _atom_type_scat_Cromer_Mann_b3 _atom_type_scat_Cromer_Mann_a4 _atom_type_scat_Cromer_Mann_b4 _atom_type_scat_Cromer_Mann_c N 12.2126 0.0057 3.1322 9.8933 2.0125 28.9975 1.1663 0.5826 -11.5290 C 2.3100 20.8439 1.0200 10.2075 1.5886 0.5687 0.8650 51.6512 0.2156 O 3.0485 13.2771 2.2868 5.7011 1.5463 0.3239 0.8670 32.9089 0.2508 SE17.0006 2.4098 5.8196 0.2726 3.9731 15.2372 4.3543 43.8163 2.8409 S 6.9053 1.4679 5.2034 22.2151 1.4379 0.2536 1.5863 56.1720 0.8669 ZN14.0743 3.2655 7.0318 0.2333 5.1625 10.3163 2.4100 58.7097 1.3041 Eleanor
Re: [ccp4bb] How to get formfactor for Zn +2.
If you will put element names in correct positions then refmac may have a chance to find it. Here is corrected positions: ATOM 1893 O HOH A 258 -8.934 52.268 49.467 0.00 66.53 O ATOM 1894 ZNZN B 1 -10.456 38.580 26.267 1.00 57.36 ZN+2 ATOM 1895 O HOH C 1 -5.932 42.917 25.589 1.00 24.02 O In your case all element names are moved towards left and B value of ZN is in incorrect position also. ATOM 1893 O UNK A 258 -8.934 52.268 49.467 0.00 66.53 O ATOM 1894 ZN+2 ZN B 1 -10.456 38.580 26.267 1.00 57.36ZN+2 ATOM 1895 O HOH C 1 -5.932 42.917 25.589 1.00 24.02 O Regards Garib On 4 Oct 2011, at 15:31, Eleanor Dodson wrote: Can anyone advise me how to get the Zn+2 formfactor from atomsf.lib The input coordinate is given atom type ZN+2 but the formfactor is that for Zn: I changed the atom name to Zn+2 but that made no difference... ATOM 1893 O UNK A 258 -8.934 52.268 49.467 0.00 66.53 O ATOM 1894 ZN+2 ZN B 1 -10.456 38.580 26.267 1.00 57.36ZN+2 ATOM 1895 O HOH C 1 -5.932 42.917 25.589 1.00 24.02 O refmac log says: loop_ _atom_type_symbol _atom_type_scat_Cromer_Mann_a1 _atom_type_scat_Cromer_Mann_b1 _atom_type_scat_Cromer_Mann_a2 _atom_type_scat_Cromer_Mann_b2 _atom_type_scat_Cromer_Mann_a3 _atom_type_scat_Cromer_Mann_b3 _atom_type_scat_Cromer_Mann_a4 _atom_type_scat_Cromer_Mann_b4 _atom_type_scat_Cromer_Mann_c N 12.2126 0.0057 3.1322 9.8933 2.0125 28.9975 1.1663 0.5826 -11.5290 C 2.3100 20.8439 1.0200 10.2075 1.5886 0.5687 0.8650 51.6512 0.2156 O 3.0485 13.2771 2.2868 5.7011 1.5463 0.3239 0.8670 32.9089 0.2508 SE17.0006 2.4098 5.8196 0.2726 3.9731 15.2372 4.3543 43.8163 2.8409 S 6.9053 1.4679 5.2034 22.2151 1.4379 0.2536 1.5863 56.1720 0.8669 ZN14.0743 3.2655 7.0318 0.2333 5.1625 10.3163 2.4100 58.7097 1.3041 Eleanor Garib N Murshudov Structural Studies Division MRC Laboratory of Molecular Biology Hills Road Cambridge CB2 0QH UK Email: ga...@mrc-lmb.cam.ac.uk Web http://www.mrc-lmb.cam.ac.uk
[ccp4bb] CALL FOR PROPOSALS FOR ESRF BEAM TIME WITH ONLINE MICROSPEC 30th Nov. to 4th Dec.: deadline 21st Oct
*CALL FOR PROPOSALS FOR ESRF BEAM TIME WITH ONLINE MICROSPEC* Proposal Deadline *21st October 2011* There will be beam time available at the ESRF for MX data collection with a setup that allows online monitoring of UV/VIS absorbance or fluorescence spectral changes of the crystal during the X-ray diffraction experiment. Users who are interested in using this beam time (including those who are members of BAG Groups) should use the following mechanism: _http://www.esrf.fr/UsersAndScience/UserGuide/Applying/ProposalGuidelines/MXnon-BAGproposal _ and *it must be clearly indicated in the title of the proposal form that the online monitoring of spectral changes is necessary for the project*. A brief description of the device is given below however users are encouraged to consult the web pages for detailed information: _http://www.esrf.fr/UsersAndScience/Experiments/MX/How_to_use_our_beamlines/Run_Your_Experiment/Microspectrophotometer_User_Guide_ The device is also described in: McGeehan, J., Ravelli, R.B., Murray, J.W., Owen, R.L., Cipriani, F., McSweeney, S., Weik, M. and Garman, E.F. (2009) Colouring cryo-cooled crystals: online microspectrophotometry. J Synchrotron Radiat., 16, 163-172. As this is not a standard