[ccp4bb] off topic question regarding SPR

[Faisal Tarique]

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

Faisal
School of Life Sciences
JNU

Re: [ccp4bb] Unidentified blobs

[Faisal Tarique]

I THINK IT IS PEG..

On Thu, May 16, 2013 at 10:20 PM, Nicholas Keep n.k...@mail.cryst.bbk.ac.uk
 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 example be some part of a PEG molecule that gets ordered round a
 more hydrophobic bit of your protein surface.
 You need to think about everything your protein has come into contact
 with, possibly even inside the cell.  It is not uncommon to carry cofactors
 right through a purification, less likely in something more surface bound
 like this.
 Best wishes
 Nick

 --
 Prof Nicholas H. Keep
 Executive Dean of School of Science
 Professor of Biomolecular Science
 Crystallography, Institute for Structural and Molecular Biology,
 Department of Biological Sciences
 Birkbeck,  University of London,
 Malet Street,
 Bloomsbury
 LONDON
 WC1E 7HX

 email n.k...@mail.cryst.bbk.ac.uk
 Telephone 020-7631-6852  (Room G54a Office)
   020-7631-6800  (Department Office)
 Fax   020-7631-6803
 If you want to access me in person you have to come to the crystallography
 entrance
 and ring me or the department office from the internal phone by the door




-- 
Regards

Faisal
School of Life Sciences
JNU

[ccp4bb] cryo condition

[Faisal Tarique]

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

[Faisal Tarique]

Thank you everybody for their nice suggestions..

On Thu, May 23, 2013 at 7:39 PM, Matthew BOWLER mbow...@embl.fr 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 quite often it occurs at relative humidity values where the
 concentration of the mother liquor components will not have increased by
 very much. Cheers, Matt.


 On 2013-05-23 15:32, Ed Pozharski wrote:

 Matt,

 with this technique, how do you prevent crystal from drying up (other
 than doing it fast)?  I know Thorne's group does this trick under oil.
 If you take no extra precautions, do you have an estimate of how often
 diffraction is destroyed by this?

 On the other hand, it's quite possible that what destroys resolution
 when crystals dry up is increase in concentration of non-volatile mother
 liquor components, which shouldn't be happening here to the same degree.

 Cheers,

 Ed.

 On Thu, 2013-05-23 at 14:38 +0200, Matthew BOWLER wrote:

 Hi Faisal,
 if your solvent channels are smaller than 40A in the largest dimension
 (most are) you can use a mesh loop to pick up the crystal and then wick
 away all of the mother liquor. You can then flash cool your crystal
 without having to transfer the crystal to another solution. Good luck,
 Matt


 --
 Matthew Bowler
 Synchrotron Science Group
 European Molecular Biology Laboratory
 BP 181, 6 rue Jules Horowitz
 38042 Grenoble Cedex 9
 France
 ==**=
 Tel: +33 (0) 4.76.20.76.37
 Fax: +33 (0) 4.76.88.29.04

 http://www.embl.fr/
 ==**=




-- 
Regards

Faisal
School of Life Sciences
JNU

[ccp4bb] sigma value of a structure file

[Faisal Tarique]

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) What is
the optimum sigma value range ?



-- 
Regards

Faisal
School of Life Sciences
JNU

[ccp4bb] sigma value in structure file

[Faisal Tarique]

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 value is
mentioned?. 3rd) and What is the optimum sigma value range ?

-- 
Regards

Faisal
School of Life Sciences
JNU

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

[Faisal Tarique]

Thank you all for your kind reply..

On Mon, Jun 17, 2013 at 7:02 PM, herman.schreu...@sanofi.com wrote:

 **
 Dear Faisal,

 I might be missing something, but why not ask the annotator instead of the
 bulletin board? He should know which value is meant. For me, a sigma
 belongs to a set of observations or parameters and without any further
 information one can only guess (as Ed just did) which set. My guess would
 be, that instead of structure file, structure factor file was meant and
 that somehow a negative sigma slipped in for one of the structure factors,
 but again that 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:* [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 value
 is mentioned?. 3rd) and What is the optimum sigma value range ?

  --
 Regards

 Faisal
 School of Life Sciences
 JNU




-- 
Regards

Faisal
School of Life Sciences
JNU

[ccp4bb] Self rotation function and translation peak

[Faisal Tarique]

*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

[Faisal Tarique]

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 manuscript preparation i have drawn the
topology diagram taking the output from STRIDE and DSSP while the overall
3D structure is from PYMOL..Will it be O.K to show some helices missing
from the output of pymol while they are present in the toplogy diagrma ? or
the reviewer will raise the issue? hope you are able to understand what i
mean to say.

Please suggest me

-- 
Regards

Faisal
School of Life Sciences
JNU

Re: [ccp4bb] visualizing G310 helices in PYMOL

[Faisal Tarique]

Thanx to all

Your suggestions really worked and solved my problem.

regards

Faisal



On Fri, Sep 27, 2013 at 2:08 AM, Parthasarathy Sampathkumar 
spart...@gmail.com wrote:

 Hi Faisal,

 you could run dssp2pdb by James Stroud (
 http://www.jamesstroud.com/software/dssp2pdb/ ) to convert dssp output
 into PDB readable format as part of the header. When you open resultant PDB
 in PyMOL, secondary structure as defined by dssp would be displayed.

 OR

 one could also define secondary structure in PyMOL manually (see at the
 end of this link:
 http://pymol.sourceforge.net/newman/user/S0260cartoons.html)

 HTH,
 Partha


 On Thu, Sep 26, 2013 at 4:02 PM, Faisal Tarique 
 faisaltari...@gmail.comwrote:


 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 manuscript preparation i have drawn the
 topology diagram taking the output from STRIDE and DSSP while the overall
 3D structure is from PYMOL..Will it be O.K to show some helices missing
 from the output of pymol while they are present in the toplogy diagrma ? or
 the reviewer will raise the issue? hope you are able to understand what i
 mean to say.

 Please suggest me

 --
 Regards

 Faisal
 School of Life Sciences
 JNU





-- 
Regards

Faisal
School of Life Sciences
JNU

[ccp4bb] rmsd

[Faisal Tarique]

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

[Faisal Tarique]

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 refinement)..My question is whether the out put from the
Pdb redo server with improved statistics can be de submitted to
protein data bank RCSB as its ?



-- 
Regards

Faisal
School of Life Sciences
JNU

[ccp4bb] resubmission of pdb

[Faisal Tarique]

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.cif.gz..Now i want to submit the same ..My question is what is
the best way to do it again..??
Should we start  from the beginning through ADIT Deposition tool and
resubmit it with a new PDB id or there is some way to submit again those
zip files which the annotator sent us after retraction..May you please
suggest what could be the easiest way to submit our structure to PDB
without much efforts.


-- 
Regards

Faisal
School of Life Sciences
JNU

[ccp4bb] apologize

[Faisal Tarique]

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

[Faisal Tarique]

Thanks everybody for their valuable suggestions..

