[ccp4bb] RMSD map
Hi community, I'd like to calculate Ca-RMSD between two related structures without any structure superposition using a running window of say few amino acids, and map them onto the mobile structure with color-coding. Does anyone have a script for the same? Thanks in advance. Ashok Nayak Post-Doctoral Fellow, Department of Physiology and Biophysics VCU Medical Centre,1101 E Marshall ST, Richmond,VA USA To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] sphere refine radius in coot 0.9.5.1
Dear community, Is it possible to increase the radius of real space refinement while manually adjusting models in Coot with the sphere refine option? Thanks in advance, Ashok Nayak Post-Doctoral Fellow, Department of Physiology and Biophysics VCU Medical Centre,1101 E Marshall ST, Richmond,VA USA To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] Cation-channel pore representation for solvent accessible area
> > Hi Everyone, > Thank you very much for all your inputs. > The easiest way that worked for me was to take the coot dot_surface output > and edit it to a .bild file as per Elaine's suggestion. > Coot dot surface output: > 243.69110 246.85279 354.96833 0.448000.471680.8 > #7278cc > 241.97888 247.57961 354.96833 0.448000.471680.8 > #7278cc > 240.15185 247.92877 354.96833 0.448000.471680.8 > #7278cc > 238.29229 247.88454 354.96833 0.448000.471680.8 > #7278cc > Chimera readable .bild file: > .color0.448000.471680.8 > .sphere243.69110 246.85279 354.96833*0.2* > .color0.448000.471680.8 > .sphere241.97888 247.57961 354.96833*0.2* > .color0.448000.471680.8 > .sphere240.15185 247.92877 354.96833*0.2* > .color0.448000.471680.8 > .sphere238.29229 247.88454 354.96833*0.2* > > The color codes are in 0-1 r g b format and the size of the dots (shown in > bold) could be controlled as well. > The script from Oliver Clarke also works. > > -regards > Ashok > To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
[ccp4bb] Cation-channel pore representation for solvent accessible area
Hi Board Members, I need to draw the solvent accessible surface representation figure for a cation channel pore from the channel coordinates. The Hole program and the documentation is already handy to obtain the 2D-plot (pore radius vs channel coordinate) and the coloured dot surface but is limiting for a publishable figure. Here is what I did I used the HOLE programs sph_process and qpt_conv to obtain the dot surface file as mentioned in http://www.holeprogram.org/doc/index.html#_plotting_a_2d_graph_of_pore_radius_vs_channel_coordinate which I sourced onto VMD. I was unable to get rid off the dots which appear more than certain radius limit. I could not control these in sph_process either. Could anyone suggest me the standard way or fine steps to circumvent this ? Ashok Nayak Post-Doctoral Fellow, Department of Physiology and Biophysics VCU Medical Centre,1101 E Marshall ST, Richmond,VA USA To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] R/Rfree values
Dear Rohit, Look at what percentage of the reflections are in the Rfree set, if its less say 5 %; and you have a good redundancy you can use 10 %. You might like to use the other Rfree set[1 if you have already used the 0 set] or consider using the whole set of reflections as a free set if need be if you suspect a bias in your Rfree set. As suggested earlier I would also look at how the Fobs and Fcalc correlate as a function of resolution from the sigma A plot or CC* values. Sometimes overestimating the resolution would add up more noise and it would give you bad R values. and If the molecule is elongated you might have diffraction anisotropy and in that case The R values don't come down. I would also like to use Refmac along with Phenix; that helped in my case. So you would like to take them one by one and figure out carefully. Best Wishes Ashok Nayak Post-Doctoral Fellow, Department of Physiology and Biophysics VCU Medical Centre,1101 E Marshall ST, Richmond,VA USA On Wed, Dec 14, 2016 at 11:12 AM, Morais, Marc C. <mcmor...@utmb.edu> wrote: > In addition to what others have mentioned, you might want to consider the > unpleasant possibility that part of your structure is simply built > incorrectly. Sometimes rebuilding a short loop or even a few residues in > that loop can do the trick. Look carefully for regions of your map with > poor density and/or regions of your model with poor geometry, and see if > there might be an alternate way to build that region. There is often a > psychological barrier to attempting these rebuilds, because they are > difficult (if they weren't we would have built correctly the first time). > However, once begun, it is often less painful than expected. SA/composite > omit maps can help. > -- > *From:* CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Eleanor > Dodson [eleanor.dod...