set-up, it might take a significant amount of time to train users, align the device, and analyze the data in order to derive relevant data collection schemes. *We will therefore schedule 24 hours for each project*. The *deadline *for this specific application is *Friday 21st October 2011*. It is strongly recommended to, beforehand, record an absorption (fluorescence) spectrum of the crystal on a home microspectrophotometer such as the 4dx one, or at an off-line facility such as the ESRF Cryobench, and to provide it in the application form. Such a spectrum would greatly help to determine the feasibility of the experiment. For optimal experimental conditions, crystals should be frozen in minimal amounts of cryosolution, especially when the crystals are small. Finally, please note that *the ESRF sample changer cannot be operated at the same time as the on-line microspec*. The use of specific LASER is possible if the device is compliant with the beam line safety system (interlock on device power). Dates of beam-time: *30th November - 4th December 2011* Storage Ring: 7/8 + 1 (200mA) Beamline: ID14-1 Energy: 13.27 keV (not tunable) Specifications: UV/VIS-range: 250-1100 nm Light source: Mikropack DH-2000-BAL (Deuterium/Halogen) Fluorescence/Actinic excitation wavelength: 405, 440, 473, 532, 561, 671 nm ODmax for UV-vis absorbance spectra: 2-2.5 Monitoring light size: 0.03 (min) - 0.15mm(max) Sampling freq (to disk): 10Hz or lower -- Dr David FLOT Beam-Line Operation Manager Tel : (+33) 4 76 88 17 63 Structural Biology GroupFax : (+33) 4 76 88 26 24 ESRF B.P. 220, 6 rue Jules Horowitz e-mail : david.f...@esrf.fr F-38043 GRENOBLE CEDEX http://www.esrf.eu
Re: [ccp4bb] How to get formfactor for Zn +2.
OK So the ATOM TYPE has ZN O C S etc in column 77/78 and the +2 etc in 79/80 Is there any documentation for this? E On 10/04/2011 03:56 PM, Garib N Murshudov wrote: If you will put element names in correct positions then refmac may have a chance to find it. Here is corrected positions: ATOM 1893 O HOH A 258 -8.934 52.268 49.467 0.00 66.53 O ATOM 1894 ZNZN B 1 -10.456 38.580 26.267 1.00 57.36 ZN+2 ATOM 1895 O HOH C 1 -5.932 42.917 25.589 1.00 24.02 O In your case all element names are moved towards left and B value of ZN is in incorrect position also. ATOM 1893 O UNK A 258 -8.934 52.268 49.467 0.00 66.53 O ATOM 1894 ZN+2 ZN B 1 -10.456 38.580 26.267 1.00 57.36ZN+2 ATOM 1895 O HOH C 1 -5.932 42.917 25.589 1.00 24.02 O Regards Garib On 4 Oct 2011, at 15:31, Eleanor Dodson wrote: Can anyone advise me how to get the Zn+2 formfactor from atomsf.lib The input coordinate is given atom type ZN+2 but the formfactor is that for Zn: I changed the atom name to Zn+2 but that made no difference... ATOM 1893 O UNK A 258 -8.934 52.268 49.467 0.00 66.53 O ATOM 1894 ZN+2 ZN B 1 -10.456 38.580 26.267 1.00 57.36ZN+2 ATOM 1895 O HOH C 1 -5.932 42.917 25.589 1.00 24.02 O refmac log says: loop_ _atom_type_symbol _atom_type_scat_Cromer_Mann_a1 _atom_type_scat_Cromer_Mann_b1 _atom_type_scat_Cromer_Mann_a2 _atom_type_scat_Cromer_Mann_b2 _atom_type_scat_Cromer_Mann_a3 _atom_type_scat_Cromer_Mann_b3 _atom_type_scat_Cromer_Mann_a4 _atom_type_scat_Cromer_Mann_b4 _atom_type_scat_Cromer_Mann_c N 12.2126 0.0057 3.1322 9.8933 2.0125 28.9975 1.1663 0.5826 -11.5290 C 2.3100 20.8439 1.0200 10.2075 1.5886 0.5687 0.8650 51.6512 0.2156 O 3.0485 13.2771 2.2868 5.7011 1.5463 0.3239 0.8670 32.9089 0.2508 SE17.0006 2.4098 5.8196 0.2726 3.9731 15.2372 4.3543 43.8163 2.8409 S 6.9053 1.4679 5.2034 22.2151 1.4379 0.2536 1.5863 56.1720 0.8669 ZN14.0743 3.2655 7.0318 0.2333 5.1625 10.3163 2.4100 58.7097 1.3041 Eleanor Garib N Murshudov Structural Studies Division MRC Laboratory of Molecular Biology Hills Road Cambridge CB2 0QH UK Email: ga...@mrc-lmb.cam.ac.uk Web http://www.mrc-lmb.cam.ac.uk
Re: [ccp4bb] How to get formfactor for Zn +2.