On 2/3/14, MARTYN SYMMONS martainn_oshioma...@btinternet.com wrote:
 Yes, thanks Robbie
 That is just my point - a structure submitted and then validated for paper
 reviewers by the PDB can be changed almost completely after the paper is
 accepted.
 The data can be changed too and only stipulation seems to be that it cannot
 be new data i.e. it has to have a date of collection _before_ submission.

 Changes are of course not bad in principle - they may be motivated by peer
 review.

 But they need to be tracked. ln a way that is understandable for users of
 the data. Perhaps they are available in the new mmCif-based deposition and
 annotation system. I have not used it yet.

 The PDB provides a comparison between obsoleted and superseding entries
 (coordinates at least). So a similar approach could be used.

 all the best
 Martyn



 
  From: Robbie Joosten robbie_joos...@hotmail.com
 To: CCP4BB@JISCMAIL.AC.UK
 Sent: Sunday, 2 February 2014, 20:13
 Subject: Re: [ccp4bb] resubmission of pdb


 Hi Martyn,

 I have recently had the same problem. But generally, the PDB will usually
 allow a further 6 months hold for review or modifications to an already
 submitted paper.
 That is good to hear. I guess the 1 year limit is mostly to avoid structures
 to stay in limbo too long.

 But what I wanted to say was that the correct term is 'withdrawal' if the
 entry
 is removed pre-release - 'retraction' carries a pejorative connotation.
 Even
 after release, pulling an entry would be called obsoleting (status OBS)
 without superseding. So some structures have been 'obsoleted' owing to
 retraction of a published paper. (Superseding is when a better structure
 replaces the original - this process is tracked by the PDB.)
 Indeed, bad choice of words on my side. Just to complete the list, the
 possible statuses are here: http://www.ebi.ac.uk/pdbe-srv/status/search/doc

 Most pre-release 'withdrawn' entries are of course subsequently released
 after re-submission. But the PDB does not seem to track these connections
 -
 although they maintain a list of withdrawn entries - which means ids
 cannot
 really be recycled.
 That's too bad, there are not that many possible PDBids.

 Interestingly, before release entries can be 'replaced' which means a new
 structure can take the place (and 4 letter code) of the old one - this
 would
 have to have the same meta-data - so source and expression - but could
 have different resolution, space group, coordinates, and small molecules.
 Changes in these could for example be motivated by referees' comments on
 the submitted paper or maybe the authors got lucky with a better crystal.
 But
 this pre-release replacement could also be potentially used to 'sex up' a
 structure - for example by adding a 'novel' small molecule 'overlooked' in
 the
 original deposition. Such changes are tracked privately by the PDB but are
 not
 publically available... even after release.
 I didn't know this was an option. It seems sensible for peer review, but
 does present a potential loop-hole. I saw a fairly recent PDB entry that was
 deposited as a C-alpha trace (in 2013), but presented as a full model in
 Table 2 of the linked publication. The model was deposited a month before
 the paper was accepted, so referees could have noticed this (in theory). But
 now I wonder I the model was not 'downgraded' before the release. Perhaps
 I'm just paranoid.

 Cheers,
 Robbie

 Even more interestingly, the ligand definitions such as bond orders can be
 modified _after_ release (as in the recent R12 case I noticed*)... I think
 this is
 owing to the lack of clear rules on small molecule changes - which means
 the
 PDB should be considered of limited value as a definitive record of small
 molecule chemistry.

 Cheers - M
 *https://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg33403.html








 From: Robbie Joosten robbie_joos...@hotmail.com
 To: CCP4BB@JISCMAIL.AC.UK
 Sent: Saturday, 1 February 2014, 12:48
 Subject: Re: [ccp4bb] resubmission of pdb


 Hi Folmer,

 Perhaps because of the one year 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 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
  Folmer Fredslund
  Sent: Saturday, February 01, 2014 10:33
  To: CCP4BB@JISCMAIL.AC.UK
  Subject: Re: [ccp4bb] resubmission of pdb
 
  Hi Faisal,
 
  There is one thing I don't understand:
 
  Some time back i had submitted a coordinate in PDB but because of
  unacceptance of the manuscript we had to retract the submission
 
  Why would you need to retract your deposited structure just because the
  paper describing the structure didn't get accepted?
 
 
  Venlig hilsen
  Folmer Fredslund
 
  On Jan 31, 2014 10:04 PM, Faisal Tarique faisaltari...@gmail.com
 wrote:
 
 
  Dear all

[ccp4bb] 3letter code

[Faisal Tarique]

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

[Faisal Tarique]

Thanks everybody for sending me the three letter code..

regards

Faisal

On 2/14/14, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote:
 -BEGIN PGP SIGNED MESSAGE-
 Hash: SHA1

 Dear Faisal,

 I find the files in the directory $CLIB/data/monomers/list very useful
 for such questions, e.g.
 # 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.

 Best,
 Tim

 On 02/13/2014 10:07 PM, Faisal Tarique wrote:
 Hi everyone

 Can anyone please tell me the three letter code for D-Ribulose
 1,5-bisphosphate..

 Thanks in advance


 - --
 - --
 Dr Tim Gruene
 Institut fuer anorganische Chemie
 Tammannstr. 4
 D-37077 Goettingen

 GPG Key ID = A46BEE1A

 -BEGIN PGP SIGNATURE-
 Version: GnuPG v1.4.12 (GNU/Linux)
 Comment: Using GnuPG with Icedove - http://www.enigmail.net/

 iD8DBQFS/eHBUxlJ7aRr7hoRAjVtAKDJbmndqLGBpIIr/WJwtl0KcWkzpACgyhlp
 UJUo2t//J/vrs3ZN7epGsCQ=
 =9P2R
 -END PGP SIGNATURE-



-- 
Regards

Faisal
School of Life Sciences
JNU

[ccp4bb] relation between redundancy and total reflection

[Faisal Tarique]

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
in the log file but i am more concerned about locating of total reflections
and no of unique reflections and its relation to redundancy..
-- 
Regards

Faisal
School of Life Sciences
JNU

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

[Faisal Tarique]

Dear Herman

Where these values can be located..i.e. total no of reflections and no of
unique reflections..which processed log file is the optimum one to look
into..??

regards

Faisal


On Thu, Apr 17, 2014 at 7:48 PM, herman.schreu...@sanofi.com wrote:

  Dear Faisal,

 redundancy is total no. of observed reflections 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 2014 16:12
 *An:* CCP4BB@JISCMAIL.AC.UK
 *Betreff:* [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
 in the log file but i am more concerned about locating of total reflections
 and no of unique reflections and its relation to redundancy..
 --
 Regards

 Faisal
 School of Life Sciences
 JNU




-- 
Regards

Faisal
School of Life Sciences
JNU

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

[Faisal Tarique]

Thank you every body..your suggestions really helped me and i got my answer
as well.


On Thu, Apr 17, 2014 at 8:15 PM, Matthew Franklin mfrank...@nysbc.orgwrote:

  Hi Faisal -

 These numbers can be found near the bottom of the Scalepack log file.  In
 HKL2000, this has a default name of scale.log but you can rename it to
 anything you want in the Scaling window of HKL2000.

