Re: [ccp4bb] sugestions on weak diffracting protein crystals

[Jacqueline Vitali]

Hi Deepak,

If this is a metalloprotein, include higher concentration of the metal in
the crystallization drop.  It may act as a glue in the interfaces and give
you a good crystal.

Jackie Vitali
Cleveland State University

On Tue, May 18, 2021 at 6:20 AM Deepak Deepak 
wrote:

> Dear all,
>
> I have got multiple crystals (see picture 1) of a protein (8kDa) with a
> helical aromatic oligoamide foldamer (5kDa) but these crystals *diffract
> very poorly *(see the diffraction pattern in picture 2).
>
> I prepare a 1.3mM:1.3mM complex of protein: foldamer in 20mM Tris, pH 7.5
> buffer. Crystals grew in 3-5 days in sitting and hanging drop at 20 Deg C
> and 25 Deg C in the following conditions:
>
> *- 20% PEG 400, 0.1M MES pH 6.0*
> *-20% PEG 400, 0.1M Sodium Cacodylate pH 6.0*
>
> *Multiple cryo used were:*
> *-25%Glycerol in mother solution*
>  -30% glycerol in water
> *-30%PEG 400,*
> *-35% PEG 400*
> *-20% PEG 8000 + 40% PEG 400 mix*
>
> Kindly suggest some methods/modifications on how can I improve the
> resolution and get better-diffracting crystals. Please let me know if you
> need more information.
>
> Kind regards,
> Deepak
> Ph.D. Student
>
> PS: The protein is a DNA binding protein and I have crystallized and
> solved the structure of this protein with its DNA partner and now I
> crystallized it with our foldamers but diffraction is not good. There are
> multiple structures of the Protein+DNA complex in literature but *no
> apo-protein structure *as the protein needs a binding partner to
> crystallize. *We already have solution studies showing a good binding.*
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
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>



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Re: [ccp4bb] Anisotropic Scaling

[Jacqueline Vitali]

There is an anisotropy server from ucla that I think you can use over the
internet,  Just google it and try it to see if it helps with your data.  I
think the data is better afterwards,

Jackie Vitali
Cleveland State University

On Sat, Jan 13, 2018 at 5:53 AM, Zhang Foggy  wrote:

> Dear Crystallographers,
>
> Sorry for the non-ccp4 topic.
>
> Recently I collected a set of diffraction data with significant diffraction
> anisotropy (two directions to 3.0A, while the other to 3.7A). The overall
> resolution can only be scaled to 3.3A (I/sigma=1.04). I have read some
> publications that they can scale the data under different directions rather
> than overall by using HKL3000 (like the table in attached figure), which
> can describe the anisotropy more accurate. Does anyone can tell me how to
> scale the data like that?
>
> Thank you in advance.
>
> Best,
>
> Liang
>

Re: [ccp4bb] Modeling protein tertiary structure

[Jacqueline Vitali]

The easiest is modeller via chimera.

You can use I-TASSER server but it decides for itself what to do...  You
have some control too.  You can use the sec structure from itasser and then
go to modeller in chimera

You can use modeller in the interfaces it provides in the web (mod web ...)
or modeller directly with command files

and finally swissmodel

Jackie Vitali
Cleveland State Univ



On Fri, Dec 9, 2016 at 4:05 PM, Myeongseon Lee (이명선) <
0e01bd27cd0f-dmarc-requ...@jiscmail.ac.uk> wrote:

> Hi, all.
>
> Could you anyone recommend me modeling programs for protein tertiary
> structure?
>
> I have 3D strunture of a template protein and amino acid sequence of my
> protein. These two proteins are very close structurally and functionally.
>
> I have done this kind of modeling with template 3D structure and amino
> acid sequence of an unknown structure long time ago for other project. But,
> unfortunately, I could not remember what program I have used at that time.
>
> Have a great day.
>
>
> Sent from my Samsung device
>

Re: [ccp4bb] Model parts rearrangement

[Jacqueline Vitali]

coot, lsq command

i have not checked chimera but it may have too. (I think so)

For coot. I used it recently for a small molecule. 

And pymol

Finally the superpose server may do it.

On Jul 8, 2015, at 3:41 PM, Bernhard Rupp (Hofkristallrat a.D.) 
hofkristall...@gmail.com wrote:

 Hi Fellows, 
 
 I seek advice for a trivial but tedious problem: I have rebuilt,
 automatically and manually, several parts of a
 structure, which of course, are all over the place in different ASUs. I also
 have a  reference model, where
 the parts form a correct ASU. 
 