I think it is a pdb rule. Here are some of the rules: http://www.wwpdb.org/documentation/format33/sect9.html Charges (confusingly) could be 2+ etc. Regards Garib On 4 Oct 2011, at 16:41, Eleanor Dodson wrote: OK So the ATOM TYPE has ZN O C S etc in column 77/78 and the +2 etc in 79/80 Is there any documentation for this? E On 10/04/2011 03:56 PM, Garib N Murshudov wrote: If you will put element names in correct positions then refmac may have a chance to find it. Here is corrected positions: ATOM 1893 O HOH A 258 -8.934 52.268 49.467 0.00 66.53 O ATOM 1894 ZNZN B 1 -10.456 38.580 26.267 1.00 57.36 ZN+2 ATOM 1895 O HOH C 1 -5.932 42.917 25.589 1.00 24.02 O In your case all element names are moved towards left and B value of ZN is in incorrect position also. ATOM 1893 O UNK A 258 -8.934 52.268 49.467 0.00 66.53 O ATOM 1894 ZN+2 ZN B 1 -10.456 38.580 26.267 1.00 57.36ZN+2 ATOM 1895 O HOH C 1 -5.932 42.917 25.589 1.00 24.02 O Regards Garib On 4 Oct 2011, at 15:31, Eleanor Dodson wrote: Can anyone advise me how to get the Zn+2 formfactor from atomsf.lib The input coordinate is given atom type ZN+2 but the formfactor is that for Zn: I changed the atom name to Zn+2 but that made no difference... ATOM 1893 O UNK A 258 -8.934 52.268 49.467 0.00 66.53 O ATOM 1894 ZN+2 ZN B 1 -10.456 38.580 26.267 1.00 57.36ZN+2 ATOM 1895 O HOH C 1 -5.932 42.917 25.589 1.00 24.02 O refmac log says: loop_ _atom_type_symbol _atom_type_scat_Cromer_Mann_a1 _atom_type_scat_Cromer_Mann_b1 _atom_type_scat_Cromer_Mann_a2 _atom_type_scat_Cromer_Mann_b2 _atom_type_scat_Cromer_Mann_a3 _atom_type_scat_Cromer_Mann_b3 _atom_type_scat_Cromer_Mann_a4 _atom_type_scat_Cromer_Mann_b4 _atom_type_scat_Cromer_Mann_c N 12.2126 0.0057 3.1322 9.8933 2.0125 28.9975 1.1663 0.5826 -11.5290 C 2.3100 20.8439 1.0200 10.2075 1.5886 0.5687 0.8650 51.6512 0.2156 O 3.0485 13.2771 2.2868 5.7011 1.5463 0.3239 0.8670 32.9089 0.2508 SE17.0006 2.4098 5.8196 0.2726 3.9731 15.2372 4.3543 43.8163 2.8409 S 6.9053 1.4679 5.2034 22.2151 1.4379 0.2536 1.5863 56.1720 0.8669 ZN14.0743 3.2655 7.0318 0.2333 5.1625 10.3163 2.4100 58.7097 1.3041 Eleanor Garib N Murshudov Structural Studies Division MRC Laboratory of Molecular Biology Hills Road Cambridge CB2 0QH UK Email: ga...@mrc-lmb.cam.ac.uk Web http://www.mrc-lmb.cam.ac.uk Garib N Murshudov Structural Studies Division MRC Laboratory of Molecular Biology Hills Road Cambridge CB2 0QH UK Email: ga...@mrc-lmb.cam.ac.uk Web http://www.mrc-lmb.cam.ac.uk
Re: [ccp4bb] How to get formfactor for Zn +2.