 You will find a table that looks like this:

 Summary of reflection intensities and R-factors by batch number
   All dataLinear
Batch # obs # obs  1   I/sigma N. Chi**2R-fac
1   873   873 5.7 2.0520.184
2  1551  1551 5.3 1.7630.178
3  1499  1499 6.0 1.5820.147
 . . . . .
  All films 1072444   1072075 6.0 1.4280.157


 The number 1072444 represents the total number of observations in this
 data set.  Directly below this table is one titled Summary of observation
 redundancies by shells.  The bottom line of that table looks like this:

  All hkl253   369   438   502   626  1647  2351  8257 24834 22607
 61631

 The number 61631 is the number of unique observations.  Divide 1072444 by
 61631 and you get 17.4, the overall redundancy for this dataset.  (I was
 trying to use high redundancy to squeeze 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

  Where these values can be located..i.e. total no of reflections and no
 of unique reflections..which processed log file is the optimum one to look
 into..??

  regards

  Faisal


 On Thu, Apr 17, 2014 at 7:48 PM, herman.schreu...@sanofi.com wrote:

  Dear Faisal,

 redundancy is total no. of observed reflections 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 2014 16:12
 *An:* CCP4BB@JISCMAIL.AC.UK
 *Betreff:* [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
 in the log file but i am more concerned about locating of total reflections
 and no of unique reflections and its relation to redundancy..
 --
 Regards

 Faisal
 School of Life Sciences
 JNU




  --
 Regards

 Faisal
 School of Life Sciences
 JNU



 --
 Matthew Franklin, Ph. D.
 Senior Scientist
 New York Structural Biology Center
 89 Convent Avenue, New York, NY 10027
 (212) 939-0660 ext. 9374




-- 
Regards

Faisal
School of Life Sciences
JNU

[ccp4bb] observed criterion sigma

[Faisal Tarique]

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

[Faisal Tarique]

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 ion bound to the protein,  specifically in the case of Mg and
Calcium..An anomalous data analyzed through Xtriage (phenix) gives a signal
of 0.097 with Magnesium while the same gives a signal of 0.1062 with
Caclium ( both data sets showing Anomalous flag as true )..can anybody shed
some light on which is more true ?? the data has maximum resolution of 2.6A
and i had kept Mg atom at the active site (  protein was incubated with 5mM
MgCl2)..just because it is not matching a typical octahedral geometry and
exact metal ion-oxygen distance as represented by Cambridge structural
database (CSD) my reviewer has asked me to check anomalous signal for both
Mg and Ca and ( he is expecting that scattering metal ion it to be Ca )
give appropriate reason for putting Mg there..please give suggestions..

your help would be greatly appreciated

-- 
Regards

Faisal
School of Life Sciences
JNU

[ccp4bb] rigid body refinement or molecular replacement.

[Faisal Tarique]

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 =39.4,64.5,117.2.
and a,b,c = 39.6,63.9,117.8 for native and complex)..My question is ..what
is the best way to solve the complex structure ??..whether it should be
done through molecular replacement with the native structure or simply by
doing rigid body refinement through mtz from complex and coordinates of the
native structures..in summary...what should be the ideal method employed
for the structure solution if the aim is to compare between the native and
complex structure of the same protein ??.

-- 
Regards

Faisal
School of Life Sciences
JNU

[ccp4bb] anomalous signal

[Faisal Tarique]

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 d'/sig and d/sig should be about 0.80. Then
in the present case is there really a signal or can be assumed no
signal..we are expecting one Ca atom bound to the protein at its active
site..the redundancy of the data is 11.6..with this signal strength can we
assume Ca to be present there or whatever little anomalous if present is
due to something elseor there is no signal at all ??...

Resl.   Inf - 8.0 - 6.0 - 5.0 - 4.0 - 3.8 - 3.6 - 3.4 - 3.2 - 3.0 - 2.8 -
2.60
 N(data) 375   493   580  1319   450   538   679   866  1081  1414  1709
 I/sig58.8  38.6  32.6  38.3  27.7  27.2  21.9  18.4  12.6   9.5   6.1
 %Complete  94.7  99.0  99.3  99.5 100.0  99.6  99.7  99.8  99.6  99.6  90.9
 d/sig   1.65  1.27  1.18  1.25  1.19  1.12  1.11  1.11  0.97  1.02  1.05



-- 
Regards

Faisal
School of Life Sciences
JNU

[ccp4bb] anomalous signal

[Faisal Tarique]

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 signal d'/sig and d/sig should be about 0.80. Then
in the present case is there really a signal or can be assumed no
signal..we are expecting one Ca atom bound to the protein at its active
site..the redundancy of the data is 11.6..with this signal strength can we
assume Ca to be present there or whatever little anomalous if present is
due to something elseor there is no signal at all ??...

Resl.   Inf - 8.0 - 6.0 - 5.0 - 4.0 - 3.8 - 3.6 - 3.4 - 3.2 - 3.0 - 2.8 -
2.60
 N(data) 375   493   580  1319   450   538   679   866  1081  1414  1709
 I/sig58.8  38.6  32.6  38.3  27.7  27.2  21.9  18.4  12.6   9.5   6.1
 %Complete  94.7  99.0  99.3  99.5 100.0  99.6  99.7  99.8  99.6  99.6  90.9
 d/sig   1.65  1.27  1.18  1.25  1.19  1.12  1.11  1.11  0.97  1.02  1.05

-- 
Regards

Faisal
School of Life Sciences
JNU

[ccp4bb] anomalous signal

[Faisal Tarique]

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 is 1.28
we can always expect some  anomalous signal out of the data..My question is
..how we will know if the anomalous signal is coming out of Sulfur or from
Calcium ?? is there any method through which we can get to know the
identity of the scattering molecule through the data..Can FFT anomalous map
from CCP4 is of any help in this direction, if yes then please tell me how
to interpret the output from this..

-- 
Regards

Faisal
School of Life Sciences
JNU

[ccp4bb] ideal rms bond and rms angle

[Faisal Tarique]

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 quality of a structure depends upon the value of these
rms deviation ? And what is the ideal value for these ?

-- 
Regards

Faisal
School of Life Sciences
JNU

[ccp4bb]

[Faisal Tarique]

which type of protein u r working on ??

On Fri, May 4, 2012 at 12:39 PM, ruby singh singh.rub...@gmail.com 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 no results. My protein is highy thermostable(till 80C) and pH stable(1
 to 13)...plz if anyone is having any idea or trick let me knw.




-- 
Regards

Faisal
School of Life Sciences
JNU

[ccp4bb]

[Faisal Tarique]

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
disulphide  bond ie to connect cysteine with bme.

