Re: [ccp4bb] Phosphatase enzymatic assay
Hi, Could you radiolabel the kinase? If yes, measuring the labeled Pi may work. Cheers, Seema To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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] ionic interaction inside a protein
The link is fine. If you still get the 'error message', then google "PIC webserver" , fullform of PIC - protein interactions calculator. Seema Nath
Re: [ccp4bb] ionic interaction inside a protein
you can try the following link: http://pic.mbu.iisc.ernet.in/ Seema Nath
Re: [ccp4bb] Off-topic Thrombin cleavage
I have used both Novagen thrombin & lyophilized thrombin of BDBioscience(dissolved in 10X thrombin dilution buffer provided by Novagen) in both 'thrombin cleavge buffer' & others (HEPES pH 7.0, Bicine pH 9.0, MOPS pH 7.8) without adding calcium chloride - all the conditions permitted the cleavge process, but addition of DTT/ BMe slowed the process
[ccp4bb] arp/warp error
I've recently installed arp/warp(7.1) in ccp4 6.2 in linux i686,the problem is whenever I'm trying to run arp/warp navigator or any other programs under arp/warp it gives the error " cannot get environment variable for warpbin" Please help. Thanks in advance. Seema Nath
Re: [ccp4bb] how to distinguish between phase separation, spherulite, and microcrystalline?
I also got something shown in pic.3 and supposed to be some oil droplet,when I tried to break them I found that was actually a hemisphere type material attached to the coverslip like a 2D circle and sphere like shape in the hanging drop, a small hanging-drop within a large one.Ammonium sulfate was used as precipitant,even I put it to run SDS-PAGE and it was (may be a quasi-crystal of) the protein of interest.
[ccp4bb] off-topic:increasing clashscore in Phenix refinement
I'm trying to solve a structure by MR using Phenix,reso. 2.69A,sg I121(imosflm), but I'm taking upto 2.9A data and sg P1 which shows 0.49 twinning(h,h-k,h-l).I've got 3monomers/asu & the R-factor/R-free is 28.97/36.34 at 2.9 using twin law,xyz-refinement,individual B factors. Now R-free becomes static,with almost a minor change in decimal place & clashscore is increasing in every steps,when I'm trying to rectify the residues listed in Ramachandran outliers/Rotamers outliers...etc. the C-N bond get collapsed/the whole residue get detached/the geometry worsen.The starting model requires atleast 20% side-chain mutation but there's almost no density for the left out large side chains.Please suggest how to overcome this problem.Thanks in advance. Regards, Ms.Seema Nath
[ccp4bb] problem with ccp4 6.1.13
Recently I've installed CCP4 6.1.13 (RHL4) to use refmac 5.5 twinning refinement (as stated in the current version) but the program list shows refmac5 instead of the current one. So I followed the thread- >Re: [ccp4bb] refmac 5.6 and the ccp4i task interface >Garib N Murshudov >Wed, 29 Sep 2010 11:50:14 -0700 >Yes. There are two ways: >1) replace $CBIN/refmac5 with refmac5.6 >2) on ccp4i click "System administration", select "configure interface" and >jus >below >"Give full path name for CCP4 programs to overcome name conflicts" click "Add >a >program" >there will appear two fields. On the right field type refmac5 and on the left >field actual address of the program. >I hope it helps >regards >Garib On 29 Sep 2010, at 16:39, Ben Eisenbraun wrote: > Is it possible to use refmac 5.6 with the ccp4i Refmac5 task? > > Can I just copy the 5.6 binary over the 5.5 binary distributed with CCP4? > It looks like the new refmac has a number of new keywords which wouldn't be > accessible doing this, but would it otherwise be compatible? If so, where > does the dictionary go? > > Is there some elegant way of letting users choose between the two? > > Thanks. > > -ben > > -- > | Ben Eisenbraun | Software Sysadmin | > | Structural Biology Grid | http://sbgrid.org | > | Harvard Medical School | http://hms.harvard.edu | I followed both the option still there is refmac5 in place of the current version. Please suggest possible solution of the problem. Thanking you Regards, Seema Nath
[ccp4bb] problem running tutorial data in phenix autosol
dear all, i was trying to run the sad tutorial data in phenix autosol. the p9 sad worked really well in the fast mode building almost the entire structure, but the se17 sad data does not give good results. it shows an fom of 34.6 and r factor of 33.2 in P41 spacegroup. autobuild built only a part of the model which was no where to the deposited structure pdb 1qqe. i would be very grateful to know the exact way to run the sec17-sad data in autosol and the post processes. seema nath
[ccp4bb] coot-scripting
Hi, I'm using COOT-0.6 following the manual,but while trying to use (calculate>scripting>)>python or (calculate>scripting>)>scheme to write any command (say,set_show_origin_marker 0) it shows "BL WARNING:: Python syntax error! (Or you attempted to use an invalid guile command...) Python error: unexpected EOF while parsing (, line 1) " Please suggest me the correction to run the command correctly. Thanking you, Seema Nath
Re: [ccp4bb] Pseudo-symmetry/refinement
Would you please explain how to proceed for "rigid body refinement against weak reflection" & "normal restrained refinement against strong reflection".
Re: [ccp4bb] crystal growth
All the crystals I got for three different proteins in same condition looked similar. I think crystal morphology may vary with the crystallizing conditions.