On Tue, Oct 4, 2011 at 4:41 PM, Eleanor Dodson c...@ysbl.york.ac.uk wrote: OK So the ATOM TYPE has ZN O C S etc in column 77/78 and the +2 etc in 79/80 Is there any documentation for this? E Yes, see: ftp://ftp.wwpdb.org/pub/pdb/doc/format_descriptions/Format_v33_A4.pdf Though this has been the format for ATOM/HETATM records ever since I can remember. Cheers -- Ian
Re: [ccp4bb] How to get formfactor for Zn +2.
I checked back and the 1992 format decscription did not use columns 77 - 80 for ATOM/HETATM records. But the 1996 document did use them. I then checked the old Newsletters and the proposed use of columns 77 - 80 was discussed in April 1995. Frances = Bernstein + Sons * * Information Systems Consultants 5 Brewster Lane, Bellport, NY 11713-2803 * * *** *Frances C. Bernstein * *** f...@bernstein-plus-sons.com *** * * *** 1-631-286-1339FAX: 1-631-286-1999 = On Tue, 4 Oct 2011, Ian Tickle wrote: On Tue, Oct 4, 2011 at 4:41 PM, Eleanor Dodson c...@ysbl.york.ac.uk wrote: OK So the ATOM TYPE has ZN O C S etc in column 77/78 and the +2 etc in 79/80 Is there any documentation for this? E Yes, see: ftp://ftp.wwpdb.org/pub/pdb/doc/format_descriptions/Format_v33_A4.pdf Though this has been the format for ATOM/HETATM records ever since I can remember. Cheers -- Ian
Re: [ccp4bb] How to get formfactor for Zn +2.
Thank you all. I had forgotten about checking pdb record formats.. Eleanor It works when you follow the rules! On 10/04/2011 05:05 PM, Frances C. Bernstein wrote: I checked back and the 1992 format decscription did not use columns 77 - 80 for ATOM/HETATM records. But the 1996 document did use them. I then checked the old Newsletters and the proposed use of columns 77 - 80 was discussed in April 1995. Frances = Bernstein + Sons * * Information Systems Consultants 5 Brewster Lane, Bellport, NY 11713-2803 * * *** * Frances C. Bernstein * *** f...@bernstein-plus-sons.com *** * * *** 1-631-286-1339 FAX: 1-631-286-1999 = On Tue, 4 Oct 2011, Ian Tickle wrote: On Tue, Oct 4, 2011 at 4:41 PM, Eleanor Dodson c...@ysbl.york.ac.uk wrote: OK So the ATOM TYPE has ZN O C S etc in column 77/78 and the +2 etc in 79/80 Is there any documentation for this? E Yes, see: ftp://ftp.wwpdb.org/pub/pdb/doc/format_descriptions/Format_v33_A4.pdf Though this has been the format for ATOM/HETATM records ever since I can remember. Cheers -- Ian
Re: [ccp4bb] How to model this type of radiation damage?
At first glance, it looks like it could be modeled by a partially reduced carboxylate (to aldehyde or carbonyl radical). Is there any precedent for such a radiation-induced photoelectron reduction? Like you, I only remember seeing decarboxylations of Asp and Glu. To get an aldehyde or carbonyl radical, it would seem you need an oxygen acceptor in the crystal matrix: thiols, which can make thiyl radicals could possibly act as oxygen or OH radical acceptors. J. Phys. Chem. Lett. 2010, 19, 2898 suggests a mechanism by which thiols can be oxidized to S-hydroxythiols under ionizing radiation conditions. This is of course all speculation. :) ___ Roger S. Rowlett Gordon Dorothy Kline Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@colgate.edu On 10/4/2011 3:16 PM, Mischa Machius wrote: Y'all, I have several instances of this feature afflicting some glutamates. The red blob is negative difference density. I assume it's a form of radiation damage, but it doesn't seem to be the typical decarboxylation type. I'd appreciate any suggestions as to what the damaged product could be and/or how to best model this feature. Thanks so much in advance. Cheers! MM
Re: [ccp4bb] Calculate real-space R-factor/corr coeff for ligand
On Tue, Oct 4, 2011 at 7:14 PM, bkziervo...@uchicago.edu wrote: Hi Adam and Ian, Thanks for your help. If I re-calculate the R-factors with the correct absolute values I get more reasonable values. However, I'm still a bit confused because the output given by the Overlapmap program is structure factor values, which are used to calculate the real-space R-factors. Should this not be Rho values instead? Additionally, a lot of my structure factors, even for the protein, which I know fits well within the experimental density, are 0 for the sidechains or negative. Any idea what's going on here? I've attached some sample data from the Overlapmap output file. Thanks in advance. Brigitte Hi Brigitte Yes I agree with you that the output is very confusing! I don't know exactly what 'Fobs' 'Fcalc' are but I'm pretty sure they can't be structure factors. I would guess that 'F' is actually rho (i.e. rho calculated by FFT from F). According to the man page overlapmap only inputs outputs maps: nowhere does it mention reading or writing SFs. Very confusing! Also why the values are small or negative, I've no idea as I've never used overlapmap. I would keep posting to the BB in the hope that someone can solve your problem. Cheers -- Ian