 Is the a program/script that can accomplish this assembly of parts onto the
 correct model given the 
 reference model?
 
 This is probably a common nuisance with a tool already available.
 
 Best regards,  BR
 -
 Bernhard Rupp
 001 (925) 209-7429
 +43 (676) 571-0536
 b...@ruppweb.org
 hofkristall...@gmail.com
 http://www.ruppweb.org/
 -
 The man who follows the crowd will get
 no further than the crowd.
 The man who walks alone will find himself
 in places where no one has been before.
 -

[ccp4bb] what happens when freezer goes down

[Jacqueline Vitali]

Dear colleagues,

I know this is not related to ccp4 but I am in need of an answer and many
of you work with cells etc.

My building had a major malfunction of electricity and the power backup did
not kick in.  My -80C freezer was without power for over 24 hours until I
found out.  Because it is small, it goes fast to room temp.  I had many
glycerol stocks in it with cells, cells with plasmids etc. as well as cell
pellets.  I am trying to rescue things.

My question is what happens to cell pellets.  I had many as I like to start
purification at the cell pellet level.  Are these destroyed when they go to
room temp for 24 hours or are they ok?

Thanks.

Jackie Vitali
Cleveland State University

Re: [ccp4bb] I/sigmaI or I/sigmaI

[Jacqueline Vitali]

Phil Jeffrey has a small program to calculate avg. I/sig for Table 1
including for resolution ranges.

Jackie Vitali




On Wed, Feb 12, 2014 at 11:20 AM, Ronald E Stenkamp 
stenk...@u.washington.edu wrote:

 How did people get I/sigmI when using HKL2000?  Ron

 On Wed, 12 Feb 2014, Phil Evans wrote:

  I/sigmaI

 On 12 Feb 2014, at 11:43, Cai Qixu caiq...@gmail.com wrote:

  Dear all,

 Does the I/sigmaI in Table 1 mean for I/sigmaI or I/sigmaI ?

 Thanks for your answer.

 Best wishes,

 Qixu Cai

Re: [ccp4bb] structural homologs as cross seeds

[Jacqueline Vitali]

I do not have experience with this but it is worth trying.


On Fri, Dec 27, 2013 at 2:29 PM, Mahesh Lingaraju mxl1...@psu.edu wrote:

 Dear all,

 I was wondering if it sounds logical to use the crystals from a possible
 structural homolog as seeds to induce nucleation ? (in terms of overall
 sequence, the proteins are considerably different but based on sequence
 alignment and structures from other related proteins, it is highly likely
 the protein would have the same structure.)

 Please comment if any of you had experience with this.

 Thank you

 Happy holidays :)

 Mahesh

Re: [ccp4bb] Align linux version

[Jacqueline Vitali]

Mintu Chandra,

align is gerson cohen's program.  Unless you talk about another align.

I googled align for linux Gerson Cohen and here is what I found  -- the
linux version
http://software.compbio.washington.edu/ramp/ramp/src/other_source/align.save.f

Test it and see if it works.

If not, there is a superpose server as well that you can use in the
internet.  just google superpose.  Also coot. Phenix has some option as I
recall I have seen it.  lsqman does the job as well.

jackie vitali



On Sun, Nov 10, 2013 at 4:09 PM, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote:

 -BEGIN PGP SIGNED MESSAGE-
 Hash: SHA1

 Dear Mintu Chandra,

 Do you mean by 'has linux compiled align version', that 'align' is a
 program you use for the alignment? I wonder because I have not heard
 of it.

 If you would be happy with any alignment software, you could use coot
 (graphical) or lsqkab (command line). Both programs areavailable once
 you installed ccp4.

 Regards,
 Tim Gruene

 On 11/10/2013 01:30 PM, Mintu Chandra wrote:
  Dear CCP4 users,
 
  We are trying to align two different structures. It would be
  helpful for us if anybody has linux compiled align version?
 