-- 
Regards

Faisal
School of Life Sciences
JNU

Re: [ccp4bb] Moleculardimensions kits

[Faisal Tarique]

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 luck

On Tue, May 29, 2012 at 9:55 PM, Barbara Medagli 
barbara.meda...@elettra.trieste.it wrote:

 Dear all,
 This is Barbara Medagli, working in the structural biology lab in Italy
 Surfing in the molecular dimensions web site
 I found this two screens: MIDAS and ProPlex.
 I was thinking in buy them as I have to order other
 items to this company
 Some of you already used those kits?
 Any experience with them?
 Thanks for the help



 Barbara Medagli, PhD
 Structural Biology Lab
 Sincrotrone Trieste SCpA
 S.S. 14, km 163.5, Loc. Basovizza
 34012 Trieste/Italy
 phone +39040 3758807/8537
 fax +39040 3758029




-- 
Regards

Faisal
School of Life Sciences
JNU

[ccp4bb] CME

[Faisal Tarique]

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, can i
show it as a modified residue CME or cys in disulfide bond with bme.

-- 
Regards

Faisal
School of Life Sciences
JNU

[ccp4bb] lithium incorporation in refmac

[Faisal Tarique]

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


-- 
Regards

Faisal
School of Life Sciences
JNU

Re: [ccp4bb] lithium incorporation in refmac

[Faisal Tarique]

thanx a lot...

On Sat, Jun 9, 2012 at 12:23 AM, Ian Tickle ianj...@gmail.com wrote:

 Hi

 You don't need a CIF file for elements or their ions, only for
 compounds.  Li and Li+1 are already in the list of scattering factors
 ($CLIBD/atomsf.lib) as indeed are all the elements with their 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 faisaltari...@gmail.com wrote:
 
  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
 
 
  --
  Regards
 
  Faisal
  School of Life Sciences
  JNU
 




-- 
Regards

Faisal
School of Life Sciences
JNU

[ccp4bb] value of observed criterion sigma

[Faisal Tarique]

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 and every resolution shell or only two
entries i.e. the maximum resolution and minimum resolution entry is enough
in the whole columns.

-- 
Regards

Faisal
School of Life Sciences
JNU

[ccp4bb] balbes solution

[Faisal Tarique]

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 loop region.   the data is of 2.5 angstrom resolution.
-- 
Regards

Faisal
School of Life Sciences
JNU

[ccp4bb] hi

[Faisal Tarique]

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
another anamolous redundancy..i want to know which one i should mention or
both if data is anamolous ?

-- 
Regards

Faisal
School of Life Sciences
JNU

Re: [ccp4bb] determination of oligomerization state of protein

[Faisal Tarique]

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 molecular weight polymeric state of that protein as it has worked in
one of my case..try some additive like arginine  glutamate while
concentrating your protein and before SEC..it works sometime..

regards

Faisal

On Tue, Aug 14, 2012 at 8:57 AM, gauri misra kamga...@gmail.com wrote:

 Hi,
 Try glutaraldehyde crosslinking of  peaks you are obtaining from SEC
 individually and see if it gives you some idea.

 Best wishes
 Gauri




-- 
Regards

Faisal
School of Life Sciences
JNU

Re: [ccp4bb] ideal rms bond length

[Faisal Tarique]

Thanx everybody for your nice suggestions..

On Wed, Oct 3, 2012 at 3:19 AM, Faisal Tarique faisaltari...@gmail.comwrote:


 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
 mine case which is as follows..


 NcycRfactRfree FOM  -LL -LLfree  rmsBOND  zBOND
 rmsANGL  zANGL rmsCHIRAL $$
 $$
0   0.2090   0.2079   0.875226315.   11985.5   0.0278  1.389
 2.718  1.261   0.198
1   0.2064   0.2284   0.850226313.   12201.1   0.0285  1.427
 2.733  1.271   0.204
2   0.2076   0.2373   0.837226944.   12289.9   0.0248  1.242
 2.598  1.200   0.187
3   0.2092   0.2429   0.828227495.   12341.7   0.0222  1.107
 2.458  1.128   0.173
4   0.2100   0.2468   0.822227753.   12372.4   0.0211  1.053
 2.377  1.086   0.166
5   0.2104   0.2500   0.818227942.   12395.7   0.0204  1.021
 2.326  1.061   0.161
6   0.2108   0.2522   0.814228075.   12411.5   0.0200  0.999
 2.289  1.042   0.158
7   0.2111   0.2537   0.812228162.   12421.8   0.0197  0.984
 2.265  1.030   0.156
8   0.2113   0.2550   0.810228228.   12430.5   0.0194  0.971
 2.243  1.020   0.154
9   0.2114   0.2559   0.809228300.   12436.1   0.0192  0.962
 2.228  1.012   0.153
   10   0.2116   0.2568   0.808228348.   12441.7   0.0191  0.957
 2.218  1.008   0.152
   11   0.2118   0.2574   0.807228394.   12446.2   0.0190  0.951
 2.210  1.004   0.151
   12   0.2119   0.2581   0.806228421.   12449.6   0.0189  0.948
 2.203  1.001   0.151
   13   0.2119   0.2585   0.805228440.   12452.7   0.0189  0.944
 2.198  0.998   0.150
   14   0.2120   0.2590   0.805228461.   12455.0   0.0188  0.941
 2.194  0.996   0.150
   15   0.2121   0.2593   0.804228480.   12456.9   0.0188  0.939
 2.190  0.995   0.150


 --
 Regards

 Faisal
 School of Life Sciences
 JNU




-- 
Regards

Faisal
School of Life Sciences
JNU

[ccp4bb] side chain density

[Faisal Tarique]

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 missing
for side chains ( in loop regions )..i have question do i need to mutate
them to alanine or leave them as such..The density fit analysis in COOT (
traffic light) showing those regions with side chain as red..

thanx in advance

Regards

Faisal
School of Life Sciences
JNU

[ccp4bb] seleno methionine labelling of protein

[Faisal Tarique]

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 Life Sciences
JNU

Re: [ccp4bb] seleno methionine labelling of protein

[Faisal Tarique]

thanx all for their nice suggestions


On Mon, Nov 12, 2012 at 6:23 PM, Chittaranjan Das c...@purdue.edu wrote:

 Tim,


 My understanding is that the D-isomer does not get incorporated. I could
 be wrong though. Bacteria may convert the D to the L-form.

 Chitta



 - Original Message -
 From: Tim Gruene t...@shelx.uni-ac.gwdg.de
 To: CCP4BB@JISCMAIL.AC.UK
 Sent: Monday, November 12, 2012 4:25:34 AM
 Subject: Re: [ccp4bb] seleno methionine labelling of protein

 -BEGIN PGP SIGNED MESSAGE-
 Hash: SHA1

 Dear ,

 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.

 Best,
 Tim

 On 11/12/2012 10:06 AM, Faisal Tarique wrote:
  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..?
 

