[ccp4bb] sigma value in structure file

Dear all During PDB deposition the annotator me to verify and review the sigma value in the structure file which in my case was -0.03. I have some basic queries and request you all to please answer them. My first question is, what actually is a "sigma value" of a structure file. 2nd) where the val

Re: [ccp4bb] AW: [ccp4bb] sigma value in structure file

t is just guessing. > > My two cents, > Herman > > > -- > *Von:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *Im Auftrag von > *Faisal Tarique > *Gesendet:* Montag, 17. Juni 2013 08:41 > *An:* CCP4BB@JISCMAIL.AC.UK > *Betreff:* [ccp4b

[ccp4bb] Self rotation function and translation peak

*Dear All *In case we have more than one molecule per asymmetric unit, how to look for the results of the self-rotation function calculation and translation peak in the native patterson. -- Regards Faisal School of Life Sciences JNU

[ccp4bb] visualizing G310 helices in PYMOL

Dear all Sorry for the off topic question. My protein has few G310 helices. It is clearly visible through STRIDE or DSSP, but when i open the structure in PYMOL it didnt show it. Other visualization graphics like CHIMERA and VMD are able to pick few of them but not all the G310 helices..For manu

Re: [ccp4bb] visualizing G310 helices in PYMOL

: > http://pymol.sourceforge.net/newman/user/S0260cartoons.html) > > HTH, > Partha > > > On Thu, Sep 26, 2013 at 4:02 PM, Faisal Tarique > wrote: > >> >> Dear all >> >> Sorry for the off topic question. >> >> My protein has few G310 hel

[ccp4bb] observed criterion sigma

Dear all I request you to please explain the "Observed criterion sigma" value required during pdb deposition. Does it depends on the methods of data integration and scaling ? if yes then what are the values for the data processed through scalepack2mtz (HKL2000) and scala (mosflm).. -- Regards F

[ccp4bb] rmsd

Dear all Can anybody please tell me if there is any sever where i can find RMSD and no of C alpha of the two structures which were aligned manually in PYMOL.. really apologize for asking off topic question.. thanks in advance -- Regards Faisal School of Life Sciences JNU

[ccp4bb] pdbredo

Dear all I have solved a structure of a protein at 2.1A..the R and free R is 21 and 26..for the betterment of its refinement statistics i submitted the coordinate and structure factor file to we based server "PDB_REDO" which improved the R and Rfree to 18 and 23, (which probably does through TLS r

[ccp4bb] resubmission of pdb

Dear all Dear Dr. PDB, Some time back i had submitted a coordinate in PDB but because of unacceptance of the manuscript we had to retract the submission. During this procedure i got few zipped file from the annotator such as 1>. rcsb0.cif-public.gz, 2>. rcsb0.pdb.gz and 3>. rcsb0-sf

[ccp4bb] apologize

My earlier mail had an aberration where i began my mail by Dear Dr PDB..i am extremely sorry for this .. -- Regards Faisal School of Life Sciences JNU

Re: [ccp4bb] resubmission of pdb

r limit of keeping PDB entries in the 'HPUB' >> status. >> >> So when a PDB entry is retracted before release, is the PDBid recycled > after >> a while? >> >> Cheers, >> Robbie >> >> > -Original Message- >> > From: CCP4 bulle

[ccp4bb] 3letter code

Hi everyone Can anyone please tell me the three letter code for D-Ribulose 1,5-bisphosphate.. Thanks in advance -- Regards Faisal School of Life Sciences JNU

Re: [ccp4bb] 3letter code

> #> grep -i ribulose * > > mon_lib_list.cif:5RP 5RP 'RIBULOSE-5-PHOSPHATE non-polymer > mon_lib_list.cif:HMS HMS '5-O-phosphono-L-ribulose > mon_lib_list.cif:RUB RUB 'RIBULOSE-1,5-DIPHOSPHATE > > points you at the RUB, as Mario already mentioned

[ccp4bb] relation between redundancy and total reflection

Dear all Can anybody please tell me how redundancy is related to total no. of observations and number of unique observations..what is the best way to identify and locate these values in a data processed through HKl2000..I know that completeness, redundancy, Rsymm, I/isig etc can easily be located

