[ccp4bb] AsCA 2018/CRYSTAL 32 conference workshops

[Christopher Squire]

[https://az659834.vo.msecnd.net/eventsairseasiaprod/production-uoaevents-public/d231daa0bdac4db99817bc87d65a4b98]


Dear Colleagues,

Registration for the AsCA 2018/CRYSTAL 32 Conference workshops which will be 
held on Sunday, 2 December 2018 is now open.

Delegates can register for a workshop at the same time as registering for the 
conference. There are four workshops which will each run concurrently. Spaces 
are strictly limited, so please register now at the following site: 
http://asca2018.org/registration/?

Workshop topics:

  *   Olex2-CCDC workshop
  *   CCP4-Autorickshaw workshop
  *   Combined workshop 1) SBGrid - Structural biology software infrastructure, 
2) Synergistic use of diffraction and spectroscopic methods at XFEL and 
synchrotron sources
  *   LCP - Lipidic cubic phase workshop

For a full description of the workshops visit http://asca2018.org/workshops/ 
and for the full programme (including times) visit 
http://asca2018.org/programme/.

Finally, a reminder that submissions are now open. Please visit the Call for 
Abstracts page for more information 
and to submit an abstract.

Should you have any queries regarding the AsCA 2018/CRYSTAL 32 Conference, 
please do not hesitate to contact us using the email address below.


Kind regards,

Event Services
University of Auckland
Email: asca2...@auckland.ac.nz



[https://az659834.vo.msecnd.net/eventsairseasiaprod/production-uoaevents-public/74ff1f66f2454a1badc85ad293b9e939]








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Re: [ccp4bb] Unidentified electron density blob

[Jan Stransky]

Hi,

seeing a "blue" map might at lower sigma levels might give some more 
insight. However, there are some caveats in doing so, like solvent 
flattening during the refinement. Phenix has options to calculate some 
fancy maps, which might give you some more "tips": Feature Enhanced Map, 
and Polder map.


Also you mention, that it is a shallow cavity on the surface, that could 
mean, that some bigger molecule (PEG, PTPE) is localised only partially. 
Or there are multiple states, combined with water etc Not helping 
much :-)


Do you have an anomalous map available? For example HEPES has a group 
with sulphur, which might be seen in anomalous map. If you see anomalous 
peaks on sulphurs of your protein, it might not be that unreasonable 
even on 1.0A-ish wavelength.


Best regards,
Jan

Dne 06.07.2018 v 16:02 Robbie Joosten napsal(a):

I'd like to add the more current CCP4 solution: AceDRG. It works really well 
and you only need to feed it the SMILES string of your compound.

Also keep in mind that many compounds are actually already in the CCP4 
dictionary. Finding out whether a compound is, is a two-step procedure:

1) Go to http://ligand-expo.rcsb.org/ and use the search option to find out 
whether the compound is already in the PDB
2) If it is, you now have a residue name. To check whether the compound is also 
in the CCP4 dictionary, just use the 'Get monomer' option in Coot.

HTH,
Robbie



-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
zaigham mahmood khan
Sent: Friday, July 06, 2018 15:30
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Unidentified electron density blob

Hey Uma

Yes, you are right that PFPE is too big for this density. Also, more experienced
scientist in this field has already commented on it.

For the second part of your query, this is how one can generate the
"crystallographic information file" - .cif for the ligand of choice (in case it 
is not
available):

1.  Using Prodrg server (http://prodrg1.dyndns.org/submit.html)
2.  Phenix Ligands (i usually use eLBOW), but this will require smile
strings for the molecules not listed in PDB (and hence 3-letter code is not
available). I use Chemdraw to obtain the Smile Strings..


Best wishes


-Z


Zaigham Mahmood Khan, PhD

Icahn School of Medicine at Mount Sinai
Department of Oncological Sciences
1470 Madison Avenue
New York

On Fri, Jul 6, 2018 at 5:42 AM, Wim Burmeister 
wrote:


Hello,
a really molecule should show up also in the 2Fo-Fc type map. This
appears not to be the case.
So indeed it is likely that your density corresponds to some alternate
conformation of the surrounding residues present with low occupancy. The
glutamic acid sidechain could be modelled, but I have some doubts about the
rest.
If the refinement is almost finished, it could simply be noise.
Best
Wim


On 03/07/2018 04:23, Uma Gabale wrote:



Dear all,


We came across a blob of unidentified electron density in a
shallow cavity of a bacterial protein structure (pictures attached). It is
surrounded by residues Asp, Arg, Gln, His, Glu, Thr, and Trp.