 - --
 - --
 Dr Tim Gruene
 Institut fuer anorganische Chemie
 Tammannstr. 4
 D-37077 Goettingen

 GPG Key ID = A46BEE1A

 -BEGIN PGP SIGNATURE-
 Version: GnuPG v1.4.12 (GNU/Linux)
 Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/

 iD8DBQFQoMCOUxlJ7aRr7hoRAopyAKD4kBksPb4zIDYDgok5r5BuuefndgCgrf3S
 r+YIxyjC50XywK1Tgc+fglk=
 =3GcK
 -END PGP SIGNATURE-




-- 
Regards

Faisal
School of Life Sciences
JNU

[ccp4bb]

[Faisal Tarique]

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 mtz file
and saw it working. i am not able to figure out whats wrong with my mtz.
its giving structure, refining well but not working with the submission
procedure.

-- 
Regards

Faisal
School of Life Sciences
JNU

[ccp4bb] how to add atoms in refmac library

[Faisal Tarique]

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

[Faisal Tarique]

Thanx to all the problem is solved now..[?]

On Fri, Feb 15, 2013 at 2:49 PM, Ganesh Natrajan ganesh.natra...@ibs.frwrote:

 Hi,

 Zinc is very much present in the Refmac library.

   ZN   zinc non-polymer   1   1C


 Are you using the correct atom id in your PDB file? It has 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
 library for the successful refinement of the coordinates.

 --
 Regards

 Faisal
 School of Life Sciences
 JNU





-- 
Regards

Faisal
School of Life Sciences
JNU
330.gif

[ccp4bb] B factor of the loop

[Faisal Tarique]

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

[Faisal Tarique]

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
at 2.5A with R/Rfree of 22 and 25)..i may be wrong but i have heard that
the data statistics generally improves after twin refinement..can anybody
please explain.

-- 
Regards

Faisal
School of Life Sciences
JNU

[ccp4bb] ionic interaction inside a protein

[Faisal Tarique]

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
residues in my  protein structure by just uploading its coordinate
file.ina nut shell i want to identify those residues in my protein
which are
taking part in ionic interaction.

-- 
Regards

Faisal
School of Life Sciences
JNU

Re: [ccp4bb] ionic interaction inside a protein

[Faisal Tarique]

Thanx everybody..PICserver is really good

On Mon, Mar 25, 2013 at 12:09 PM, Seema Nath seema.n...@saha.ac.in 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 Sciences
JNU

Re: [ccp4bb] Twinning problem

[Faisal Tarique]

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 follows:

operator k,h,-l
type pseudomerohedral
brotton alpha 0.019
h alpha 0.023
m alpha 0.22

it seems the probable twin fraction in my case is 0.2, now the question is
does it mean that in another twin domain ie. twin operator h,k,l the twin
fraction will be 0.8 ?




On Tue, Mar 26, 2013 at 9:07 PM, vellieux frederic.velli...@ibs.fr wrote:

  Hello,

 I would suggest to use several tools (in addition to Phenix's) - CCP4's
 detwin, the plots generated by truncate before detwinning, the Yeates
 twinning server and there might be others - to get a good idea of what the
 twinning fraction is.

 Here we've had success using CCP4's detwin to detwin diffraction data.
 The resulting mtz file is not equivalent to an mtz file containing data
 recorded from an untwinned crystal - this detwinning operation is not a
 perfectly accurate operation... In our case we used the estimate of the
 twinning fraction obtained from Phenix (which was lower).

 HTH,

 Fred.


 On 26/03/13 15:45, Liang Zhang wrote:

 Hi, All,

  I got a set of P2(or P21) data for MR. However, the Phenix-Xtriage
 indicated that it could be a pseudo-merohedral twinning. Does anyone know
 how to deal with such kind of twinning problem? Thanks.

  Best,

  Liang



 --
 Fred. Vellieux (B.Sc., Ph.D., hdr)
 ouvrier de la recherche
 IBS / ELMA
 41 rue Jules Horowitz
 F-38027 Grenoble Cedex 01
 Tel: +33 438789605
 Fax: +33 438785494




-- 
Regards

Faisal
School of Life Sciences
JNU

Re: [ccp4bb] STRAP secondary structure

[Faisal Tarique]

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 perturb-w...@hotmail.com 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. Using
 STRAP i can got alignment nicely, but did not know the tips to add
 secondary structure on top.
 Anybody of experienced can give me a hand? Tutorial-like instruction would
 be much helpful. Your kindness is greatly appreciated.

 Thanks
 Mike




-- 
Regards

Faisal
School of Life Sciences
JNU

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

[faisal tarique]

is these site is meant for this purpose ?

On 12/24/10, Bosch, Juergen jubo...@jhsph.edu 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 Hopkins Malaria Research Institute
 615 North Wolfe Street, W8708
 Baltimore, MD 21205
 Phone: +1-410-614-4742
 Lab:  +1-410-614-4894
 Fax:  +1-410-955-3655
 http://web.mac.com/bosch_lab/http://web.me.com/bosch_lab/

 On Dec 24, 2010, at 3:07 AM, Sudhir Kumar wrote:

 I did my recharge on
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Re: [ccp4bb] off-topic replay: glycerol in protein stock solutions

[faisal tarique]

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
India

On 3/5/11, Van Den Berg, Bert lambertus.vandenb...@umassmed.edu wrote:
 Hi Tom,

 Adding glycerol to (crystallization) buffers is a very common practice when
 working with membrane proteins. Many membrane proteins have been
 crystallized (perhaps even the majority) with glycerol, even up to 30% v/v.
 So, at least for membrane proteins, there is no problem.

 Bert


 On 3/4/11 8:25 PM, Brett, Thomas tbr...@dom.wustl.edu wrote:

 Hi guys:
 I know this has been asked before, but I want to get (current) opinions and
 observations once again. Every once in a while, you work with a protein that
 needs to have a little something added to the buffer to keep it soluble. The
 most common trick is addition of glycerol (usually 5-10%). I'm looking for
 general observations on this. I was of the opinion that this was usually a
 bad thing to do with protein stock that you intend to cyrstallize because
 glycerol will coat the protein in a non-homogeneous manner and make your
 homogeneous protein prep heterogeneous (in a way). Or do people usually have
 good luck crystallizing proteins that have to be stored in some glycerol? Or
 is there a better additive? Also, when having to use glycerol, do you put it
 on your sizing columns, etc? I am concerned with putting glycerol on my
 columns I may never be able to completely wash it away. What are your
 thoughts, community?
 thanks in advance,
 -tom

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

[faisal tarique]

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 be opted first.

regards

faisal

On 3/7/11, Annie Hassell annie.m.hass...@gsk.com wrote:
 Hi Tom--

 We have had good luck crystallizing proteins with 5-10% glycerol.  In the
 majority of these cases, the glycerol was included in the buffer for the
 final purification step.  We have also seen several cases where
 1,2-propanediol worked much better than glycerol.