[ccp4bb] Finding a sequence motif with BLAST
Dear Crystallographers, I cannot get BLAST to find all proteins with the motif cxcxcxc or at least cxcxc. It seems to think of x as an actual amino acid rather than a wildcard. There must be some easy way to do this? Ordinarily to find a short motif, I would just paste the sequence and get the answer, but here the C's are an absolute requirement and there is no constraint on the x's except that they be only one residue. JPK -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program cel: 773.608.9185 email: j-kell...@northwestern.edu ***
Re: [ccp4bb] Calculate real-space R-factor/corr coeff for ligand
Thanks Ian, I'll keep posting :) Brigitte Original message Date: Tue, 4 Oct 2011 21:19:40 +0100 From: Ian Tickle ianj...@gmail.com Subject: Re: [ccp4bb] Calculate real-space R-factor/corr coeff for ligand To: bkziervo...@uchicago.edu Cc: Adam Ralph adam.ra...@maths.nuim.ie, CCP4 bulletin board CCP4BB@jiscmail.ac.uk On Tue, Oct 4, 2011 at 7:14 PM, bkziervo...@uchicago.edu wrote: Hi Adam and Ian, Thanks for your help. If I re-calculate the R-factors with the correct absolute values I get more reasonable values. However, I'm still a bit confused because the output given by the Overlapmap program is structure factor values, which are used to calculate the real-space R-factors. Should this not be Rho values instead? Additionally, a lot of my structure factors, even for the protein, which I know fits well within the experimental density, are 0 for the sidechains or negative. Any idea what's going on here? I've attached some sample data from the Overlapmap output file. Thanks in advance. Brigitte Hi Brigitte Yes I agree with you that the output is very confusing! I don't know exactly what 'Fobs' 'Fcalc' are but I'm pretty sure they can't be structure factors. I would guess that 'F' is actually rho (i.e. rho calculated by FFT from F). According to the man page overlapmap only inputs outputs maps: nowhere does it mention reading or writing SFs. Very confusing! Also why the values are small or negative, I've no idea as I've never used overlapmap. I would keep posting to the BB in the hope that someone can solve your problem. Cheers -- Ian
Re: [ccp4bb] Finding a sequence motif with BLAST
Hi Jacob, SCAN PROSITE http://prosite.expasy.org/scanprosite/ will do precisely what you want. C-X-C-X-C-X-C or C-X-C-X-C would be the pattern using Prosite syntax. Cheers, Dave David C. Briggs PhD Father, Structural Biologist and Sceptic University of Manchester E-mail: david.c.bri...@manchester.ac.uk http://manchester.academia.edu/DavidBriggs (v.sensible) http://xtaldave.wordpress.com/ (sensible) http://xtaldave.posterous.com/ (less sensible) Twitter: @xtaldave Skype: DocDCB On 4 October 2011 21:34, Jacob Keller j-kell...@fsm.northwestern.eduwrote: Dear Crystallographers, I cannot get BLAST to find all proteins with the motif cxcxcxc or at least cxcxc. It seems to think of x as an actual amino acid rather than a wildcard. There must be some easy way to do this? Ordinarily to find a short motif, I would just paste the sequence and get the answer, but here the C's are an absolute requirement and there is no constraint on the x's except that they be only one residue. JPK -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program cel: 773.608.9185 email: j-kell...@northwestern.edu ***
[ccp4bb] Overlapmap
Hi, I am using the program Overlapmap to calculate real-space R-factors and correlation coefficients in order to find ligand conformations that fit best within the density. I'm confused by the Overlapmap output, which includes Fobs and Fcalc values that are used to calculate the R-factors and corr coeff. However, I'm not sure what these F values are as they should not be structure factors since the program seems to only deal with maps. Additionally, in many cases the Fobs and Fcalc values are either 0 or negative values, even for protein residues that are well-defined in the density. Has anyone used this program before or have an idea of what could be going on here? I have been supplying the program with a refmac mtz file with ligand unmodeled as map 1 and a pdb file with both protein and ligand coordinates to calculate the map 2. Any suggestions or ideas of better ways to score ligand fits are appreciated, thanks. Brigitte
Re: [ccp4bb] Installation of ccp4 on 64bit fedora core 13