Re: [ccp4bb] AW: [ccp4bb] relation between redundancy and total reflection

flections divided by no. of unique > reflections, i.e. how often each unique reflection has been measured on > average. > > Herman > > > > *Von:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *Im Auftrag von > *Faisal Tarique > *Gesendet:* Donnerstag, 17. April 2

Re: [ccp4bb] AW: [ccp4bb] relation between redundancy and total reflection

a bit more resolution out of a > weakly diffracting crystal.) In recent versions of HKL, the redundancy > values are printed in a table as well. > > Hope that helps, > > Matt > > > > > On 4/17/14 10:25 AM, Faisal Tarique wrote: > > Dear Herman >

[ccp4bb] observed criterion sigma

Dear all I request you please tell me what is the value of Observed criterion sigma (F) and Observed criterion sigma (I) for any data processed by imosflm and scala ? -- Regards Faisal School of Life Sciences JNU

[ccp4bb] anomalous signal for Mg and Calcium

Dear all Just in the continuation of my previous mail i again want to ask few question on the metalloprotiens..Apart from factors like occupancy, B factor, coordination sphere and metal ion-ligand distances to distinguish Mg or calcium, can anomalous signal tell the identity and the type of metal

[ccp4bb] rigid body refinement or molecular replacement.

Dear all I have a high resolution (2A) native structure of a protein and structure factors for a relatively low resolution (2.6A) of the same protein bound with its substrate (complex) having same space group and cell parameters (P212121 is the space group and cell parameters are a,b,c =39.4,64.5,

[ccp4bb] anomalous signal

Dear all written below is the log file of an anomalous data processed through SHELXC..my question is ..what is the strength of anomalous signal ?? as it is said "For zero signal and should be about 0.80". Then in the present case is there really a signal or can be assumed no signal..we are expec

[ccp4bb] anomalous signal

Dear all sorry about my previous mail where i forgot to mention that the data was collected on home source at Cuk alpha and at 1.54A. written below is the log file of an anomalous data processed through SHELXC..my question is ..what is the strength of anomalous signal ?? as it is said "For zero s

[ccp4bb] anomalous signal

Dear all I am working on a metalloprotein which probably contains Ca at its active site..The sulfur containing amino acid constitutes almost 5.4% of the total amino acid residues of this protein..I have collected the data at home source (CuKalpha=1.54A)..Since f'' of Sulfur is 0.56 and that of Ca

[ccp4bb] ideal rms bond and rms angle

Dear all I request you to please tell me the ideal rms bond and rms angle for a perfectly refined structure..As we can see in order to have optimum R and Rfree we often adjust the weighing factor in Refmac so as the R and Rfree changes it brings changes in rms bond and rms angle as well..Does the

[ccp4bb] citation for shelxc and hkl2000

Dear all i request you to please tell me the name of paper required for citing shelxC and hkl2000.. Thanx in advance -- Regards Faisal School of Life Sciences JNU

[ccp4bb] Difference between different b factors values

Dear all I request you to please tell me the difference between wilson B-factor and average B, all atoms ?? I have two structures one native at 2A resolution, having mean b factor of 24 and the other a complex structure of the same protein with a ligand (at 2.6A resolution) has mean b factor of 23

[ccp4bb] CC-half value

Dear all How CC-half value of a data set determines the resolution limit for the data processing ?? Although much we know about the Rsym and I/Isig values of the highest resolution shell while processing the data, what are the parameters we need to check related to CC-half values ?? -- Regards

[ccp4bb] CC-half value ??

Dear all How CC-half value of a data set determines the maximum resolution limit during data processing ?? Although much we know about the Rsym and I/Isig values of the highest resolution shell while processing the data, what are the parameters we need to check related to CC-half values ?? -- Re

[ccp4bb] cc1/2 value in hkl2000

Hello everyone Can anybody please tell me where to locate the Corelation value between half sets (CC1/2) of a data processed through HKL2000 ?? -- Regards Faisal School of Life Sciences JNU

Re: [ccp4bb] CC-half value ??