 Hope this helps!
 annie



 -Original Message-
 From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Brett,
 Thomas
 Sent: Friday, March 04, 2011 8:26 PM
 To: CCP4BB@JISCMAIL.AC.UK
 Subject: [ccp4bb] off-topic replay: glycerol in protein stock solutions

 Hi guys:
 I know this has been asked before, but I want to get (current) opinions and
 observations once again. Every once in a while, you work with a protein that
 needs to have a little something added to the buffer to keep it soluble. The
 most common trick is addition of glycerol (usually 5-10%). I'm looking for
 general observations on this. I was of the opinion that this was usually a
 bad thing to do with protein stock that you intend to cyrstallize because
 glycerol will coat the protein in a non-homogeneous manner and make your
 homogeneous protein prep heterogeneous (in a way). Or do people usually have
 good luck crystallizing proteins that have to be stored in some glycerol? Or
 is there a better additive? Also, when having to use glycerol, do you put it
 on your sizing columns, etc? I am concerned with putting glycerol on my
 columns I may never be able to completely wash it away. What are your
 thoughts, community?
 thanks in advance,
 -tom

[ccp4bb] webserver for molscript

[faisal tarique]

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

[ccp4bb] citation for shelxc and hkl2000

[Faisal Tarique]

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

[Faisal Tarique]

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..Why
there is a difference in the b factor for these two coordinates with the
later having (low resolution) lower value than the previous (high
resolution)..?? is this a normal phenomenon or the stability is due to
bound ligand molecule, which is stabilizing the whole structure ?? Please
pour some light in this direction..

-- 
Regards

Faisal
School of Life Sciences
JNU

[ccp4bb] CC-half value ??

[Faisal Tarique]

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 ??

-- 
Regards

Faisal
School of Life Sciences
JNU

[ccp4bb] cc1/2 value in hkl2000

[Faisal Tarique]

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 ??

[Faisal Tarique]

Thank you for your valuable suggestions..it really helped me a lot..


On Fri, Aug 15, 2014 at 8:38 PM, Phil Evans p...@mrc-lmb.cam.ac.uk 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 you should look at the curve and not just the
 number estimated. I would look at I/sigI as well, and anisotropy to decide
 the resolution. However, the final cutoff should probably be based on
 refinement, and also I don't think the exact cutoff makes a huge difference
 (see http://www.ncbi.nlm.nih.gov/pubmed/23793146)

 Phil

 On 15 Aug 2014, at 15:54, Ed Pozharski pozharsk...@gmail.com wrote:

  Same here.  Ultimately, the KD test must be used in the end to finalize
 the resolution (keeping in mind recently discussed issues of effective
 resolution given data completeness).  I just want to add that at least some
 versions of aimless report overestimated resolution based on CC1/2 cutoff
 when outliers are present (e.g. due to ice rings or salt diffraction). It
 seems that aimless just picks the highest resolution bin where cc1/2 0.5
 even if some lower resolution bins are below 0.5 as well. I have written a
 script for more robust automated evaluation of these curves.  In a
 nutshell, it fits CC1/2 (d) curve to 1/(1+exp (-x)) and returns the
 resolution at midpoint.  I'm pretty sure that theoretical CC1/2 (d)
 dependence is different from this, but it seems good enough for a rough
 estimate.
 
 
  Sent on a Sprint Samsung Galaxy S® III
 
 
 
 
 
 
 
 
   Original message 
  From: Roger Rowlett
  Date:08/14/2014 5:44 PM (GMT-05:00)
  To: CCP4BB@JISCMAIL.AC.UK
  Subject: Re: [ccp4bb] CC-half value ??
 
  Exactly. Aimless will give you suggested resolution cutoffs based on CC
 1/2 in the log file.
 
  Roger Rowlett
 
  On Aug 14, 2014 5:04 PM, conan仙人指路 conan_...@hotmail.com wrote:
  Hi Faisal,
 
CC-half standard is valuable in evaluating the cut-off of highest
 resolution. Sometimes even if I/sigI is close to 1 and completeness is not
 as high, if CC-half is still significant, it may be worth incorporate the
 extra high-res shell data and extend the resolution. Again, if only the
 reliability and unbias are carefully confirmed, and the apparent
 significant CC-half is not due to an artifact of some other factors like
 ice ring etc.
  (Ref: Karplus PA and Diederichs K. 2012 Science 336, 1030-1033
 https://www.pubmed.com/pubmed/22628654)
 
It has yet to be appreciated by most population of the crystallography
 society, unlike the I/sigI, completeness, Rsym. In particular, Rsym has
 gradually less a direct measurement of the data quality and or determinant
 of resolution cut-off.
 
  Best,
  Conan
 
  Hongnan Cao, Ph.D.
  Department of Biochemistry
  Rice University
 
  Date: Fri, 15 Aug 2014 01:39:48 +0530
  From: faisaltari...@gmail.com
  Subject: [ccp4bb] CC-half value ??
  To: CCP4BB@JISCMAIL.AC.UK
 
  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 ??
 
  --
  Regards
 
  Faisal
  School of Life Sciences
  JNU
 




-- 
Regards

Faisal
School of Life Sciences
JNU

[ccp4bb] calculation of active site area

[Faisal Tarique]

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

[Faisal Tarique]

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 showed maximum activity with Zn2+..while in others it is
Mn2+..What could be the chemical or physical phenomenon for this
difference ??..Can anybody suggest or name some good paper for this
explanation..

-- 
Regards

Faisal
School of Life Sciences
JNU

[ccp4bb] 3 letter code

[Faisal Tarique]

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

[Faisal Tarique]

Thank you..i got it

On Thu, Oct 2, 2014 at 5:04 PM, Andreas Förster docandr...@gmail.com
wrote:

 I took the liberty of googling this for you.  I trust that other search
 engines will give the same answer.  Try your favorite next time.

 http://www.ebi.ac.uk/pdbe-srv/pdbechem/chemicalCompound/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

 Faisal
 School of Life Sciences
 JNU


 --
   Andreas Förster
  Crystallization and X-ray Facility Manager
Centre for Structural Biology
   Imperial College London




-- 
Regards

Faisal
School of Life Sciences
JNU

Re: [ccp4bb] 3 letter code

[Faisal Tarique]

Thank you every one..

On Thu, Oct 2, 2014 at 5:27 PM, Robbie Joosten robbie_joos...@hotmail.com
wrote:

 Hi Faisal,

 You can also look in LigandExpo http://ligand-expo.rcsb.org/index.html

 If you don't find a result immediately, you can also search by formula,
 even
 without hydrogens.

 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 code
 
  On 02/10/14 11:50, Faisal Tarique wrote:
  
  
   I request you to please tell me the 3 letter code for p nitrophenyl
   phosphate..
  
 
  No.  But here's how to find it yourself:
 
  Go to rcsb.org
  nitrophenyl phosphate - Search
  Top hit in Chemical Name table.
 
  or similarly File - Search Monomer Library in Coot.
 
  Paul.




-- 
Regards

Faisal
School of Life Sciences
JNU

[ccp4bb] 3 letter code for pyridoxine

[Faisal Tarique]

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] Bin R and Rfree values

[Faisal Tarique]

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 more than Rfree although overall values are fine. Apart from this, when
i am generating table 1 by Phenix, the output is giving the bin values as
16% and 18% for R and Rfree respectively.
Can anybody suggest what need to be done?

