Re: [ccp4bb] Bad density for chains
Thank you for the reply. On Thu, Jan 26, 2017 at 9:07 PM, <herman.schreu...@sanofi.com> wrote: > Dear Pooja, > > > > A few remarks: > > > > -Matthews does not show 4 chains in the asymmetric unit, it > suggests 4 chains. However, in reality it can be more or less chains, > although rare, 75% solvent (2 chains) is not unheard of. > > -An initial Rfree of 38% is ok, 32% after refinement is a bit > high > > -Disordered loops do exist and you may have to live with them > (not be able to build them). > > -To correct for anisotropy, I suggest the staraniso server from > global phasing. > > -Unless you ran your molecular replacement in P1, Zanuda will > confirm the space group you choose for MR. So run MR in P1 (if your > symmetry is not too high) and run Zanuda again. (Have someone) look > critical at the assigned space group and assess whether another choice > might also be possible. > > > > Good luck! > > Herman > > > > *Von:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *Im Auftrag von > *Pooja Kesari > *Gesendet:* Donnerstag, 26. Januar 2017 15:12 > *An:* CCP4BB@JISCMAIL.AC.UK > *Betreff:* Re: [ccp4bb] Bad density for chains > > > > We have a 2.6 A structure showing four chains in an asymmetric unit. Our > protein is 360 residues around 40 kDa . Mattews shows four chain in an > assymetric unit (solvent 49% mattews coeff 2.44). The template has about > 60% homologous with our protein. The molecular replacement against this > template gave an initial free R of 38. We did chain tracing and found that > we have good density (2Fo-Fc) for chain A and B but poor density for C and > D. > > > > 1. The density for a particular stretch of 10 amino acids (disordered loop > region) is absent in all the chains. We could not found density for this > flexible loop region in any of the already known structures. Any suggestion > on how can we build this region? > > > > 2. We did not find density for most of the loop regions in chain C and D > which were well traced in chain A and B. How can we improving the density > for these two chains based on chain A and B (Density modification)? > > > > 3. We analysed the data using phenix xtriage and found that our data shows > severe anisotropy. Any suggestion of anisotropy correction? > > > > Pointless and Ctruncate analyses didn't show twinning or NCS. I have > checked the space group using Zanuda. We are stuck at a free value of 32. > > > > On Thu, Jan 26, 2017 at 4:47 PM, Eleanor Dodson <eleanor.dod...@york.ac.uk> > wrote: > > This is a bit too vague to help much. > > How did you solve the structure? > > Eleanor > > > > On 26 January 2017 at 03:50, Pooja Kesari <pkesar...@gmail.com> wrote: > > Dear All, > > Thank you all for reply. > > We have checked the data for twinning. > > Our protein is 360 residues around 40 kDa protein. > > We have tried TLS refinement. > > chain A and B don't superimpose well with chain C and D. (A and B chains > also share slight difference ) > > Since we don't have proper density for *some regions* chain C and D, we > are not sure whether these chain have similar or different conformations. > > We tried anisotropy correction and the model refined a bit. > > > > > > On Wed, Jan 25, 2017 at 10:32 AM, Debanu <debanu@gmail.com> wrote: > > Hi Pooja, > > > > Are you positive you have the correct space group and there are no other > issues like twinning, etc? > > > > If sure, did you define NCS groups in refinement? TLS refinement? Try > different refinement programs? > > > > How big is the molecule? Was it solved by MR or experimental phasing? > > > > You can try superimposing A/B on C/D and refinement with tight NCS then > adjust NCS restraints during model adjustments based on local differences > or also see if phenix autobuild helps. > > > > Best, > > Debanu > > -- > > Debanu Das > > Accelero Biostructures > > > > > On Jan 24, 2017, at 8:42 PM, Pooja Kesari <pkesar...@gmail.com> wrote: > > Dear All, > > I have a 2.6 A resolution structure having four chains in an asymmetric > unit. > > The chain A and B have density for almost all residues however we don't > have proper residue density in chain C and D.What can be tried to build > chain C and D ? > > > > > > Many Thanks > > Pooja > > > > > > -- > > Thanks & Regards, > Pooja Kesari > > Research Scholar > > Department Of Biotechnology > > Indian Institute of Technology Roorkee > > INDIA > > > > > > > > > > -- > > Thanks & Regards, > Pooja Kesari > > Research Scholar > > Department Of Biotechnology > > Indian Institute of Technology Roorkee > > INDIA > > > -- Thanks & Regards, Pooja Kesari Research Scholar Department Of Biotechnology Indian Institute of Technology Roorkee INDIA