Thank you for your valuable suggestions..it really helped me a lot.. On Fri, Aug 15, 2014 at 8:38 PM, Phil Evans wrote: > I should make the estimation in Aimless more robust, and curve fitting > sounds like a good idea (but what function?). Outliers are a difficult > problem, but anyway I think

[ccp4bb] calculation of active site area

Dear all Please tell me the names of good servers / tools which calculate the size and surface area of the active site pocket of a protein.. -- Regards Faisal School of Life Sciences JNU

[ccp4bb] variation in metal ion requirement

Hello everybody Why sometimes same enzyme of a homologous series from different organism show different affinity towards type of metal ion for its activity..Lets say threonine dehydratase from H pylori show maximum activity with Mg2+ as a cofactor while the same enzyme from Entamoeba histolytica

[ccp4bb] 3 letter code

Hello everyone I request you to please tell me the 3 letter code for p nitrophenyl phosphate.. -- Regards Faisal School of Life Sciences JNU

Re: [ccp4bb] 3 letter code

complete/4NP > > > Andreas > > > > > On 02/10/2014 11:50, Faisal Tarique wrote: > >> >> Hello everyone >> >> I request you to please tell me the 3 letter code for p nitrophenyl >> phosphate.. >> -- >> Regards >> >

Re: [ccp4bb] 3 letter code

gens. > > Cheers, > Robbie > > > -Original Message- > > From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of > > Paul Emsley > > Sent: Thursday, October 02, 2014 13:31 > > To: CCP4BB@JISCMAIL.AC.UK > > Subject: Re: [ccp4bb] 3 letter

[ccp4bb] 3 letter code for pyridoxine

Hello everyone Wishing you all a very happy new year.. I request you to please tell me the three letter code for pyridoxine.. -- Regards Faisal School of Life Sciences JNU

[ccp4bb] deposition through ADIT or wwPDB Deposition & Annotation (D&A) System

Hello everyone Is coordinate deposition through ADIT is still valid or it has to be done by the newly arrived wwPDB Deposition & Annotation (D&A) System of the RCSB..OR both are fine ? -- Regards Faisal School of Life Sciences JNU

[ccp4bb] Bin R and Rfree values

Hi everbody, I have one question with regards to the Bin R and Rfree values. My overall R and Rfree values for (resolution1.4 angstrom) is 15% and 19% respectively. But, the values in bin as shown in PDB header after the refinement from the REFMAC are 15.7% for R and 14.5% for Rfree. In this R is

[ccp4bb] cryo condition

Hello everyone Can anybody suggest me a cryo condition for a crystal obtained in MIDAS screen of Molecular Dimension: G1> 0.1MTris8.0G10.1Mpotassium chloride25% v/vSOKALAN®CP7 0.1MHEPES7.0 G2>0.3Mammonium formate20% v/vSOKALAN® CP 5 0.1MHEPES7.0 Crystals are in beautiful cuboid shaped but all s

Re: [ccp4bb] Cryo protection

Cryo On 5 May 2015 13:51, faisaltari...@gmail.com wrote: Thank you everyone..I have got some hints from this discussion and will definitely try some of them to check its efficacy for my case...Thanx again for your valuable suggestions.. On 5 May 2015 13:48, "Anthony Savill" wrote: Dear colleag

[ccp4bb] Cryo-EM

Hi everyone A bit off topic..but..I request you to please suggest me some good readings related to Cryo-EM.. Thanx in advance -- Regards Faisal School of Life Sciences JNU

Re: [ccp4bb] Cryo-EM

Hi everyone Thanx a lot..Your suggestions are really informative and a valuable source of knowledge.. regards Faisal On 5/20/15, Takanori Nakane wrote: > Hi Faisal, > > Recordings of MRC-LMB EM-course last year are available at > http://www2.mrc-lmb.cam.ac.uk/groups/scheres/impact.html > > Bes

[ccp4bb] Difference in the substrate specificity for TMP and CMP

Hello everyone I am working on a 5'-nucleotidase (Mg as a cofactor) and have a decent structure of the same at 2A resolution..While doing its biochemical characterization i found it hydrolyzing TMP: Thymine-5'-monophosphate at much higher rate than CMP Cytosine-5'-monophosphate (40 fold difference