Hi folks, Anyone know if this site is temporarily down or is it more permanent? http://bioscreencastwiki.com/Crystallography_Howtos/Installing_ccp4-6.0.99e_on_64_bit_Ubuntu Cheers Joel _ Joel Tyndall, PhD Senior Lecturer in Medicinal Chemistry National School of Pharmacy University of Otago PO Box 56 Dunedin 9054 New Zealand Skype: jtyndall http://www.researcherid.com/rid/C-2803-2008 Pukeka Matua Te Kura Taiwhanga Putaiao Te Whare Wananga o Otago Pouaka Poutapeta 56 Otepoti 9054 Aotearoa Ph / Waea +64 3 4797293 Fax / Waeawhakaahua +64 3 4797034 -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Edward A. Berry Sent: Tuesday, 9 August 2011 2:28 p.m. To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Installation of ccp4 on 64bit fedora core 13 유상헌 wrote: Dear all, First I’m a beginner of linux and I’m trying to install CCP4 on my 64bit Fedora 13. If there is anyone who successfully installed ccp4 on 64bit fedora13, please, instruct me how to install this program in detail. I recently installed CCP4-6.1.3 from source on fedora 14, 64-bit. After googling solved a few problems it went easily. Maybe the problems are all fixed in 6.2 so try that first. Un-tar the package- read INSTALL (or INSTALL.html or .ps) in the top directory Try to follow the instructions for installing from source and see where you get stuck. Check the list of problems reported and see if there are solutions at http://www.ccp4.ac.uk/problems.php For me, this site had most of the answers: http://bioscreencastwiki.com/Crystallography_Howtos/Installing_ccp4-6.0.99e_on_64_bit_Ubuntu For fedora, use yum install instead of apt-get install and yum provides (or whatprovides) instead of apt-file search (And unless you are a mac person, you might be more comfortable becoming root rather than prepending every privilege-requiring command with sudo) If you have trouble with TCL/TK read below-quoted message. Mosflm site has more suggestions. better yet: http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/CCP4_on_Fedora_12 Mark Del Campo wrote: Okay, I got the problem resolved in the following way (thanks go to Clint Leysath): 1. removed the tcltk++ directory that came with my ccp4 download 2. installed Activestate's tcltk 8.4.19.2 from https://www.activestate.com/activetcl/downloads/ 3. downloaded blt2.4z.tar.gz and the blt2.4z-patch-2 from http://sourceforge.net/projects/blt/files/ 4. unpacked blt2.4z.tar.gz and moved the patch file into the blt2.4z directory 5. patched the blt installation (patch -p1 -i blt2.4z-patch-2) 6. then reordered statements in blt2.4z/src/bltTree.c [this is detailed at http://www.ccp4.ac.uk/ccp4i/install_tcltkblt.html under the heading Compilation failure in bltTree on 64-bit machines] 7. configured the blt install (./configure --with-tcl=/path/to/ActiveTcl-8.4) 8. installed blt (make) 9. for some reason bltwish did not end up in /path/to/ActiveTcl-8.4/bin even though the configure script said that is where it would be put, so I moved it to /path/to/ActiveTcl-8.4/bin 10. edited 1 line in ccp4.setup-bash (setenv CCP4I_TCLTK /path/to/ActiveTcl-8.4/bin/) 11. opened a new terminal window ccp4i works
Re: [ccp4bb] Finding a sequence motif with BLAST
Thanks everybody, I tried using --toolkit tuebingen mpi --Scanprosite I think my regex syntax was different from the Tuebingen site's, but scanprosite worked well and found many hits, although without really hitting paydirt. I think both of these programs would do the job well, though. Thanks very much for your speedy help (this BB is truly amazing!), Jacob On Tue, Oct 4, 2011 at 3:47 PM, David Briggs drdavidcbri...@gmail.com wrote: Hi Jacob, SCAN PROSITE http://prosite.expasy.org/scanprosite/ will do precisely what you want. C-X-C-X-C-X-C or C-X-C-X-C would be the pattern using Prosite syntax. Cheers, Dave David C. Briggs PhD Father, Structural Biologist and Sceptic University of Manchester E-mail: david.c.bri...@manchester.ac.uk http://manchester.academia.edu/DavidBriggs (v.sensible) http://xtaldave.wordpress.com/ (sensible) http://xtaldave.posterous.com/ (less sensible) Twitter: @xtaldave Skype: DocDCB On 4 October 2011 21:34, Jacob Keller j-kell...@fsm.northwestern.edu wrote: Dear Crystallographers, I cannot get BLAST to find all proteins with the motif cxcxcxc or at least cxcxc. It seems to think of x as an actual amino acid rather than a wildcard. There must be some easy way to do this? Ordinarily to find a short motif, I would just paste the sequence and get the answer, but here the C's are an absolute requirement and there is no constraint on the x's except that they be only one residue. JPK -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program cel: 773.608.9185 email: j-kell...@northwestern.edu *** -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program cel: 773.608.9185 email: j-kell...@northwestern.edu ***
Re: [ccp4bb] Overlapmap
Hi,
On Tue, Oct 4, 2011 at 1:55 PM, Brigitte Ziervogel bkziervo...@uchicago.edu
wrote:
(...)