Re: [ccp4bb] Bad density for chains
We have a 2.6 A structure showing four chains in an asymmetric unit. Our protein is 360 residues around 40 kDa . Mattews shows four chain in an assymetric unit (solvent 49% mattews coeff 2.44). The template has about 60% homologous with our protein. The molecular replacement against this template gave an initial free R of 38. We did chain tracing and found that we have good density (2Fo-Fc) for chain A and B but poor density for C and D. 1. The density for a particular stretch of 10 amino acids (disordered loop region) is absent in all the chains. We could not found density for this flexible loop region in any of the already known structures. Any suggestion on how can we build this region? 2. We did not find density for most of the loop regions in chain C and D which were well traced in chain A and B. How can we improving the density for these two chains based on chain A and B (Density modification)? 3. We analysed the data using phenix xtriage and found that our data shows severe anisotropy. Any suggestion of anisotropy correction? Pointless and Ctruncate analyses didn't show twinning or NCS. I have checked the space group using Zanuda. We are stuck at a free value of 32. On Thu, Jan 26, 2017 at 4:47 PM, Eleanor Dodson <eleanor.dod...@york.ac.uk> wrote: > This is a bit too vague to help much. > How did you solve the structure? > Eleanor > > On 26 January 2017 at 03:50, Pooja Kesari <pkesar...@gmail.com> wrote: > >> Dear All, >> Thank you all for reply. >> >> We have checked the data for twinning. >> Our protein is 360 residues around 40 kDa protein. >> We have tried TLS refinement. >> chain A and B don't superimpose well with chain C and D. (A and B chains >> also share slight difference ) >> Since we don't have proper density for *some regions* chain C and D, we >> are not sure whether these chain have similar or different conformations. >> We tried anisotropy correction and the model refined a bit. >> >> >> On Wed, Jan 25, 2017 at 10:32 AM, Debanu <debanu@gmail.com> wrote: >> >>> Hi Pooja, >>> >>> Are you positive you have the correct space group and there are no other >>> issues like twinning, etc? >>> >>> If sure, did you define NCS groups in refinement? TLS refinement? Try >>> different refinement programs? >>> >>> How big is the molecule? Was it solved by MR or experimental phasing? >>> >>> You can try superimposing A/B on C/D and refinement with tight NCS then >>> adjust NCS restraints during model adjustments based on local differences >>> or also see if phenix autobuild helps. >>> >>> Best, >>> Debanu >>> -- >>> Debanu Das >>> Accelero Biostructures >>> >>> >>> On Jan 24, 2017, at 8:42 PM, Pooja Kesari <pkesar...@gmail.com> wrote: >>> >>> Dear All, >>> >>> I have a 2.6 A resolution structure having four chains in an asymmetric >>> unit. >>> The chain A and B have density for almost all residues however we don't >>> have proper residue density in chain C and D.What can be tried to build >>> chain C and D ? >>> >>> >>> >>> Many Thanks >>> Pooja >>> >>> >> >> >> -- >> Thanks & Regards, >> Pooja Kesari >> Research Scholar >> Department Of Biotechnology >> Indian Institute of Technology Roorkee >> INDIA >> >> > -- Thanks & Regards, Pooja Kesari Research Scholar Department Of Biotechnology Indian Institute of Technology Roorkee INDIA
Re: [ccp4bb] Bad density for chains
Dear All, Thank you all for reply. We have checked the data for twinning. Our protein is 360 residues around 40 kDa protein. We have tried TLS refinement. chain A and B don't superimpose well with chain C and D. (A and B chains also share slight difference ) Since we don't have proper density for *some regions* chain C and D, we are not sure whether these chain have similar or different conformations. We tried anisotropy correction and the model refined a bit. On Wed, Jan 25, 2017 at 10:32 AM, Debanu <debanu@gmail.com> wrote: > Hi Pooja, > > Are you positive you have the correct space group and there are no other > issues like twinning, etc? > > If sure, did you define NCS groups in refinement? TLS refinement? Try > different refinement programs? > > How big is the molecule? Was it solved by MR or experimental phasing? > > You can try superimposing A/B on C/D and refinement with tight NCS then > adjust NCS restraints during model adjustments based on local differences > or also see if phenix autobuild helps. > > Best, > Debanu > -- > Debanu Das > Accelero Biostructures > > > On Jan 24, 2017, at 8:42 PM, Pooja Kesari <pkesar...@gmail.com> wrote: > > Dear All, > > I have a 2.6 A resolution structure having four chains in an asymmetric > unit. > The chain A and B have density for almost all residues however we don't > have proper residue density in chain C and D.What can be tried to build > chain C and D ? > > > > Many Thanks > Pooja > > -- Thanks & Regards, Pooja Kesari Research Scholar Department Of Biotechnology Indian Institute of Technology Roorkee INDIA