Resolution range (Ã...)

31.42  - 1.4 (1.45  - 1.4)

Multiplicity

6.4 (6.4)

Completeness (%)

98.06 (97.16)

Mean I/sigma(I)

18.51 (12.82)

Wilson B-factor

14.51

R-merge

0.0948 (0.1303)

R-meas

0.1036

CC1/2

0.99 (0.986)

CC*

0.997 (0.996)

R-work

0.1578 (0.1660)

R-free

0.1944 (0.1869)






Faisal
School of Life Sciences
JNU

[ccp4bb] deposition through ADIT or wwPDB Deposition Annotation (DA) System

[Faisal Tarique]

Hello everyone

Is coordinate deposition through ADIT is still valid or it has to be
done by the newly arrived wwPDB Deposition  Annotation (DA) System
of the RCSB..OR both are fine ?

-- 
Regards

Faisal
School of Life Sciences
JNU

[ccp4bb] cryo condition

[Faisal Tarique]

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

G20.3Mammonium formate20% v/vSOKALAN® CP 5 0.1MHEPES7.0

Crystals are in beautiful cuboid shaped but all sorts of PEG
combinations and Glycerol formulation failed to prevent it from
cracking and dissolving.

Has anybody faced a similar situation as mentioned above and what
precaution was taken to prevent it from cracking or dissolving.

Your suggestions will be of immense help

Thanks in advance
-- 
Regards

Faisal
School of Life Sciences
JNU

Re: [ccp4bb] Cryo protection

[Faisal Tarique]

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 t...@moleculardimensions.com wrote:



Dear colleagues,



Having followed the CCP4 BB discussion on cryoprotection I thought you
might be interested to know that with the help of work from Enrico Stura's
lab Molecular Dimension have introduced two kits now to take some of the
trial and error out of finding an effective cryoprotectant.



http://www.moleculardimensions.com/shopdisplayproducts.asp?id=205cat=CryoKits



Vera, L., Stura, E. A. (2013) Strategies for protein cryocrystallography.

Crystal Growth  Design,

http://pubs.acs.org/doi/full/10.1021/cg301531f





Tony Savill

Molecular Dimensions Ltd.

Unit 6 Goodwin Business Park

Willie Snaith Road

Newmarket, Suffolk.

UK CB8 7SQ



Tel: +44 1638 561051

Fax: +44 1638 660674



Registered Office

Salisbury House

Station Road

Cambridge

CB1 2LA



Registered in England and Wales:

Registration number 1794026

[ccp4bb] Cryo-EM

[Faisal Tarique]

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

[Faisal Tarique]

Hi everyone

Thanx a lot..Your suggestions are really informative and a valuable
source of knowledge..

regards

Faisal

On 5/20/15, Takanori Nakane takanori.nak...@bs.s.u-tokyo.ac.jp 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

 Best regards,

 Takanori Nakane

 On 2015/05/20 2:36, Yi-Wei Chang wrote:
 Hi Faisal,

 Here is a new series of lecture video called Getting Started in
 Cryo-EM made by Prof. Grant Jensen at Caltech/HHMI.

 http://cryo-em-course.caltech.edu/

 There are 14.5 hours of lecture total, which starts with the basic
 anatomy of electron microscopes, an introduction to Fourier transforms,
 and the principles of image formation.  Building upon that foundation,
 the lecture then covers sample preparation issues, data collection
 strategies, and basic image processing workflows for tomography, single
 particle analysis, and 2-D crystallography.  It is an excellent
 introduction that will prepare people for real practical training on the
 microscope or to engage in serious conversations about cryo-EM: a great
 way to get started for anyone just joining a cryo-EM lab, or anyone who
 wants to be sure they have the basic concepts down.

 Cheers,
 Yi-Wei




-- 
Regards

Faisal
School of Life Sciences
JNU

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

[Faisal Tarique]

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).
Since the structure of TMP and CMP are very similar what could be the
possible explanation for this difference or how one should approach to
explain this difference..Can modelling, docking and energy minimization
give an insight into this direction, if yes then what parameters should be
looked into..To summarize..Theoretically how it is possible to explain this
difference..??

Thanks in advance

-- 
Regards

Faisal
School of Life Sciences
JNU

[ccp4bb] topdraw

[Faisal Tarique]

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

Re: [ccp4bb] Help needed finding hit condition

[khaja faisal tarique]

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 from the hit
itself which diffracted to 2.2A resolution. But it is still a mystery for
us but this is all crystallography is. Strange things happen.

Faisal
Postdoc
PHRI, NJ, USA

On Jul 31, 2017 5:19 PM, "Janet Newman"  wrote:

> ​Hi Jonathan,
>
>
> Hopefully you know about the trick of making any precious condition last
> longer - use the 'magic' solution only in the drop itself, and use the best
> approximation you can make in the reservoir of the experiment (if you are
> doing vapour diffusion)
>
>
> Regards, Janet
>
>
> Janet Newman
> Principal Scientist / Director, Collaborative Crystallisation Centre (C3)
> CSIRO Material Science and Engineering
> 343 Royal Parade
> Parkville.  VIC. 3052
> Australia
> Tel +613 9662 7326 <+61%203%209662%207326>
> Email janet.new...@csiro.au
> --
> *From:* CCP4 bulletin board  on behalf of Jonathan
> Bailey 
> *Sent:* 31 July 2017 22:34
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* [ccp4bb] Help needed finding hit condition
>
>
> Dear CCP4bb community
>
>
> I apologies for the slightly off topic post.
>
>
> We have recently had success crystallizing a membrane protein (diffraction
> > 3 Å at a synchrotron source) using the *in meso* method, the hit
> condition was from the Jena Bioscience screen Pi-minimal condition number
> #57.
>
>
> Hit condition – 47.1 % w/v PEG1000, 150 mM Tris pH 8.0, 80 mM Potassium
> bromide
>
>
> The screen is old and expired 12/20/2013 (lot # JBS00013133), we have
> tried to reproduce the crystals using homemade optimization screens around
> the hit condition but have not had any success. We have tried reproducing
> the hit using a new (not expired) Pi-minimal screen but had no success. We
> are only able to reproduce the crystals using the expired screen and we do
> not have much of it left.
>
>
>
> We went back and tested the pH of the condition that had given crystals,
> the expected pH was 7.9 but we found it to be 6 – 6.5 using a pH indicator
> strip. We believe the drop in pH is caused by oxidative degradation of the
> PEG1000 resulting in the formation of carboxylic acid species.
>
>
> We have contacted Jena Bioscience to try and get some of the old screen
> stock but unfortunately they do not have any.
>
>
> My question is does anyone out there happen to have any expired screen
> stocks of this Pi-minimal condition (#57), ideally from the same lot (lot #
> JB200013133), that they would be willing to send us.
>
>
>
> Does anyone have any advice as to how to reproduce the condition? We’ve
> considered bubbling oxygen through and heating the sample to accelerate the
> oxidation process.
>
>
>
> King Regards
>
>
> Jonathan Bailey (PhD student)
>
>
> Professor Martin Caffrey Lab MS group Trinity College Dublin
>

[ccp4bb] Off-topic question

[khaja faisal tarique]

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]



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[ccp4bb] saving coordinates with respect to map in ChimeraX

[khaja faisal tarique]

Hello everyone

While doing rigid body fit we know that after placing the coordinate to its
correct position we can save it with respect to the map. Does anyone know
if a similar feature exists in ChimeraX ?  Is there a way where the
coordinates .pdb/cif file can be saved with respect to its map in ChimeraX ?