  Regards,
 
  Mintu Chandra
 

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

 GPG Key ID = A46BEE1A
 -BEGIN PGP SIGNATURE-
 Version: GnuPG v1.4.15 (GNU/Linux)
 Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/

 iD8DBQFSf/YeUxlJ7aRr7hoRAvhHAJ4+LUkvSIMPWjbTkKdw3+6LMtztfQCgztjN
 lG+aflDaFBmC8kBvJYA4WoE=
 =Vpsr
 -END PGP SIGNATURE-

[ccp4bb] use only companies that you know to purchase chemicals

[Jacqueline Vitali]

Dear all,

I used the guidechem chemical network to obtain a compound that is not sold
in US.  Many people responded and I was persuaded to try to buy it from

SHANGHAI JIEKE BIOTECHNOLOGY LIMITED COMPANY

Adress：NO.1008 Qigangroad,FengXianZone,ShangHai,China

Tel  ：+86-031-97265503
Fax  ：+86-031-97265320
Site  ： http://www.jiekechem.com/


 My University send the money as they requested the money to be paid in
advance.  I saw no compound and the person disappeared when she obtained
the information of my University.  My university requested the wire back
but the recipients cannot be reached and the bank in China closed the
request to return the funds because it could not reach the recipients.  Yet
the recipients still have an account in this bank.


I reported to guidechem and they ignored me.


(1) Do not trust companies that you do not know especially in other
countries.  There are many unreliable places.  Do not take a chance like I
did.


(2) Is there any way to get the money back?


The bank information and account are
This is our bank information:
COMPANY NAME :  SHIJIAZHUANG DUNAO CHEMICAL CO., LTD
Name: BANK OF CHINA SHIJIAZHUANG ,ZHONGSHAN BR.
Address:NO.83WEST  ZHONGSHAN  ROAD,
SHIJIAZHUANG,  HEBEI,  CHINA
Account No.: 100391967084
Swift Code : BKCHCNBJ220

I feel very bad about the whole thing.

Can anyone advise how to get the money back?

Jackie

[ccp4bb] question about arginine sepharose 4B

[Jacqueline Vitali]

Dear all,

Arginine sepharose 4B is an affinity column.  If you have used it please
let me know where you purchased it.

GE Lifesciences used to sell it but discontinued it.

I found it in China in the site http://www.pharmaceutical-sales.net
and I corresponded with their sales representative

Does anyone know this company?  Are their products reliable?  It is the
only place I found this product.

I would appreciate any information about this company or any place that may
sell arg sepharose.

Thank you.

Jackie Vitali

[ccp4bb] Fwd: request for reprint

[Jacqueline Vitali]

Dear Colleagues,

Does anyone have access to this article?  It is not in my library and they
cannot find it via interlibrary loan.  I know the limitations and that it
is best not to ask papers via the newsgroup but I have even tried to ask
the author for a reprint and my email was returned to me.

Thank you.

Jackie Vitali
Cleveland State University



Cell Mol Biol 
(Noisy-le-grand).http://www.ncbi.nlm.nih.gov/pubmed/15529744#2004
Jun;50(4):347-52.
Cooperativity and high pressure: stabilization of the R conformation of the
allosteric aspartate transcarbamylase under the influence of pressure.
Hervé 
Ghttp://www.ncbi.nlm.nih.gov/pubmed?term=Herv%C3%A9%20G%5BAuthor%5Dcauthor=truecauthor_uid=15529744,
Schmitt 
Bhttp://www.ncbi.nlm.nih.gov/pubmed?term=Schmitt%20B%5BAuthor%5Dcauthor=truecauthor_uid=15529744,
Serre 
Vhttp://www.ncbi.nlm.nih.gov/pubmed?term=Serre%20V%5BAuthor%5Dcauthor=truecauthor_uid=15529744
.

Re: [ccp4bb] offtopic: AKTA prime

[Jacqueline Vitali]

Yes, it has happened to me more than once.  It is not a good pump.  Acta
Prime Plus has a better one.  They still have parts.  Call GE technical
support and they will tell you what to do.

The part costs some money (it is not cheap - probably $500).  I think the
Akta Prime will keep on running as long as you maintain it.  They can come
to your lab to do the job for you but I do not know how much it is per
hour.  This team is called labcrew and they are very good.

I would call them and try to arrange with them.

Make sure you have your solutions elevated above the pump.  Even though it
is a pump you need to help it.  Also do not use viscous solutions with it.
(I do not use glycerol because of the pump).  Finally clean it up with 20%
ethanol after each use to avoid mold.

On Thu, Jul 12, 2012 at 5:09 PM, Peter Hsu hsuu...@u.washington.edu wrote:

 Hi all,

  We've got an old Akta prime that I think is on the verge of kicking it.
 Hearing some high pitched sounds coming from the pump when we're running
 it. Line A seems clogged and makes a thudding noise when we try to do a
 pump wash through that line. Does anyone have any experience w/fixing
 one/replacing the pump? Or any idea how much it's going to set us back to
 get it fixed?

 Sorry for the off topic question/thanks in advance for any thoughts and
 ideas.