[ccp4bb] Bad density for chains
Dear All, I have a 2.6 A resolution structure having four chains in an asymmetric unit. The chain A and B have density for almost all residues however we don't have proper residue density in chain C and D.What can be tried to build chain C and D ? Many Thanks Pooja
[ccp4bb] BALBES exits after searching the internal database
Hi all Im trying to use BALBES locally to perofrm MR. I have given mtz file and sequence file as input. Upon successful completion of program it is giving an message #---# # Search for Structures with Similar Cell and Space Group # #---# No structure of similar cell and space group was found #---# # Model Database Analysis # #---# number of amino acids in the input sequence file is 377 null BALBES exits after searching the internal database #CCP4I TERMINATION STATUS 1 #CCP4I TERMINATION TIME 23 Jan 2015 16:46:18 #CCP4I TERMINATION OUTPUT_FILES /home/user1/projects/pramod/fmt_all/ccp4/167_balbes/167_balbes_MR_SEARCH_MOD.pdb /home/user1/projects/pramod/fmt_all/ccp4 /home/user1/projects/pramod/fmt_all/ccp4/167_balbes #CCP4I MESSAGE Task completed successfully help?? -- Thanks Regards, Pooja Kesari Indian Institute of Technology Roorkee INDIA
[ccp4bb] imosflm error
Dear All,
Whenever I start imosflm there was an error message
*iMosflm version 7.1.1, 24th March 2014ipmosflm is not compatible.Please
configure iMosflm with the correct executable.on configure*
the imosflm window is closed and there
*Tcl platform is unix x86_64 Linux 2.6.32-431.23.3.el6.x86_64TclTk version
from info patchlevel is 8.4.19Tk windowing system is x11Error in startup
script: invalid command name while executing$::session
setMultipleImageFiles 0while constructing object ::.mosflmExecutable
in ::Fileopen::constructor (body line 145)invoked from withinFileopen
.mosflmExecutable -type open -initialdir [pwd] -filtertypes {{All
Files {.*}}}(object ::.c method ::Controller::initialize body
line 115)invoked from within.c initialize(file
/home/programs/ccp4-6.4.0/share/ccp4i/imosflm/src/imosflm.tcl line
472)invoked from withinsource $env(IMOSFLM)(file
/home/programs/ccp4-6.4.0/share/ccp4i/imosflm/imosflm.tcl line
159) MOSDIR is /home/user1/projects/lpxa_all/ccp4ill,Whenever I start
imosflm from the data processing and analysis using Mosflm.there was an
error message iMosflm version 7.1.1, 24th March 2014ipmosflm is not
compatible.Please configure iMosflm with the correct executable.on
configurethe imosflm window is closed and there Tcl platform is unix x86_64
Linux 2.6.32-431.23.3.el6.x86_64TclTk version from info patchlevel is
8.4.19Tk windowing system is x11Error in startup script: invalid command
name while executing$::session setMultipleImageFiles 0while
constructing object ::.mosflmExecutable in ::Fileopen::constructor (body
line 145)invoked from withinFileopen .mosflmExecutable -type open
-initialdir [pwd] -filtertypes {{All Files {.*}}}(object ::.c
method ::Controller::initialize body line 115)invoked from within.c
initialize(file
/home/programs/ccp4-6.4.0/share/ccp4i/imosflm/src/imosflm.tcl line
472)invoked from within*
*source $env(IMOSFLM)(file
/home/programs/ccp4-6.4.0/share/ccp4i/imosflm/imosflm.tcl line
159) MOSDIR is /home/user1/projects/lpxa_all/ccp4i*
please help!!!
--
Thanks Regards,
Pooja Kesari
Research Scholar
Department Of Biotechnology
Indian Institute of Technology Roorkee
INDIA
Re: [ccp4bb] 3 letter code
Hi Faisal The 3letter code for p nitrophenyl phosphate would be 4NP http://www.rcsb.org/pdb/explore/explore.do?structureId=1D1Q On Thu, Oct 2, 2014 at 4:20 PM, Faisal Tarique faisaltari...@gmail.com wrote: Hello everyone I request you to please tell me the 3 letter code for p nitrophenyl phosphate.. -- Regards Faisal School of Life Sciences JNU -- Thanks Regards, Pooja Kesari Research Scholar Department Of Biotechnology Indian Institute of Technology Roorkee INDIA