[ccp4bb] topdraw

Dear all Can anybody provide me the link to download or install " TopDraw " a topology drawing interface in CCP4..? Thanks -- Regards Faisal School of Life Sciences JNU

[ccp4bb] webserver for molscript

Hello everyone Is there any online server which could convert 3D structure of a protein into 2D image, the way program molscript does ? -- Regards Faisal School of Life Sciences JNU

Re: [ccp4bb] sudhir.1...@gmail.com is inviting you to freecharge.in

is these site is meant for this purpose ? On 12/24/10, Bosch, Juergen wrote: > I only drink Lavazza sorry. Donations can be sent to below address. Thank > you ! > > Jürgen > - > Jürgen Bosch > Johns Hopkins Bloomberg School of Public Health > Department of Biochemistry & Molecular Biology > Johns

Re: [ccp4bb] off-topic replay: glycerol in protein stock solutions

hello Bert u can also add 50mM to 100 mM Argine and glutamate either alone or combined together..it really works fine..although it will increase the protein stability many fold but i dont know whether it will impede crystallization or not.. others comments are welcome.. Faisal SLS, JNU New Delhi

Re: [ccp4bb] off-topic replay: glycerol in protein stock solutions

hello everybody how does arginine and glutamate affect crystallization..what will be the better stabilizing agent during protein purification which wont affect crystallization or have minimal affect on crystallization..example..glycerol, sorbitol, glycine, poline, arginine, glutamate..what should

Re: [ccp4bb] kinase purification

Kendall is absolutely correct.. Faisal On 3/30/11, Kendall Nettles wrote: > There is a paper from John Kuriyan on co-expressing a phosphatase with c-Src > kinase domain to enable bacterial expression of homogenous protein ( > PMID: > 16260764). Also look at work from E. Goldsmith (PMID: 16829129

[ccp4bb]

which type of protein u r working on ?? On Fri, May 4, 2012 at 12:39 PM, ruby singh wrote: > Dear all, > > Im a PhD student who started working on Protein crystallization. Its been > years im trying to get any crystal of that protein. I have tried all > crystallization screens available. > but n

[ccp4bb]

Dear All I have one query, i have solved one structure where in which near cys residues i can see density for beta mercaptoethanol (which i have used in my crystallization cocktail ). i have one query when i am taking BME from coot library, i can fit it in density but i do not know how to make di

Re: [ccp4bb] Moleculardimensions kits

hi i dont know about the midas but proplex is good..but if u really wanna go for some molecular dimension screen then opt for morpheus..it is damn good..if any protein is ever going to crystallize, it will also give crystal in this screen too.. u could find a hit in this screen also.. best of luc

[ccp4bb] CME

Dear All, I have one query while fitting residues into the density i came across the cysteine residue which as per me is fitting nicely as Cys in disulfide bond with beta mercaptoethanol, so from coot i have taken CME which is infact cysteine plus bme, my query is how to proceed with submission,

[ccp4bb] lithium incorporation in refmac

Dear all i have downloaded lithium coordinates for the density i guess is for lithium but i think while refinement in refmac is not taking lithium into the consideration. i want to know how to obtain cif file for lithium and incorporate it into the refmac for refinement.. thanx in advance l --

Re: [ccp4bb] lithium incorporation in refmac

common > ions. Are you sure you have the atom name in the right columns on the > HETATM record (e.g. Li in 13-14 and LI1+ in 77-80)? > > Cheers > > -- Ian > > On 8 June 2012 19:35, Faisal Tarique wrote: > > > > Dear all > > > > i have downloaded li

[ccp4bb] large difference between r & rfree during refinement

Dear all i have two basic queries 1> while refining my structure (of resolution 2.2A) i face problem with the gap in R & Rfree which is around 8. The mosaicity of my data is 1.8. is this difference is due to large mosaicity or twinning though for twinning i got nothing when i checked with Xtriag

[ccp4bb] value of observed criterion sigma

Dear all i have two basic queries 1) i have processed my data in HKL 2000 and during pdb submission i need to know the value of observed criterion sigma (F) and observed criterion sigma (I). 2) during entering data in category resolution shell whether one needs to mention the statistics of each

