[ccp4bb] the B facot of soaked substrate
Dear All: I am refining a protein structure with a soaked substrate. The resolution is 2.5 A. The B factor of protein is around 40, while the B factor of the soaked substrate is as high as 80. The density looks fine. Is this structure acceptable? Or is there anyone who can give me an example of this situation in the PDB bank? Thanks. -- Jiamu Du State Key Laboratory of Molecular Biology Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences (CAS)
Re: [ccp4bb] the B facot of soaked substrate
Dear Herman: It is due to the occupancy obviously. Previously, someone mensioned that in this resolution it is not suitable to refine the occupancy. So I think it is better for me to keep the occupancy to 1. Do you have some case for this situation in the PDB bank? Thanks. On 11/1/07, [EMAIL PROTECTED] [EMAIL PROTECTED] wrote: Deart Jamu, You probably do not have full occupancy. Set the occupancy of the inhibitor to say 0.6 and refine again and see what happens to the B-factors. Herman ** -- *From:* CCP4 bulletin board [mailto:[EMAIL PROTECTED] *On Behalf Of *Jiamu Du *Sent:* Thursday, November 01, 2007 1:05 PM *To:* CCP4BB@JISCMAIL.AC.UK *Subject:* [ccp4bb] the B facot of soaked substrate Dear All: I am refining a protein structure with a soaked substrate. The resolution is 2.5 A. The B factor of protein is around 40, while the B factor of the soaked substrate is as high as 80. The density looks fine. Is this structure acceptable? Or is there anyone who can give me an example of this situation in the PDB bank? Thanks. -- Jiamu Du State Key Laboratory of Molecular Biology Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences (CAS) -- Jiamu Du State Key Laboratory of Molecular Biology Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences (CAS)
Re: [ccp4bb] carving up maps (was re: pymol help)
Having put the make my density look publishable (mapcover) command in BobScript, my conscience wouldn't ever let me use it as it gives a false impression of experimental maps! It is useful, though, in a couple of cases: where the map is not representing electron density but calculated from the structure (e.g. binding pockets...) and - artistic tip for the day - to draw a map in two colours which I have used in presentations to help show ligand density. You draw the map in one colour, then increase the map line width ever so slightly and draw it again with map cover and in a different colour. The ligand density is then highlighted but the rest of the structure and noise are still visible. However, the original question seemed to be targeted at obscuring information (the ligand structure) rather than showing it. I assume this is not for academic purposes! My suggestion there would be to use a low resolution map (say calculated to 3.5A) covering where the ligand is and the full resolution map for the rest of the molecule. (Effectively rendering the ligand density as a blob). Otherwise Tassos is spot on... use Illustrator... Cheers, Robert
Re: [ccp4bb] the B facot of soaked substrate
Thank you all. I think I have know how to deal with this situation. Best Regards. On 11/1/07, [EMAIL PROTECTED] [EMAIL PROTECTED] wrote: Dear Jiamu, This is a matter of debate, but I prefer to publish something as close as possible to the true situation. Publishing a structure with artificially inflated B-factors is, in my opinion, further from the truth than publishing a structure with an estimated occupancy, even with a relatively large error, which, by the way, will be less than the error you create when you let the B-factors soak-up the occupancy problem. The problem is that occupancy and B-factors are linked at the resolution you have, so you cannot refine them independently. You have the following options (decreasingly accurate, but increasingly easy and robust to implement). 1) refine individual B-factors and a group occupancy for the substrate. Unless the substrate gets cleaved, it will enter or leave the active site as one piece. If it does get cleaved, you could try to refine group occupancies for the two parts as the would be formed after cleavage. 2) fix the B-factors of the substrate to those of the surrounding protein and refine a (group)occupancy, but no B-factors. (if you can refine B-factors, you can refine occupancies with similar accuracy, but you can not refine the two at the same time). Then fix the occupancy of the substrate to the refined value (if you used individual occupancies, you have to take the average value) and do another round of B-factor refinement. 