 Peter

Re: [ccp4bb] Monomers in COOT

[Jacqueline Vitali]

try file  search monomer library.  Hit search without typing anything.  It
will give you what it has.
Jackie Vitali

2011/10/12 Dr. STEPHEN SIN-YIN, CHUI chui...@hkucc.hku.hk

 Dear All,

 For all monomers (3 letter) used in COOT, where can i find the full names
 of the
 whole library? Many thanks

 stephen

 --
 Dr. Stephen Sin-Yin Chui (徐先賢)
 Assistant Professor,
 Department of Chemistry,
 The University of Hong Kong, Pokfulam Road,
 Hong Kong SAR, China.
 Tel: 22415814 (Office), 22415818 (X-ray Diffraction Laboratory)

[ccp4bb] Linux vs MacOS for crystallographic software

[Jacqueline Vitali]

Dear colleagues,

I need some advice for a new computer.

(1) I have the option of an HP Z210  8 GB with a low end Quadro Nvidia 400
512 MB.

--How does Coot run with this card?

--I am happy with any Linux.  However, the system needs updates for security
purposes (the University requires it).  Do I have to remake the NVidia
driver every time there is a kernel update or is there a way around it for
this NVidia card?  Do you suggest another NVidia card (inexpensive) that is
good for coot and automatically updates when the kernel is updated?

(2) Second option is an IMAC 4 GB 2.5 GHz with AMD Radeon HD 6750M 512 MB
GDDRS.

--How does Coot work with this graphics card?

--Should I get more memory for Lion?

--Is this platform advisable for crystallographic software for the next four
years?

Thank you in advance for any advice.

Jackie Vitali
Cleveland State University

[ccp4bb] glycerol on three-fold axis

[Jacqueline Vitali]

Dear colleagues,

Has anyone seen glycerol on a three-fold axis?

THis is possible as the glycerol can be disordered but I want to know if
there is an actual case.

Any information would be greatly appreciated.

Jackie Vitali

[ccp4bb] cryosleeves with ID 22 mm

[Jacqueline Vitali]

Dear colleagues,

I needed cryo -sleeves 22 mm ID so that I could put standard epitubes in
cryo canes and protect them.  The epitubes do not hold as good as the cryo
vials in the cryo canes.

All commercially available cryo sleeves are 16 mm ID and are made for cryo
vials.  Some of us put cultures in epitubes.

I was able to have them custom made for me by www.papertube.com.  They are
made out of cardboard.

I would like to give the reference of this company to all in case someone
else encounters the same problem.

Jackie Vitali

Reference:




 *James P. Rose*
 *Jonesville Paper Tube Corporation*
 *540 Beck Street, P.O. Box 39*
 *Jonesville, MI  49250*
 *517-849-9963*
 www.papertube.com


---

Re: [ccp4bb] Off topic question. NACCESS

[Jacqueline Vitali]

I think one of the options of PISA is to calculate accessibilities -- I
recall when I was learning how to use pisa that I saw this option.

Also DSSP outputs accessibilities per residue

Areaimol in ccp4 does too.

I have seen many programs in the internet, google accessibilities,
accessible surface area.  what_if does something like this too.

On Sun, Jun 19, 2011 at 5:09 PM, VAN RAAIJ , MARK JOHAN 
mjvanra...@cnb.csic.es wrote:

 Dear Armando,
 don't know about NACCESS, but I guess it is superseded by AREAIMOL in CCP4
 (also in CCP4i); it outputs the accessible volume per atom in the pdb file
 and per residue and per chain and some other statistics in the log-file.
 Mark

 Quoting Armando Albert:

  Does anyone has got some information about how to get a mac version
  (intel), of the old unix program naccess?. It was meant  to calculate
  the solvent accessibility per residue from a pdb file.
  Armando

 Mark J van Raaij
 Laboratorio M-4
 Dpto de Estructura de Macromoléculas
 Centro Nacional de Biotecnología - CSIC
 c/Darwin 3, Campus Cantoblanco
 28049 Madrid
 tel. 91 585 4616
 email: mjvanra...@cnb.csic.es

Re: [ccp4bb] diverging Rcryst and Rfree

[Jacqueline Vitali]

Hi,

I have seen this happening when I had NCS and did not include it in
refinement.  Rwork drops and Rfree increases. In this case the difference
became small when I included the NCS.

Also if your Rmerge is high and you include all reflections in refinement,
Rfree is high.  In my experience, by excluding F  sigma reflections you
drop Rfree a lot.