@york.ac.uk] > *Sent:* Wednesday, December 14, 2016 9:49 AM > *To:* CCP4BB@JISCMAIL.AC.UK > *Subject:* Re: [ccp4bb] R/Rfree values > > es - look carefully at your data quality indicators - batch scales, Wilson > plot - moments etc.. tHese can show up if there is a problem with ice rings > or crystal decay or whatever. > Then I always look at the REFMAC plot of v > If they overlap well - good - but problems with scaling will show up there. > > Eleanor > > On 14 December 2016 at 15:21, Mark J van Raaij <mjvanra...@cnb.csic.es> > wrote: > >> Dear Rohit, >> >> I wouldn’t judge a structure just by the Rwork and Rfree values, but also >> by the validation and other statistics (bond lengths, angles, Ramachandran >> plot, map quality, fit to map, average B values). If these are all ok, you >> should be able to “get away with” an Rfree of 33%. >> In your email you state that you have already made a significant effort >> in different refinement strategies, so perhaps there is no improvement to >> be made there. >> The reason for the high-ish Rfree could be that the data is not so good, >> and reprocessing might help. Although the most likely outcome is that you >> can’t significantly improve it, but at least trying will put your mind more >> at ease. >> In the end, the only way to improve the structure, and R-factors, may be >> to grow a better crystal, cryo-protect better and/or collect better data - >> this particular crystal may just have some kind of disorder. >> >> Greetings, >> >> Mark J van Raaij >> Dpto de Estructura de Macromoleculas >> Centro Nacional de Biotecnologia - CSIC >> calle Darwin 3 >> E-28049 Madrid, Spain >> tel. (+34) 91 585 4616 >> http://wwwuser.cnb.csic.es/~mjvanraaij >> >> >> >> >> >> >> >> > On 14 Dec 2016, at 16:02, rohit kumar <rohit...@gmail.com> wrote: >> > >> > Dear All, >> > >> > I am solving a data of 2.5 A (C121 space group). Right now the R/Rfree >> values are 26/33, after many cycles of refinements (With or With out water) >> the R/Rfree values still same. Zanuda suggests that the space group seems >> to be correct and the model is looking fine in coot. >> > Some one suggest what is the main problem. >> > Should I again process my data? And what is the best way to fine right >> space group (If problem with space group). >> > Please tell me if you need any information regarding may data. >> > >> > -- >> > WITH REGARDS >> > Rohit Kumar Singh >> > Lab. no. 430, >> > P.I. Dr. S. Gourinath, >> > School of Life Sciences, >> > Jawaharlal Nehru University >> > New Delhi -110067 >> > > --
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Re: [ccp4bb] How to fit BioSAXS shape to the Structure
Dear Weifei, It can also be done manually in Pymol by changing the mouse mode from 3 button viewing to 3 button editing and later moving the envelope onto the X-ray structure or vice-versa, however the best fit can be achieved in SUPCOMB. regards Ashok Nayak CSIR-CDRI, Lucknow India
[ccp4bb] A query regarding GST tag protein purification
Hello one and all !! I have been working on cloning and purification aspects on a Leishmanial cysteine peptidase (pI= 8.2) for quite some time. I had cloned it in pGEX expression vector. Expression seemed quite okay when induced with 0.5 and 1mM IPTG, so did the solubility in 4 buffers at different pH conditions. i. e. Tris (6.8), HEPES (7.5), Bicine (pH = 9) and Glycine (pH=10). The problem is when I purify it using glutathione sepharose column I get only GST (size wise estimation; no western tried ) i.e. a prominent 25 KD band. At the same time I get the fusion protein in the load, equilibration and wash fractions. When I increased salt concentration to 400 mM I only could exclude the fusion protein band from wash. I had tried protease inhibitors like PMSF, sigma cocktail, and DTT in the lysate before sonication. I had also tried reduced glutathione upto 40mM in the elution buffer with two different pH at 8 and 9. I also read from the literature from similar proteases the behavior is unaltered even after doing mutagenesis of the Cysteine residue at its active site .Should I try ion exchange or affinity chromatography using any inhibitor of this enzyme?? Can anyone suggest me some tip?? Guys help me out. i am kind of struck here Ashok Ranjan Nayak Research Scholar Molecular and Structural Biology Division Central Drug Research Institute, Lucknow