3) run several refinement trials with different fixed occupancy, say 0.3, 0.4, 0.5 etc. Steps of 0.1 are more than fine enough. Say with value results in R-factors in the range of the surrounding protein. Again, I would advice against publishing a structure with B-factors you are sure they are wrong. Herman -- *From:* Jiamu Du [mailto:[EMAIL PROTECTED] *Sent:* Thursday, November 01, 2007 1:23 PM *To:* Schreuder, Herman SMA/DE *Cc:* ccp4bb@jiscmail.ac.uk *Subject:* Re: [ccp4bb] the B facot of soaked substrate Dear Herman: It is due to the occupancy obviously. Previously, someone mensioned that in this resolution it is not suitable to refine the occupancy. So I think it is better for me to keep the occupancy to 1. Do you have some case for this situation in the PDB bank? Thanks. On 11/1/07, [EMAIL PROTECTED] [EMAIL PROTECTED] wrote: Deart Jamu, You probably do not have full occupancy. Set the occupancy of the inhibitor to say 0.6 and refine again and see what happens to the B-factors. Herman ** -- *From:* CCP4 bulletin board [mailto:[EMAIL PROTECTED] *On Behalf Of *Jiamu Du *Sent:* Thursday, November 01, 2007 1:05 PM *To:* CCP4BB@JISCMAIL.AC.UK *Subject:* [ccp4bb] the B facot of soaked substrate Dear All: I am refining a protein structure with a soaked substrate. The resolution is 2.5 A. The B factor of protein is around 40, while the B factor of the soaked substrate is as high as 80. The density looks fine. Is this structure acceptable? Or is there anyone who can give me an example of this situation in the PDB bank? Thanks. -- Jiamu Du State Key Laboratory of Molecular Biology Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences (CAS) -- Jiamu Du State Key Laboratory of Molecular Biology Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences (CAS) -- Jiamu Du State Key Laboratory of Molecular Biology Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences (CAS)
Re: [ccp4bb] converting structure factor files to mtz files
The crystallographic model-building and display program MIFit can read mmCIF diffraction data directly and compute the map internally i.e. you don't need any other software. There is a tutorial (lesson 16) on this exact application. MIFit runs on Windows and Linux and is free to academics users. There is an installer for Windows and gzipped tar file for Linux http://mi.active-sight.com/download.html There is a lot of flexibility in rendering and image export. Thanks John Badger, Director of Structural Biology, ActiveSight
Re: [ccp4bb] carving up maps (was re: pymol help)
Along those lines, one of the things you can do with PyMOL is color map density based on the color of the nearest atom (if any): Example image at: http://delsci.com/img/map_color.jpg Example script: load ref.pdb load map.xplor isomesh mesh, ref, 1.0 ramp_new ramp, ref, [0,1.5,2], [-1, -1, grey70] color ramp, mesh Cheers, Warren -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Robert Esnouf Sent: Thursday, November 01, 2007 5:06 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] carving up maps (was re: pymol help) Having put the make my density look publishable (mapcover) command in BobScript, my conscience wouldn't ever let me use it as it gives a false impression of experimental maps! It is useful, though, in a couple of cases: where the map is not representing electron density but calculated from the structure (e.g. binding pockets...) and - artistic tip for the day - to draw a map in two colours which I have used in presentations to help show ligand density. You draw the map in one colour, then increase the map line width ever so slightly and draw it again with map cover and in a different colour. The ligand density is then highlighted but the rest of the structure and noise are still visible. However, the original question seemed to be targeted at obscuring information (the ligand structure) rather than showing it. I assume this is not for academic purposes! My suggestion there would be to use a low resolution map (say calculated to 3.5A) covering where the ligand is and the full resolution map for the rest of the molecule. (Effectively rendering the ligand density as a blob). Otherwise Tassos is spot on... use Illustrator... Cheers, Robert