[ccp4bb] balbes solution

Dear all i submitted one job in BALBES at YSBL server. The final outcome are showing the result to be definite solution by stating it to be a 99%solution. but when i am refining with refmac, Rwork and Rfree is not coming down despite my several tries. In COOT i can see tye missing density for lo

[ccp4bb] hi

Dear all A mtz output from mosflm when fed to SCALA gives information about total no of reflection, uique reflection, R merge, redundancy etc. i have two questions. 1. is there anyway to use sca files from HKL2000 with SCALA. 2. SCALA gives two multiplicity, one along with binary reflection and

Re: [ccp4bb] determination of oligomerization state of protein

Hi you can also try dynamic light scattering of different fraction of the peak.it will help you to know the exact molecular size of individual peak..glutaraldehyde crosslinking is also a good option..increasing the concentration of protein may shift the equilibrium in the direction of higher mole

Re: [ccp4bb] ideal rms bond length

Thanx everybody for your nice suggestions.. On Wed, Oct 3, 2012 at 3:19 AM, Faisal Tarique wrote: > > Dear all > > i request you to please answer my basic query about the ideal acceptable > rmsbond length obtained during refmac refinement..is the data acceptable in > min

[ccp4bb] side chain density

Dear all i have solved a structure ( at 2A resolution) whose Rwork and Rfree is 22 and 25 respectively..the Ramachandran plot shows 90% of the residues in the most favorable region and with 6 residues in generously allowed and no residues in disallowed region. But in some areas i can see density m

[ccp4bb] seleno methionine labelling of protein

Dear All just want to ask the difference between labelling your protein with D L selenomethionine mixture and L selenomethionine alone..will it make difference in anomalous diffraction,detection of Se signal and extraction of phases. Or will be the same for both..? -- Regards Faisal School of L

Re: [ccp4bb] seleno methionine labelling of protein

I am not up to date, but is there an expression system that allows you > to incorporate D-amino acids into proteins? In terms of phasing only > the Se-atom is a point or sphere, so the signal won't be altered > provided the position of that atom is the same in either case. > >

[ccp4bb]

Dear all I have solved one structure at resolution 2.6 Angstrom in the space group P212121. The R/ Rfree are 22 / 26 with FOM of .806, but when i am trying to upload on the online validation server its not working. Just to cross check there is no problem with my mtz i took altogether unrelated m

[ccp4bb] how to add atoms in refmac library

Dear all My protein has Zinc atom but the refmac does not identifies it during refinement..Can anybody please tell me how to add Zinc atom into the refmac library for the successful refinement of the coordinates. -- Regards Faisal School of Life Sciences JNU

Re: [ccp4bb] how to add atoms in refmac library

to be ZN. > > > > Ganesh > > > Le 14/02/13 21:28, Faisal Tarique a écrit : > > Dear all >> >> My protein has Zinc atom but the refmac does not identifies it during >> refinement..Can anybody please tell me how to add Zinc atom into the refmac >> li

[ccp4bb] B factor of the loop

Dear all Can B factor in the crystal structure be the criteria to look into the flexibility of a region or domain.? Also if two structures are at different resolutions. Faisal --

[ccp4bb] twinned data

Dear all Lately i have found my crystals to be pseudomerohedrally twinned with a twin fraction of 0.22..but on doing twin refinement nothing much is changing in terms of statistics as compared to the previously solved data which did not include twin refinement (in present case the data is solved a

[ccp4bb] ionic interaction inside a protein

Dear all I am working on a thermostable protein and i have read that the stability to high temperature is due to various ionic interactions among the amino acid residues of the protein itself..I request you all to tell me any web server which can show all the ionic interactions between amino acid

Re: [ccp4bb] ionic interaction inside a protein

Thanx everybody..PICserver is really good On Mon, Mar 25, 2013 at 12:09 PM, Seema Nath wrote: > The link is fine. If you still get the 'error message', then google "PIC > webserver" , fullform of PIC - protein interactions calculator. > > > > Seema Nath > -- Regards Faisal School of Life Sc

Re: [ccp4bb] Twinning problem

Hello everyone sorry for the intervention with some basic questions regarding twinning In continuation with the discussion with Liang i would like to ask a question which i faced..i have also solved a structure and the statistics depending on twin laws as described through xtriage, phenix is as f