Re: [ccp4bb] crystal growth
I used NaF in the precipitant thrice for three different proteins to be crystallized & each time I got crystals and they were all salt crystals ! I thought low solubility of NaF causes this quick crystallization of salt. Recently I got crystals of a protein at 20 degree grown in gradient concentration of AmSO4 as precipitant.In some cover-slips I got precipitate initially but I kept the tray at RT for mounting at home-source & after some time I saw small crystals appeared in those drops which contained precipitate initially.Though the small crystals never grew enough for mounting. Some drops were used for seeding,small crystals appeared but they dissolved/disappeared at RT, again reappeared after several weeks as larger one.
Re: [ccp4bb] "CCP4i has no longer control of the current database error"
Please check the "project directory" & "temporary directory" is correct or not. Initially I faced the same problem for not assigning the correct project directory (I use it Windows, but the problem also occured in Linux system). If you are running CCP4 in Windows make sure that the folder "CCP4 DATABASE" contains 2 .DEF files -1. database & 2. tmp_database & also assign correct directories. For Linux,check the directories.
Re: [ccp4bb] ? steps after detwinning
@R.Brown Resolution 3.2A DENZO suggests P6. Angles are 90,90,120 Data completeness ~95% R-merge-0.06 Wilson B-factor 42.0
Re: [ccp4bb] ? steps after detwinning
@R.Brown I'm using DENZO I'm trying POINTLESS but I don't understand "unmerged data" -what's that? is it the spot images which are used for "peak search" during data processing? Both SFCHECK & phenix.xtriage showed the information about pst & twinning. However I've tried a thorough process of reindexing,phaser,refmac ...etc. & now in P31 is showing R-factor & R-free as 0.37 & 0.40 respectively with a poly-ala model.I think I'm going towards correct solution. Many many thanks for your help.
Re: [ccp4bb] ? steps after detwinning
@R.Brown I've already tried POINTLESS but due to some reasons it failed and it isyet to be fixed.I've used SFCHECK which shows the PST vectors.I'm alreadyusing PHASER with "all choices of alternative space groups". N.B.:I've mailed you twice but each time the mail is undelivered.
Re: [ccp4bb] ? steps after detwinning
@R.Brown I regret to say that I can't tell what the actual translation is but regarding no. of monomers/asu,I got three non-overlapping monomers.My problems are - 1.actual space-group is not clear yet. 2.no. of monomers/asu ? 3.how to proceed with the technique where data having pseudosymmetry & twinning are firstly solved in lower symmetry space-group until the R-factor & R-free come to stand still and then tranference to a higher symmetry space-group.Is the solution in lower symmetry sg used in higher symmetry sg or the raw data is individually processed in both lower & higher sg? I've mentioned the detailed problem in the ccp4bb on 27th september'10
Re: [ccp4bb] ? steps after detwinning
I've used phenix.xtriage and it showed that in all three cases i.e. (P31,P61 & P6122 space groups) "translational pseudosymmetry is very likely present). Again, when I used molrep in ccp4,it showed "translational pseudosymmetry is detected".
Re: [ccp4bb] ? steps after detwinning
After running phenix.xtriage the possible point group is P622 and possible spacegroups are P622,P6122,P6522,P6222,P6422,P6322. Using this information when I run PHASER, P6322 is shown to be the most probable one.After 5 cycles of phenix.refine R-& R-free - 57 & 60 respectively. From other crystallization papers, I found that data having translational pseudosymmetry had been solved in low-symmetry spacegroup firstly and then in higher symmetry.My query is:Is the data in lower symmetry spacegroup used for higher symmetry or the raw-data is processed individually in higher symmetry? if raw data is used,then why not starting with higher symmetry directly? if data got in lower symmetry group is used,then what is the procedure?Are the .mtz & .pdb files generated in Refmac used for higher symmetry? Thanks in advance.
[ccp4bb] problem in heavy metal soaking
I'm working with a protein which crystallizes in a mixture of PEG6K with 0.2M AmSO4,my question is if there's any problem if I want to soak heavy metal derivatives in this crystallizing condition? Does AmSO4 interfere in heavy-metal soaking ? if yes, what's the reason? Thank you in advance.
[ccp4bb] ? steps after detwinning
my crystals have 0.401 alpha-twinning fraction,which on detwinning reduced to 0.22 & also pseudo-translation ~48.5,the resolution is poor,3.7 angstorm,please suggest next step after detwinning thanks in advance ..
[ccp4bb] problem in CCP4
Recently I've downloaded CCP4 in my home-computer having windowsXP.It has been successfully installed but whenever I'm trying to run any program,there's an error message saying"Database Access Failure.This instance of CCP4i no longer has control of the current database. This is probably because another CCP4i is running and has taken control of the current database over from this one." Please suggest a solution . Thanks in advance. Regards, Seema
[ccp4bb] data & contrast
I've got a data at 3.7 angstrom resolution,P3 space group but smallest cell volume as predicted by marIndex is very large in comparison to the 90 residue small protein & I'm supposed to solve it using auto-MR and CNS, now when I'm using auto-MR to search CRF & TF peaks with lowest R-factor & appreciable corelation co-efficient using a model pdb having 43% homology, the solution gives 7-10 monomers and a message"No contrast available". Please tell me what's the solution of this problem? Thanking you in advance !!