Thank you

-- 
Faisal Tarique Khaja



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

[khaja faisal tarique]

Hi Tristan

I have posted my question in ChimeraX mailing list as well and waiting for
their reply.

What you are suggesting is for Chimera. I dont see any such option in
ChimeraX. That save relative to section does not appear here or may be
there is a different way of saving model relative to map in ChimeraX.

Please correct me if I am wrong.

Faisal

On Mon, 28 Jun 2021, 2:44 pm Tristan Croll,  wrote:

> Hi Faisal,
>
> This is really a question for the ChimeraX-users list (
> chimerax-us...@cgl.ucsf.edu). But the quick run-down: using the File/Save
> dialogue, you'll 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 khaja
> faisal tarique 
> *Sent:* 28 June 2021 09:43
> *To:* CCP4BB@JISCMAIL.AC.UK 
> *Subject:* [ccp4bb] saving coordinates with respect to map in ChimeraX
>
> Hello everyone
>
> While doing rigid body fit we know that after placing the coordinate to
> its correct position we can save it with respect to the map. Does anyone
> know if a similar feature exists in ChimeraX ?  Is there a way where the
> coordinates .pdb/cif file can be saved with respect to its map 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=1
>



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

[khaja faisal tarique]

Thanks all. I am almost there making similar figs as in ILLUSTRATE. It is
amazing. Just wondering if we can make similar stuffs in ChimeraX ?.

Faisal

On Tue, 15 Aug 2023, 23:22 Jared Sampson, 
wrote:

> Hi Faisal -
>
> In addition to the `specular`, `ray_trace_mode`, and `ray_trace_gain`
> settings Blaine pointed out, you can also adjust the `direct` and `ambient`
> lighting settings, as well as `light_count` (which I believe only affects
> direct and specular lighting, not ambient).  For example, these worked
> pretty well for me:
>
> ```
> set ray_trace_mode, 3
> set ray_trace_gain, 0
> set specular, 0
> set direct, 0
> set ambient, 0.9
> ```
>
> Note that you'll have to ray trace (`ray`) to see the outlines.  Also it
> looks like the tRNA image on the CCSB Illustrate site uses slightly
> different colors for different parts of the molecule (phosphate, sugar,
> base), which is a nice effect.
>
> Hope that helps.
>
> Cheers,
> Jared
>
>
> On Tue, Aug 15, 2023 at 10:40 PM Mooers, Blaine H.M. (HSC) <
> blaine-moo...@ouhsc.edu> wrote:
>
>> Hi Faisal,
>>
>> I made a number of such figures several years ago.
>> I finally found the code.
>>
>> Load the molecule of interest into PyMOL
>> and paste the following code onto the command line
>> just below the command history window.
>> I was using our school colors: crimson and cream.
>> Ligands are colored crimson. Change to suit
>> your needs.
>>
>>
>> as surface
>> set_color crimsom, [165,42,42];
>> set_color cream, [221,203,164];
>> color crimsom, org;
>> color cream, not org;
>>
>> remove solvent
>> set_color bground, [252,250,249];
>> bg_color bground;
>> # set the view
>> # orient all within 8 of org
>> # set the lights, ray tracing setttings
>> # to get the Goodsell-like rendering
>> unset specular
>> set ray_trace_gain, 0
>> set ray_trace_mode, 3
>> bg_color white
>> set ray_trace_color, black
>> set depth_cue, 0
>> #ray
>> png Goodsell1test.png, 1200,1200,600,1
>>
>>
>> Best regards,
>>
>> Blaine
>>
>> Blaine Mooers, Ph.D.
>> Associate Professor
>> Department of Biochemistry and Molecular Biology, College of Medicine
>> Director of the Laboratory of Biomolecular Structure and Function
>> Academic Director, Biomolecular Structure Core, COBRE in Structural
>> Biology
>> Full Member, Cancer Biology Program, Stephenson Cancer Center
>> University of Oklahoma Health Sciences Center
>>
>> Mailing Address:
>> 975 NE 10th Street, BRC 466
>> Oklahoma City, OK 73104-5419
>> Office: 405-271-8300 Lab: 405-271-8312
>>
>> Websites:
>> Faculty page:
>> https://basicsciences.ouhsc.edu/bmb/Faculty/bio_details/mooers-blaine-hm-phd
>> BSC-OKC (LBSF):
>> https://research.ouhsc.edu/Core-Facilities/Laboratory-of-Biomolecular-Structure-and-Function
>> COBRE in Structural Biology: https://www.ou.edu/structuralbiology
>> --
>> *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
>> <https://urldefense.com/v3/__https://pymolwiki.org/index.php/APBS__;!!GNU8KkXDZlD12Q!9eD_ProG0wUZ-JErjGALFQIrpgJlQO_bYGkQ0_iklgY0qfFv6IblDBIQ_JwWVq4rFViNFwN_v8t_mnr6vVLzKnD4$>
>> *Pius Padayatti*
>>
>>
>>
>>
>> On Tue, Aug 15, 2023 at 5:20 PM khaja faisal tarique <
>> khajafaisaltari...@gmail.com> wrote:
>>
>> Hi everyone
>>
>> Is there any way to make surface representation of a protein structure
>> similar to the 'Illustrate: Non-photorealistic Biomolecular
>> Illustration' (https://ccsb.scripps.edu/illustrate/
>> <https://urldefense.com/v3/__https://ccsb.scripps.edu/illustrate/__;!!GNU8KkXDZlD12Q!9eD_ProG0wUZ-JErjGALFQIrpgJlQO_bYGkQ0_iklgY0qfFv6IblDBIQ_JwWVq4rFViNFwN_v8t_mnr6vekgjdM7$>)
>> using scripts in Pymol ? It will be really helpful if someone can share
>> this with me.
>>
>> Thanks
>>
>> Faisal
>>
>>
>> --
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>> <https://urldefense.com/v3/__https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1__;!!GNU8KkXDZlD12Q!9eD_ProG0wUZ-JErjGALFQIrpgJlQO_bYGkQ0_iklgY0qfFv6IblDBIQ_JwWVq4rFViNFwN_v8t_mnr6vZS2nRni$>
>>
>>
>> --

Re: [ccp4bb] ILLUSTRATE in PYMOL

[khaja faisal tarique]

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 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
>
>



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[ccp4bb] ILLUSTRATE in PYMOL

[khaja faisal tarique]

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



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