My limited experience suggests errors in the data and/.or in the way you
handle  the data.

Jackie Vitali
On Mon, Oct 25, 2010 at 5:10 PM, Rakesh Joshi rjo...@purdue.edu wrote:

 Hi all,

 Can anyone comment, in general, on diverging Rcryst and Rfree
 values(say7%) for
 structures with kind of low resolutions(2.5-2.9 angstroms)?

 Thanks
 RJ

Re: [ccp4bb] molecule on symmetry axis

[Jacqueline Vitali]

Dear colleagues,

Thank you for your suggestions.  I was able to do the refinement of the
sulfates and tartaric acid in phenix by changing the occupancies to 0.33 and
0.5,

It appears to me (from the log file and from graphics afterwards) that the
program automatically turns off the interaction with the symmetry mate when
one puts the right occupancy..

Jackie Vitali

[ccp4bb] molecule on symmetry axis

[Jacqueline Vitali]

Dear colleagues,

I have a tartaric acid on a two fold axis with its two halves related
by the two fold.  How do I refine this in Phenix?

Also I have a SO4 on a 3 fold with S and one O on tthe 3 fold.  The
other 3 oxygens are related by the 3-fold.  How do I refine this in
phenix?  I can put S and one O occupancy 1, what occupancy do I put
for the 3 oxygens that overlap their symmetry mates?

And how do I maintain stereochemistry around the symmetry axis?  These
are not just one atom. For the tartaric acid the 2 fold goes through
the middle of the bond.  I could split it in two halves but I do not
see how to keep stereochemistry.

I would appreciate all suggestions.

I apologize because the question should go to another newsgroup but I am
still working with my subscription in phenixbb.

Jackie Vitali

[ccp4bb] question on the effect of a fire alarm on crystallization

[Jacqueline Vitali]

Dear all,

Does anyone know the effect of a fire alarm placed in the same room where
one grows crystals?

(1) On trays placed inside styrofoam boxes

(2) On trays placed inside an incubator which has not been tested as
vibration free.

Thank you.

Jackie Vitali

[ccp4bb] effect of high mosaicity on atomic coordinates

[Jacqueline Vitali]

Dear all,

I have a high mosaic spread for a structure (1.2 deg).  It refines well to
low R values.  The temp factors become very high in this structure.  I
assume the reason is the high mosaicity.  Are the coordinates also affected
by high mosaicity?

I would appreciate any input.

Thanks.

Jackie Vitali

[ccp4bb] question on Akta Prime

[Jacqueline Vitali]

Dear colleagues,

I have an Akta Prime.  I have always had problem with the reproducibility of
the peak heights of the various peaks.  Recently the pump is breaking.  Does
anyone have an idea what can cause the pump to break?  It is more than once.

Jackie Vitali

[ccp4bb] MSCAN or DSCAN

[Jacqueline Vitali]

Dear colleagues,

Does anyone have a copy of the old program DSCAN or MSCAN by S.T. Rao?

It calculates torsion angles in small molecules.

Alternatively, does anyone have a program to calculate torsion angles
and their ESD's for small molecules?

Thanks.

Jackie Vitali

[ccp4bb] cuvette for dynapro 99-CP

[Jacqueline Vitali]

Dear colleagues,

I am trying to find a cuvette for Dynapro 99-CP.  Wyatt does not seem to
have these cuvettes.  If anyone knows where I can get one please let me
know.

Thanks.

Jackie Vitali

Re: [ccp4bb] about anisotrophic diffraction

[Jacqueline Vitali]

Look at the paper (search in pubmed) by B. M. Schick and F. Jurnak on
cryoprotection of TuTs.  He changes the reservoir in 24 steps using a 24
well cryschem plate.  There are some references there that are important
too.

Jackie Vitali
On Mon, Jun 23, 2008 at 8:14 PM, Ji lee [EMAIL PROTECTED] wrote:

 Dear,

 I have a crystal diffracted anisotrophically. I tested with a few
 different cryo conditions like oil, glycerol in different
 concentration to get a better data but these conditions didn't help
 any.
 Using capillary method improved the diffraction (isotrophic) but the
 crystal couldn't survive during the data collection.
 Is there any methods or cryo conditions I can use to improve my
 diffraction data?
 This crystal grew in 2.5M Ammonium Sulfate.

 Thank you so much.

 Ji

[ccp4bb] dissolving L-alanosine

[Jacqueline Vitali]

Dear colleagues:

I added a few lamdas of NaOH and dissolved it.  Thank you all for the
responses.

Jackie Vitali