[ccp4bb] Structure-function PhD position (UK only)
Dear all, I have a PhD position in my laboratory, starting in September 2015. The position will be looking to elucidate the biosynthetic pathway for two unusual sugars from Coxiella, and will have good opportunities for interesting structural work. Unfortunately due to the funding it is only suitable for students in the UK. If anyone knows a good student who might be interested, the position is online at http://www.findaphd.com/search/ProjectDetails.aspx?PJID=60313&LID=503, and I am very happy to take queries. Deadline is Friday 16th January. Best regards, Nicholas Harmer University of Exeter
Re: [ccp4bb] Bulk solvent
Dear Alaistair, this sound a little like the SQUEEZE command in Platon (with dummies placed at the spurious regions), although I am not an expert about what SQUEEZE does in detail. If your structure is not too large, you could give it a try. The Polymerase is too large for Platon, but it works with insulin ;-) best, Tim On 01/11/2015 08:05 PM, Alastair Fyfe wrote: > A related/follow-on question, hopefully on the same topic: > > When mask-based solvent modeling leads to problems caused by calculation > of an inappropriate mask (eg inclusion of disordered loops or > inaccessible pockets as bulk-solvent volume) it seems that a feasible > workaround is to (a) output the calculated mask via MSKOUT (b) edit it > to remove spurious regions (c) calculate partial structure factors for > the new solvent region using refmac's previous kSol, bSol estimates (d) > include the partial structure factors in a second round of refinement by > specifying "SOLVENT NO", FPART and SCPART. > > However, this does not re-calculate kSol and bSol to reflect the > modified mask. Is there a way to simply supply the mask to be used > rather than have refmac calculate it ? > Thanks, > Alastair Fyfe > > > On 01/11/2015 08:04 AM, Eleanor Dodson wrote: >> Yes. If the model is incomplete it is obviously not sensible to use the >> mask based solvent - you will tend to lose the unmodelled features. It >> also >> gives unrealistically low R factors for a crystal with high solvent >> content. However the best test would be to analyse maps and try to decide >> if & when the different procedures work best.. A project for a student >> dissertation perhaps?? >>Eleanor >> >> On 9 January 2015 at 20:13, Roberts, Sue A - (suer) >> >> wrote: >> >>> I always try both methods - usually there is little difference. >>> However, >>> >>> For CueO (multicopper oxidase) where there are about 25 disordered >>> (unseen) residues in a loop, using Babinet scaling instead of the >>> default >>> refmac scaling reduced the R factors by about 2% (both R and Rfree) and >>> improved the quality of the maps substantially. >>> >>> From Dirk's comment, I'd guess this is because the mask-based solvent >>> model is putting solvent where there is (disordered) protein, which is >>> different from real bulk solvent. >>> >>> Sue >>> >>> Dr. Sue A. Roberts >>> Dept. of Chemistry and Biochemistry >>> University of Arizona >>> 1306 E. University Blvd, Tucson, AZ 85721 >>> Phone: 520 621 4168 >>> s...@email.arizona.edu >>> >>> >>> >>> -Original Message- >>> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of >>> Armando Albert >>> Sent: Friday, January 09, 2015 12:56 AM >>> To: CCP4BB@JISCMAIL.AC.UK >>> Subject: [ccp4bb] Bulk solvent >>> >>> Dear all, >>> Is there any reason for using Babinet scaling for bulk solvent >>> correction >>> instead of mask based scaling? >>> Armando >>> > -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A signature.asc Description: OpenPGP digital signature
Re: [ccp4bb] Bulk solvent
A related/follow-on question, hopefully on the same topic: When mask-based solvent modeling leads to problems caused by calculation of an inappropriate mask (eg inclusion of disordered loops or inaccessible pockets as bulk-solvent volume) it seems that a feasible workaround is to (a) output the calculated mask via MSKOUT (b) edit it to remove spurious regions (c) calculate partial structure factors for the new solvent region using refmac's previous kSol, bSol estimates (d) include the partial structure factors in a second round of refinement by specifying "SOLVENT NO", FPART and SCPART. However, this does not re-calculate kSol and bSol to reflect the modified mask. Is there a way to simply supply the mask to be used rather than have refmac calculate it ? Thanks, Alastair Fyfe On 01/11/2015 08:04 AM, Eleanor Dodson wrote: Yes. If the model is incomplete it is obviously not sensible to use the mask based solvent - you will tend to lose the unmodelled features. It also gives unrealistically low R factors for a crystal with high solvent content. However the best test would be to analyse maps and try to decide if & when the different procedures work best.. A project for a student dissertation perhaps?? Eleanor On 9 January 2015 at 20:13, Roberts, Sue A - (suer) wrote: I always try both methods - usually there is little difference. However, For CueO (multicopper oxidase) where there are about 25 disordered (unseen) residues in a loop, using Babinet scaling instead of the default refmac scaling reduced the R factors by about 2% (both R and Rfree) and improved the quality of the maps substantially. From Dirk's comment, I'd guess this is because the mask-based solvent model is putting solvent where there is (disordered) protein, which is different from real bulk solvent. Sue Dr. Sue A. Roberts Dept. of Chemistry and Biochemistry University of Arizona 1306 E. University Blvd, Tucson, AZ 85721 Phone: 520 621 4168 s...@email.arizona.edu -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Armando Albert Sent: Friday, January 09, 2015 12:56 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Bulk solvent Dear all, Is there any reason for using Babinet scaling for bulk solvent correction instead of mask based scaling? Armando