The protein was expressed in E. coli BL21(DE3) and purified
on Ni-NTA followed by gel filtration. The purification buffers included Tris,
crystallization condition had HEPES and PEG3350; perfluoropolyether was
used as a cryoprotectant.

We would appreciate any help in identifying it.​


Thanks and regards,


Uma.

--
Uma Gabale, PhD
Research Associate
Molecular and Cellular Biochemistry
Indiana University Bloomington






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--


Wim Burmeister
Professeur
Institut de Biologie Structurale (IBS) CIBB
71 avenue des Martyrs


CS 20192
38044 Grenoble Cedex 9, FRANCE
E-mail: wim.burmeis...@ibs.fr
Tel:+33 (0) 457 42 87 41   Fax: +33 (0) 476 20 94 00
website 
map










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Re: [ccp4bb] Clear segid

[Pavel Afonine]

This should work in latest nightly builds:

phenix.pdbtools model.pdb clear_seg_id=true

If it doesn't please report a bug (on appropriate Phenix lists).

Good luck!
Pavel


On Thu, Jul 5, 2018 at 4:33 AM, Eugene Osipov  wrote:

> Hello everyone,
> is there any simple way in CCP4 to clear segid field?
> I used phenix.pdbtools but version 1.13 does not work anymore.
>
> --
> Eugene Osipov
> Junior Research Scientist
> Laboratory of Enzyme Engineering
> Research Center of Biotechnology
> Russian Academy of Sciences
> Leninsky pr. 33, 119071 Moscow, Russia
> e-mail: e.m.osi...@gmail.com
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>



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[ccp4bb] PISA command line

[wtempel]

Hi,
has anyone of you performed a PISA command line analysis using the version
distributed with CCP4 on ubuntu-16.04? My attempt to "-list interfaces"
after seemingly successful "-analysis" resulted in a core dump:


 PISA v.2.1.1 built 05-04-2017   with SSM v.1.4.0, SRS v.1.0.0, MMDB
v.2,0.17
 Session some_name
Segmentation fault (core dumped)


Any suggestions?
Thanks.
Wolfram Tempel



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[ccp4bb] CCP4/SPring-8 workshop 1-6 October 2018

[Ballard, Charles (STFC,RAL,CSE)]

Dear All

I am pleased to announce the second CCP4/Spring-8 (RIKEN) workshop running from 
1-6 October 2018.

This workshop will cover data collection, processing and structure solution.  
Details are available at
http://www.ccp4.ac.uk/schools/Japan-2018 , with more to follow.  Registration 
is on the same site.  Registration will
close on 24 August.

Topics will include XDS (Kay Diederichs), DIALS (Graeme Winter), the CCP4 suite 
(myself and others),
 PDB_REDO (Robbie Joosten), COOT and others. The format will cover data 
collection, lectures, tutorials and 
problem solving, so students are encourages to bring their own data to work on.

Charles and Kunio.



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Re: [ccp4bb] Unidentified electron density blob

[Robbie Joosten]

I'd like to add the more current CCP4 solution: AceDRG. It works really well 
and you only need to feed it the SMILES string of your compound. 

Also keep in mind that many compounds are actually already in the CCP4 
dictionary. Finding out whether a compound is, is a two-step procedure:

1) Go to http://ligand-expo.rcsb.org/ and use the search option to find out 
whether the compound is already in the PDB
2) If it is, you now have a residue name. To check whether the compound is also 
in the CCP4 dictionary, just use the 'Get monomer' option in Coot.