Any suggestions or ideas of better ways to score ligand fits are
appreciated, thanks.
another alternative:
phenix.model_vs_data model.pdb data.mtz comprehensive=true
will list triplet of numbers: {map CC, 2mFo-DFc value, mFo-DFc value} for
each atom or residues in your structure. Low map CC, low 2mFo-DFc density
value, or /and significantly non-zero mFo-DFc values will point out
problems.
More info:
http://www.phenix-online.org/documentation/model_vs_data.htm
Let me know if you have questions,
Pavel
Re: [ccp4bb] Fwd: Installing ccp4-6.0.99e on 64 bit Ubuntu - Bioscreencast Wiki (works for 32-bit also)
Dear all, I tend to use Google's cached versions or The web archive http://www.archive.org/web/web.php leading to http://web.archive.org/web/20100814204611/http://www.bioscreencastwiki.com/Crystallography_Howtos/Installing_ccp4-6.0.99e_on_64_bit_Ubuntu Hope this helps someone... Best regards, Folmer 2011/10/4 Edward A. Berry ber...@upstate.edu I think I captured most of it in the attached. Hope this doesn't violate anyone's copyright: -- Folmer Fredslund, Ph.D.
[ccp4bb] software for surface curvature
Dear All, These days, I want to calculate the surface curvature for my proteins in a quantitative way and show the results in a graphics software such as Pymol. Does someone have a good idea of which program will do a nice job? Thanks in advance, Best, Jun Liao Dept. of Physiology UTSW medical center at Dallas
Re: [ccp4bb] Finding a sequence motif with BLAST
Just for kicks, check out this sequence I found in the process (conjecture: maybe when the virus causes its synthesis, it uses up all the cysteines/methionines!): sp|Q69566|U88_HHV6U Uncharacterized protein U88 OS=Human herpesvirus 6A (strain Uganda-1102) GN=U88 PE=4 SV=1 MYVSVSVHVSVHVSVRVSVRVSVCVSVRVSVHVSVRVSVSVRVSVRVSVSVRVSVRVSVSVHVSVRVSVRVSVSVRVSVCARVCARVCVCARVCVCARVCVCARVCVCARVCARVCVCACVCVCACLCVCACLCVCACLCVCACLCVCACLCVCACLCVCACLCVCACLCVCVCVCLCVCVCLCVCVCLCVCVCLCVCVCLCVCVCLCVCVCLCVCVCLCVCVCLCVCVCLCVCVCVCVCVCVCVCVCVCVCVCVCLCVCVCLCVCLCVCLCVCVCVCVCLCVCLCVCLCVCVCVCVCLLCMSLCMCMCMCMCMCMCMCMCMSLCMSLCMCMCMCMCMCMCICMCMCICICMCMCMCMCMCMCMCMCMCMCMCMCMCMCMCMCMCMCMCMCMCMCMCMCMCMCMCMCIIEGNK Maybe it's just a sequencing glitch? JPK On Tue, Oct 4, 2011 at 4:05 PM, Jacob Keller j-kell...@fsm.northwestern.edu wrote: Thanks everybody, I tried using --toolkit tuebingen mpi --Scanprosite I think my regex syntax was different from the Tuebingen site's, but scanprosite worked well and found many hits, although without really hitting paydirt. I think both of these programs would do the job well, though. Thanks very much for your speedy help (this BB is truly amazing!), Jacob On Tue, Oct 4, 2011 at 3:47 PM, David Briggs drdavidcbri...@gmail.com wrote: Hi Jacob, SCAN PROSITE http://prosite.expasy.org/scanprosite/ will do precisely what you want. C-X-C-X-C-X-C or C-X-C-X-C would be the pattern using Prosite syntax. Cheers, Dave David C. Briggs PhD Father, Structural Biologist and Sceptic University of Manchester E-mail: david.c.bri...@manchester.ac.uk http://manchester.academia.edu/DavidBriggs (v.sensible) http://xtaldave.wordpress.com/ (sensible) http://xtaldave.posterous.com/ (less sensible) Twitter: @xtaldave Skype: DocDCB On 4 October 2011 21:34, Jacob Keller j-kell...@fsm.northwestern.edu wrote: Dear Crystallographers, I cannot get BLAST to find all proteins with the motif cxcxcxc or at least cxcxc. It seems to think of x as an actual amino acid rather than a wildcard. There must be some easy way to do this? Ordinarily to find a short motif, I would just paste the sequence and get the answer, but here the C's are an absolute requirement and there is no constraint on the x's except that they be only one residue. JPK -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program cel: 773.608.9185 email: j-kell...@northwestern.edu *** -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program cel: 773.608.9185 email: j-kell...@northwestern.edu *** -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program cel: 773.608.9185 email: j-kell...@northwestern.edu ***
