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
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
*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
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
:
> 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
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
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
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
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
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
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
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
> #> 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
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
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
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
>
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
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
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,
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
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
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
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
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
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
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
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
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
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
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
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
Hello everyone
I request you to please tell me the 3 letter code for p nitrophenyl
phosphate..
--
Regards
Faisal
School of Life Sciences
JNU
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
>>
>
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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,
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
--
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
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
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
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
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
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
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
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
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
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.
>
>
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
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
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
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
--
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
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
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
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
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
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
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
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
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
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
in ChimeraX ?
Thank you
--
Faisal Tarique Khaja
To unsubscribe from the CCP4BB list, click the following link:
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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
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
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]
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
>> *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
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
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