HTH,
Robbie


> -Original Message-
> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
> zaigham mahmood khan
> Sent: Friday, July 06, 2018 15:30
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Unidentified electron density blob
> 
> Hey Uma
> 
> Yes, you are right that PFPE is too big for this density. Also, more 
> experienced
> scientist in this field has already commented on it.
> 
> For the second part of your query, this is how one can generate the
> "crystallographic information file" - .cif for the ligand of choice (in case 
> it is not
> available):
> 
> 1.Using Prodrg server (http://prodrg1.dyndns.org/submit.html)
> 2.Phenix Ligands (i usually use eLBOW), but this will require smile
> strings for the molecules not listed in PDB (and hence 3-letter code is not
> available). I use Chemdraw to obtain the Smile Strings..
> 
> 
> Best wishes
> 
> 
> -Z
> 
> 
> Zaigham Mahmood Khan, PhD
> 
> Icahn School of Medicine at Mount Sinai
> Department of Oncological Sciences
> 1470 Madison Avenue
> New York
> 
> On Fri, Jul 6, 2018 at 5:42 AM, Wim Burmeister 
> wrote:
> 
> 
>   Hello,
>   a really molecule should show up also in the 2Fo-Fc type map. This
> appears not to be the case.
>   So indeed it is likely that your density corresponds to some alternate
> conformation of the surrounding residues present with low occupancy. The
> glutamic acid sidechain could be modelled, but I have some doubts about the
> rest.
>   If the refinement is almost finished, it could simply be noise.
>   Best
>   Wim
> 
> 
>   On 03/07/2018 04:23, Uma Gabale wrote:
> 
> 
> 
>   Dear all,
> 
> 
>   We came across a blob of unidentified electron density in a
> shallow cavity of a bacterial protein structure (pictures attached). It is
> surrounded by residues Asp, Arg, Gln, His, Glu, Thr, and Trp.
> 
> 
>   The protein was expressed in E. coli BL21(DE3) and purified
> on Ni-NTA followed by gel filtration. The purification buffers included Tris,
> crystallization condition had HEPES and PEG3350; perfluoropolyether was
> used as a cryoprotectant.
> 
>   We would appreciate any help in identifying it.​
> 
> 
>   Thanks and regards,
> 
> 
>   Uma.
> 
>   --
>   Uma Gabale, PhD
>   Research Associate
>   Molecular and Cellular Biochemistry
>   Indiana University Bloomington
> 
> 
> 
> 
> 
> 
>   To unsubscribe from the CCP4BB list, click the following link:
>   https://www.jiscmail.ac.uk/cgi-
> bin/webadmin?SUBED1=CCP4BB=1  bin/webadmin?SUBED1=CCP4BB=1>
> 
> 
>   --
> 
> 
>   Wim Burmeister
>   Professeur
>   Institut de Biologie Structurale (IBS) CIBB
>   71 avenue des Martyrs
>  ce=g>
> 
>   CS 20192
>   38044 Grenoble Cedex 9, FRANCE
>   E-mail: wim.burmeis...@ibs.fr
>   Tel:+33 (0) 457 42 87 41   Fax: +33 (0) 476 20 94 00
>   website  replication-machines-group-m-jamin/team-03/article/poxvirus-replication-
> machinery-presentation/>
>   map
>  /45.20762/5.69255>
> 
> 
> 
> 
> 
> 
> 
> 
> 
>   To unsubscribe from the CCP4BB list, click the following link:
>   https://www.jiscmail.ac.uk/cgi-
> bin/webadmin?SUBED1=CCP4BB=1  bin/webadmin?SUBED1=CCP4BB=1>
> 
> 
> 
> 
> 
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Re: [ccp4bb] Please share your experience about "ugly" crystals showing good diffraction

[Edward Snell]

I couldn’t agree more with Patrick which is often the case.

To echo some of his comments, in the High-Throughput Crystallization Screening 
Center we see many examples where the visual images of initial crystallization 
hits are very poor and experienced (or inexperienced) crystallographers would 
typically ignore them. SONICC and UV two photon fluorescence images can 
indicate something far more promising. Optimization of the visually ‘crappy’ 
crystals (or even things that really don’t look like crystals to the eye) that 
have strong SONICC or UV two photon fluorescence very often produces beautiful 
results. We published a short paper on this  “The detection and subsequent 
volume optimization of biological nanocrystals, Luft JR, et al.. Struct Dyn. 
2015 May 15;2(4):041710 and have seen many examples since. The crystallization 
research page of the High-Throughput Screening Center (http://getacrystal.org) 
has a link to this paper under the Crystallization Research section and there 
is a more extensive literature related to this research are on the website in 
my signature.

Excuse the shameless plug, but if you don’t have SONICC and UV-two photon 
detection, this is a standard part of the crystallization screening center 
available to all and run by Dr. Sarah Bowman 
(https://hwi.buffalo.edu/scientist-directory/sbowman/) – Details at 
http://getacrystal.org. There is also some news on automated outcome 
classification just to put a teaser of things to come out there.

Best,

Eddie

Edward Snell Ph.D.