Re: [ccp4bb] STRAP secondary structure

Dear John you can try Promal3D..it will work hopefully.. bye and take care On Sat, Apr 27, 2013 at 6:27 AM, Mike John wrote: > Hello, Every one, > > I am preparing a ppt presentation in an emergency style. What I want is a > graph of sequence alignment with secondary structure on the top. Usin

[ccp4bb] off topic question regarding SPR

Dear all i have a basic question regarding SPR experiment and that is: What is the recommended glycerol concentration in the protein sample for doing SPR experiment and getting the best possible result.? i have kept 10% Glycerol in my protein preparation..is it O.K ? Thanx in advance -- Regards

Re: [ccp4bb] Unidentified blobs

I THINK IT IS PEG.. On Thu, May 16, 2013 at 10:20 PM, Nicholas Keep wrote: > It is most likely to be something in your crystallisation condition, your > cryoprotectant, or the buffer you stored your protein in. > Could be a detergent carried through several steps of purification > Could for exam

[ccp4bb] cryo condition

Dear all Can anybody tell me the appropriate cryo condition for the crystals obtained in 2M Ammonium sulphate and tris pH8.5..I tried to add 10% glycerol to it but still the ice ring is forming.. Thanx in advance -- Regards Faisal School of Life Sciences JNU

Re: [ccp4bb] cryo condition

Thank you everybody for their nice suggestions.. On Thu, May 23, 2013 at 7:39 PM, Matthew BOWLER wrote: > I keep sending mails by accident today - apologies for the spam. The last > sentence of my should read: > > This could of course be due to too high a concentration of mother liquor > but qu

[ccp4bb] sigma value of a structure file

Dear all After PDB deposition i got a reply from the annotator to verify and review the sigma value in the structure file which in my case is -0.03. My first question is, what actually is a "sigma value" of a structure file. 2nd) where it is mentioned i mean where and how to see this value. 3rd) W

[ccp4bb] saving coordinates with respect to map in ChimeraX

in ChimeraX ? Thank you -- Faisal Tarique Khaja 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 member

Re: [ccp4bb] saving coordinates with respect to map in ChimeraX

see a checkbox with "Save relative to model: " and then a > drop-down menu. Just choose the map in the drop-down menu, and you should > get the result you want. > > Best regards, > Tristan > -- > *From:* CCP4 bulletin board on behalf of k

Re: [ccp4bb] Help needed finding hit condition

Hello everyone. I remember the screen was again from Jenabioscience and this had happened with one of my protein. The screen was very old and the condition was peg3350, tris pH 8, lithium sulfate and NaCl as the salt. Hit was obtained which was never reproducible. Luckily I solved the structure fr

[ccp4bb] Off-topic question

Hi everyone, I was wondering can anyone suggest me how to project the primary sequence conservation calculated through the Consurf server. Any help or suggestion will be appreciated. I have pasted a figure from an article just for reference. Best Khaja [image: image.png]

[ccp4bb] ILLUSTRATE in PYMOL

Hi everyone Is there any way to make surface representation of a protein structure similar to the 'Illustrate: Non-photorealistic Biomolecular Illustration' ( https://ccsb.scripps.edu/illustrate/) using scripts in Pymol ? It will be really helpful if someone can share this with me. Thanks Faisal

Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] ILLUSTRATE in PYMOL

>> *From:* CCP4 bulletin board on behalf of Pius >> Padayatti >> *Sent:* Tuesday, August 15, 2023 8:24 PM >> *To:* CCP4BB@JISCMAIL.AC.UK >> *Subject:* [EXTERNAL] Re: [ccp4bb] ILLUSTRATE in PYMOL >> >> https://pymolwiki.org/index.php/APBS >> &l

Re: [ccp4bb] ILLUSTRATE in PYMOL

Thanks everyone for their valuable feedback. It helped a lot. Best Faisal On Tue, 15 Aug 2023, 19:19 khaja faisal tarique, < khajafaisaltari...@gmail.com> wrote: > Hi everyone > > Is there any way to make surface representation of a protein structure > similar to th