Re: [ccp4bb] Finding a sequence motif with BLAST
Maybe it's just a sequencing glitch? Not so--BLAST showed there are a whole cadre of these things in various genomes. Go figure. JPK JPK On Tue, Oct 4, 2011 at 4:05 PM, Jacob Keller j-kell...@fsm.northwestern.edu wrote: Thanks everybody, I tried using --toolkit tuebingen mpi --Scanprosite I think my regex syntax was different from the Tuebingen site's, but scanprosite worked well and found many hits, although without really hitting paydirt. I think both of these programs would do the job well, though. Thanks very much for your speedy help (this BB is truly amazing!), Jacob On Tue, Oct 4, 2011 at 3:47 PM, David Briggs drdavidcbri...@gmail.com wrote: Hi Jacob, SCAN PROSITE http://prosite.expasy.org/scanprosite/ will do precisely what you want. C-X-C-X-C-X-C or C-X-C-X-C would be the pattern using Prosite syntax. Cheers, Dave David C. Briggs PhD Father, Structural Biologist and Sceptic University of Manchester E-mail: david.c.bri...@manchester.ac.uk http://manchester.academia.edu/DavidBriggs (v.sensible) http://xtaldave.wordpress.com/ (sensible) http://xtaldave.posterous.com/ (less sensible) Twitter: @xtaldave Skype: DocDCB On 4 October 2011 21:34, Jacob Keller j-kell...@fsm.northwestern.edu wrote: Dear Crystallographers, I cannot get BLAST to find all proteins with the motif cxcxcxc or at least cxcxc. It seems to think of x as an actual amino acid rather than a wildcard. There must be some easy way to do this? Ordinarily to find a short motif, I would just paste the sequence and get the answer, but here the C's are an absolute requirement and there is no constraint on the x's except that they be only one residue. JPK -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program cel: 773.608.9185 email: j-kell...@northwestern.edu *** -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program cel: 773.608.9185 email: j-kell...@northwestern.edu *** -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program cel: 773.608.9185 email: j-kell...@northwestern.edu *** -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program cel: 773.608.9185 email: j-kell...@northwestern.edu ***
Re: [ccp4bb] software for surface curvature
On 10/05/2011 07:25 AM, Jun Liao wrote: Dear All, These days, I want to calculate the surface curvature for my proteins in a quantitative way and show the results in a graphics software such as Pymol. Does someone have a good idea of which program will do a nice job? If you are a C++ expert and have some strong computational geometry knowledge: http://www.cgal.org/Manual/latest/doc_html/cgal_manual/Jet_fitting_3/Chapter_main.html Maybe by post-processing the output of MSMS (which gives surface normals) you can get something working, more easily. Regards, F. Thanks in advance, Best, Jun Liao Dept. of Physiology UTSW medical center at Dallas
[ccp4bb] Database access failure during program execution
Dear All, I am getting the following error message when trying to execute any program. Database Access Failure This instance of CCP4i no longer has control of the current database.. It is recommending to close the interface and restart, but it is coming back with the same error even after restarting the computer. How can overcome this issue? Thanks. Jobi
Re: [ccp4bb] Database access failure during program execution
Dear All, Some more details. I am running a Ubuntu 11.04 system. The ccp4i is recently installed. I looked into our previous posts and tried to locate the ccp4.LOCK file, but I cannot find one in my system. Also tried to reinstall the whole ccp4i but hasn't solved the issue. Also tried to delete the CCP4-database directory and its contents. Jobi On Wed, Oct 5, 2011 at 9:59 AM, Jobichen Chacko jobich...@gmail.com wrote: Dear All, I am getting the following error message when trying to execute any program. Database Access Failure This instance of CCP4i no longer has control of the current database.. It is recommending to close the interface and restart, but it is coming back with the same error even after restarting the computer. How can overcome this issue? Thanks. Jobi