Biological Small Angle Scattering Theory and Practice, Eaton E. Lattman, Thomas 
D. Grant, and Edward H. Snell.
Available through all good bookshops, or direct from Oxford University Press

Director of the NSF BioXFEL Science and Technology Center
President and CEO Hauptman-Woodward Medical Research Institute
BioInnovations Chaired Professorship, University at Buffalo, SUNY
700 Ellicott Street, Buffalo, NY 14203-1102
hwi.buffalo.edu
Phone:   (716) 898 8631 Fax: (716) 898 8660
Skype:eddie.snell Email: esn...@hwi.buffalo.edu
Webpage: https://hwi.buffalo.edu/scientist-directory/snell/

[cid:image001.png@01D4150E.CF9BD9D0]
Heisenberg was probably here!

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Patrick 
Shaw Stewart
Sent: Friday, July 6, 2018 7:08 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Please share your experience about "ugly" crystals 
showing good diffraction


Hi All

I have a comment, based on my old supervisor's explanation, which seemed to 
make sense.

Crystals usually grow layer by layer.  Once a new layer is formed it quickly 
expands to cover the whole surface.  That's why crystals normally have flat 
surfaces and sharp edges - the layers/steps expand rapidly until they get to 
the edges.

However it doesn't have to be like that.  Sometimes new layers can form roughly 
as quickly as the previous layers can spread.  The result is crystals with 
curved surfaces - or even just blobs.

Just because the new layers form at a rate that is comparable to the spreading 
doesn't mean that the crystals won't be ordered, and won't diffract well.

Once I understood that I understood what I was seeing better when I checked my 
drops.

Best wishes Patrick


On 5 July 2018 at 22:06, Sanishvili, Ruslan 
mailto:rsanishv...@anl.gov>> wrote:

Hi Anirban,

It would be great if you could share the compilation of relevant responses to 
your request. I think many others in the community could use these examples for 
educational purposes.

Best,

Nukri


Ruslan Sanishvili (Nukri), Ph.D.
Macromolecular Crystallographer
GM/CA@APS
X-ray Science Division, ANL
9700 S. Cass Ave.
Lemont, IL 60439

Tel: (630)252-0665
Fax: (630)252-0667
rsanishv...@anl.gov


From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> 
on behalf of Anirban Banerjee mailto:ani...@gmail.com>>
Sent: Thursday, June 28, 2018 7:07 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Please share your experience about "ugly" crystals showing 
good diffraction


Dear all,

Apologies for the non-CCP4 related question.

If you have concrete experience about visually unappealing, i.e. ugly crystals 
( your own take on ugly is fine)  diffracting better than comparably similar 
sized nicer looking crystals of the same protein, will you please share here ? 
Even better if that led to a published structure. Might you also have pictures ?

We have all heard anecdotes about not using visual appearance to judge the 
quality of crystals as far as their ability to give good diffraction data is 
concerned but I am trying to gather some concrete pointers here to motivate 
trainees.

Thanks very much for any help.

Best,

Anirban

P.S. I know that there is probably a lot of thought and wisdom  on this this 
specific topic but I am really looking for actual experience.



To 

Re: [ccp4bb] COOT: adding xylose to a plant glycosylation chain

[Paul Emsley]

Opps sorry - that's the wrong format. Try this instead.