Re: [ccp4bb] Bulk solvent
Yes. If the model is incomplete it is obviously not sensible to use the mask based solvent - you will tend to lose the unmodelled features. It also gives unrealistically low R factors for a crystal with high solvent content. However the best test would be to analyse maps and try to decide if & when the different procedures work best.. A project for a student dissertation perhaps?? Eleanor On 9 January 2015 at 20:13, Roberts, Sue A - (suer) wrote: > I always try both methods - usually there is little difference. However, > > For CueO (multicopper oxidase) where there are about 25 disordered > (unseen) residues in a loop, using Babinet scaling instead of the default > refmac scaling reduced the R factors by about 2% (both R and Rfree) and > improved the quality of the maps substantially. > > From Dirk's comment, I'd guess this is because the mask-based solvent > model is putting solvent where there is (disordered) protein, which is > different from real bulk solvent. > > Sue > > Dr. Sue A. Roberts > Dept. of Chemistry and Biochemistry > University of Arizona > 1306 E. University Blvd, Tucson, AZ 85721 > Phone: 520 621 4168 > s...@email.arizona.edu > > > > -Original Message- > From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of > Armando Albert > Sent: Friday, January 09, 2015 12:56 AM > To: CCP4BB@JISCMAIL.AC.UK > Subject: [ccp4bb] Bulk solvent > > Dear all, > Is there any reason for using Babinet scaling for bulk solvent correction > instead of mask based scaling? > Armando >
Re: [ccp4bb] correction of Ramachandran outlier by Coot
Not easy to do that in the abstract! Look for obvious errors - is there a CISpeptide near by which has been labelled wrongly in the PDB? Is there a genuine error - too many residues, lost residues etc? Or is it just that the density is poor, and it is hard to fit any coordinates and equally hard to refine them sensibly. If you are sure there are no obvious errors to correct the is a rEFINE option to improve the Ramachandran plot - or you can restrain the ramachandran angles.. But if there is an error the plot is correctly trying to alert you and the error needs creating Eleanor On 11 January 2015 at 12:06, Dialing Pretty < 03f1d08ed29c-dmarc-requ...@jiscmail.ac.uk> wrote: > Dear All, > > Will you please introduce me the ways to correct Ramachandran outlier by > Coot? > > Dialing >
Re: [ccp4bb] CCP4 Scalepack2mtz problem: Anisotropy correction failed
Well - I really need to see the output.sca file with the reflection list to test the problem properly, but this log file does show your reflections at the highest resolution are very weak, and maybe not useful. Try cutting the resolute a bit and see what happens. Eleanor On 11 January 2015 at 00:08, Xiao Lei wrote: > Hi Eleanor, > > Thanks for the input, I attach the scale log file here. > > On Sat, Jan 10, 2015 at 2:16 PM, Eleanor Dodson > wrote: > >> Certainly a negative eigen value is bad - can you attach the data? There >> may be some obvious problem.. >> Eleanor >> >> On 10 January 2015 at 04:42, Xiao Lei wrote: >> >>> Dear All, >>> >>> I tried to convert my x-ray diffraction sca data from HKL200 (.sca file) >>> to mtz in CCP4 using Scalepack2mtz and it failed, I do not know what should >>> I supposed to do next to correct the problem, any suggestions are >>> appreciated. I pasted the message from part of log file below: >>> >>> >>> ANISOTROPY ANALYSIS (using intensities): >>> >>> >>> Eigenvalues: -0.5668 0.1479 0.3584 >>> >>> Eigenvalue ratios: -1.5815 0.4128 1. >>> >>> ctruncate: Anisotropy correction failed - negative eigenvalue. >>> >>> Times: User: 0.4s System: 0.0s Elapsed: 0:00 >>> >>> >>> *** >>> >>> * Information from CCP4Interface script >>> >>> >>> *** >>> >>> The program run with command: /Applications/ccp4-6.4.0/bin/ctruncate >>> -hklin "/LAB/CCP4/TEMP/RelADD_12212014ALS502_3_1_mtz.tmp" -hklout >>> "/LAB/CCP4/TEMP/RelADD_12212014ALS502_3_3_mtz.tmp" -colin >>> "/*/*/\[IMEAN,SIGIMEAN\]" -colout P1_12 >>> >>> has failed with error message >>> >>> ctruncate: Anisotropy correction failed - negative eigenvalue. >>> >>> ObjectCache: Leaked 0005 refs to >>> >>> >>> *** >>> >>> >>> >>> #CCP4I TERMINATION STATUS 0 " ctruncate: Anisotropy correction failed - >>> negative eigenvalue. ObjectCache: Leaked 0005 refs to >>> >>> " >>> >>> #CCP4I TERMINATION TIME 09 Jan 2015 19:55:50 >>> >>> #CCP4I MESSAGE Task failed >>> >>> >>> >>> >> >
[ccp4bb] correction of Ramachandran outlier by Coot
Dear All, Will you please introduce me the ways to correct Ramachandran outlier by Coot? Dialing
