Re: [ccp4bb] Fo-Fc map in WinCoot
Yes that works like magic. Never noticed that little box before. WinCoot is jsu wonderful. Hours of endless fun awaits me. Many thanks Ray Brown On Monday, August 26, 2019, 10:47:51 AM EDT, Jonathan Cooper <0c2488af9525-dmarc-requ...@jiscmail.ac.uk> wrote: When you open the map, in the window which comes up there is a little box to tick which says "Is difference map?" in the lower left hand corner from memory. Then it will display the -ve contours. Sent from Yahoo Mail on Android On Mon, 26 Aug 2019 at 15:34, Raymond Brown wrote: Hi folks, I notice that WinCoot does not appear to display the negative peaks in Fo-Fc difference maps. Is there a fix for this? Best Ray Brown To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
[ccp4bb] Fo-Fc map in WinCoot
Hi folks, I notice that WinCoot does not appear to display the negative peaks in Fo-Fc difference maps. Is there a fix for this? Best Ray Brown To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] Refinement
Hi, Run your data through POINTLESS to check space group. Ray On Sun, 3/24/19, StrBio wrote: Subject: [ccp4bb] Refinement To: CCP4BB@JISCMAIL.AC.UK Date: Sunday, March 24, 2019, 12:17 AM ALL. I have data at 2.4 A in P21 sp gr, helical protein. Refined to Rwork 29 Rfree 34 with nice density map and all nice statistics oither Rfactor (by Phenix). Refmac quit same. Should I deposit it or look better data?Any suggestion? To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] Protein modeling issue
Yes you are absolutely right. I believe the problem is the difficulty of fitting valine, leucine and isoleucine rotomers and sidechains to what are essentially "blobs" of map density. Refinement has a hard time with this. I guess we have to stick with the experimental density. Best Ray On Sun, 3/10/19, Eleanor Dodson <176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote: Subject: Re: [ccp4bb] Protein modeling issue To: CCP4BB@JISCMAIL.AC.UK Date: Sunday, March 10, 2019, 3:40 PM Both REFMAC and COOT have an option to regularise (coot) or idealise (refmac) a structure. These options will correct bad gemetry if possible, but pay no attention to the fit to density. In general i think it is sensible to inspect the map for regions where there are serious errors high lighted. However if the resolution is low, or the region of the protein is poorly ordered, it may be difficult to see what needs fixing. Eleanor On Sat, 9 Mar 2019 at 21:23, Raymond Brown wrote: Hi folks, The WHATIF server found the following issue in evaluating a protein structure. Structure Z-scores, positive is better than average: chi-1 / chi-2 rotamer normality : -7.278 (bad ( -3.8, 1.6) ) RMS Z-scores, should be close to 1.0: Improper dihedral distribution : 2.025 (loose) Does anyone have a suggestion of what can be done for example in Coot or Refmac5 to improve or fix these results? Many thanks Ray Brown To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] Refmac5 refinement question
Hi Robbie, Thank you for your very clear explanation and suggestions. Am I right in thinking that what this means is that the zBOND and zANGLE values in Refmac5 refinement should be made to be close to 1.000? Best Ray On Tue, 3/12/19, Robbie Joosten wrote: Subject: Re: [ccp4bb] Refmac5 refinement question To: CCP4BB@JISCMAIL.AC.UK Date: Tuesday, March 12, 2019, 4:58 AM Hi Ray, This is how I see it: Because different bond length and angle target tolerances/sigmas you cannot compare them on an absolute scale. What is less likely? A two 0.020A deviation in the CD1-CG in PHE or a the same deviation in the CD1-CG bond in LEU. If you think they are equally likely, you can use rmsd, if not you probably realise that you are comparing apples and oranges. Enter rmsZ. Instead of comparing the absolute deviations you compare the deviations expressed in sigma (the Z-score). This brings everything on the same scale so you can actually compare them (provided the restraints themselves, especially the sigmas, make sense). Now let's assume that your deviations (expressed as Z-scores) have a normal distribution. Then the rmsZ says something about the broadness of this distribution. With rmsZ equal to 1 your distribution is as wide as that of the source of the restraints (i.e. small molecule structures in the COD, in the case of Refmac). Assuming that your data are a bit worse, you can argue that you do not have any strong evidence to allow wider distributions. That means your rmsZ should not be greater than 1. There seems to be a bit of a downward trend with resolution and rmsZ: lower resolution, lower rmsZ. However the correlation is not very strong and therefor I would say that any rmsZ < 1.00 is fine. Refmac gives these numbers for bond lengths and angles, not for chiral volumes, but those all have the same sigma (AFAIK). Don't go for hard numbers with deviations, unless you find a good rationale to do so (if you do, please share it). I've seen too many case of grossly over/underrestrained models where a much better fit to the data (and other validation criteria) can be obtained by just playing a bit with the geometric restraint weights. HTH, Robbie -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Raymond Brown Sent: Monday, March 11, 2019 17:11 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Refmac5 refinement question Hi folks, What are acceptable values for RMS Bond length, RMS Bond angle and RMS Chiral volume? The tutorial suggests RMS Bond length of 0.0200? I would like to hear your suggestions and/or rationale. Many thanks Ray Brown To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
[ccp4bb] Refmac5 refinement question
Hi folks, What are acceptable values for RMS Bond length, RMS Bond angle and RMS Chiral volume? The tutorial suggests RMS Bond length of 0.0200? I would like to hear your suggestions and/or rationale. Many thanks Ray Brown To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
[ccp4bb] Protein modeling issue
Hi folks, The WHATIF server found the following issue in evaluating a protein structure. Structure Z-scores, positive is better than average: chi-1 / chi-2 rotamer normality : -7.278 (bad ( -3.8, 1.6) ) RMS Z-scores, should be close to 1.0: Improper dihedral distribution : 2.025 (loose) Does anyone have a suggestion of what can be done for example in Coot or Refmac5 to improve or fix these results? Many thanks Ray Brown To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
[ccp4bb] Compositeomit job failed
Hi folks, Calculate Composite Omit Map job fails with output message: *** * Information from CCP4Interface script *** The program run with command: comit -stdin has failed with error message child killed: segmentation violation *** #CCP4I TERMINATION STATUS 0 "child killed: segmentation violation" #CCP4I TERMINATION TIME 27 Feb 2019 13:05:33 #CCP4I MESSAGE Task failed Running on CCP4 version 7.0.0.71 and Windows 7. Seems to be nothing wrong with MTZ file. Please send any thoughts and suggestions in plain English. Best Ray Brown To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