Paul



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--- lib/data/monomers/list/mon_lib_list.cif-orig2018-07-06 
14:28:55.0 +0100
+++ lib/data/monomers/list/mon_lib_list.cif 2018-07-06 14:28:32.0 
+0100
@@ -16785,6 +16785,7 @@
 ACYSNN  ACY  ACYmod  .  SNN  SNNmod  .  'ACYSNN'
 ALASNN  .ALAmodpeptide  SNN  SNNmod  .  'ALASNN'
 XYPa-XYP   XYP   XYPmod1   .XYP  XYPmod2 .  XYP-XYP
+XYP-BMA XYP  XYPmol1  . BMA  DEL-HO2.  
bond_XYP-C1B=_BMA-O2
 TPN-TPN  TPN  TPNmodC  .  TPN  TPNmodN  .
  TPN-TPN
 PEP-ORN  .  DEL-OXTpeptideORN  ORN-NE   .  PEP-ORN
@@ -19056,6 +19057,48 @@
 _chem_link_chir.volume_sign
  XYPa-XYP chir_08  1 C1B2 O4B1 C2B1 O5B   both
 #
+data_link_XYP-BMA
+
+loop_
+_chem_link_bond.link_id
+_chem_link_bond.atom_1_comp_id
+_chem_link_bond.atom_id_1
+_chem_link_bond.atom_2_comp_id
+_chem_link_bond.atom_id_2
+_chem_link_bond.type
+_chem_link_bond.value_dist
+_chem_link_bond.value_dist_esd
+ XYP-BMA 1 C1B2 O2single  1.4260.020
+
+loop_
+_chem_link_angle.link_id
+_chem_link_angle.atom_1_comp_id
+_chem_link_angle.atom_id_1
+_chem_link_angle.atom_2_comp_id
+_chem_link_angle.atom_id_2
+_chem_link_angle.atom_3_comp_id
+_chem_link_angle.atom_id_3
+_chem_link_angle.value_angle
+_chem_link_angle.value_angle_esd
+ XYP-BMA 2 C2 2 O2 1 C1B 111.8003.000
+ XYP-BMA 2 O2 1 C1B1 H1B 109.4703.000
+ XYP-BMA 2 O2 1 C1B1 C2B 109.4703.000
+ XYP-BMA 2 O2 1 C1B1 O5B 109.4703.000
+
+loop_
+_chem_link_chir.link_id
+_chem_link_chir.id
+_chem_link_chir.atom_centre_comp_id
+_chem_link_chir.atom_id_centre
+_chem_link_chir.atom_1_comp_id
+_chem_link_chir.atom_id_1
+_chem_link_chir.atom_2_comp_id
+_chem_link_chir.atom_id_2
+_chem_link_chir.atom_3_comp_id
+_chem_link_chir.atom_id_3
+_chem_link_chir.volume_sign
+ XYP-BMA chir_08  1 C1B2 O2 1 C2B1 O5B   both
+#
 data_link_ZN-CYS
 #
 loop_



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Re: [ccp4bb] COOT: adding xylose to a plant glycosylation chain

[Paul Emsley]

On 05/07/2018 15:00, Yoder, Marilyn wrote:


I'm having problems adding XYP (beta-xylose) to my glycosylation chain in a 
plant protein.


Hello again Marilyn,

Having reflected on the problem, I hope that I can offer a bit more insight than "use the latest version" - 
so here's another attempt.


As you may know, Coot uses the standard Refmac monomer library, which (amongst other things) contains a list 
of descriptions of carbohydrate linkages in list/mon_lib_list.cif.  As it sets up a refinement, Coot 
compares pairs of monomers against this list of linkages, so that, for example, an (ASN, NAG) pair will use 
the NAG-ASN link description, a (NAG, NAG) pair will use the BETA1-4 link description (and so on). I now 
recall that while developing this module we discovered that the monomer library did not contain a link for 
(XYP, BMA). Which meant that as the refinement was turned on, the XYP "rapidly wiggled away" (as you'd put 
it). So I made a new link and added it to list/mon_lib_list.cif. Coot was happy again.


So my guess is that you are using a version of the monomer library for which the XYP-BMA link description 
has not percolated through the necessary hoops (as it were).


Patch attached - you may need to dedos your dictionary - I did (not sure why).

Regards,

Paul.



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16787a16788
> XYP-BMA XYP  XYPmol1  . BMA  DEL-HO2.  
> bond_XYP-C1B=_BMA-O2
19058a19060,19101
> data_link_XYP-BMA
> 
> loop_
> _chem_link_bond.link_id
> _chem_link_bond.atom_1_comp_id
> _chem_link_bond.atom_id_1
> _chem_link_bond.atom_2_comp_id
> _chem_link_bond.atom_id_2
> _chem_link_bond.type
> _chem_link_bond.value_dist
> _chem_link_bond.value_dist_esd
>  XYP-BMA 1 C1B2 O2single  1.4260.020
> 
> loop_
> _chem_link_angle.link_id
> _chem_link_angle.atom_1_comp_id
> _chem_link_angle.atom_id_1
> _chem_link_angle.atom_2_comp_id
> _chem_link_angle.atom_id_2
> _chem_link_angle.atom_3_comp_id
> _chem_link_angle.atom_id_3
> _chem_link_angle.value_angle
> _chem_link_angle.value_angle_esd
>  XYP-BMA 2 C2 2 O2 1 C1B 111.8003.000
>  XYP-BMA 2 O2 1 C1B1 H1B 109.4703.000
>  XYP-BMA 2 O2 1 C1B1 C2B 109.4703.000
>  XYP-BMA 2 O2 1 C1B1 O5B 109.4703.000
> 
> loop_
> _chem_link_chir.link_id
> _chem_link_chir.id
> _chem_link_chir.atom_centre_comp_id
> _chem_link_chir.atom_id_centre
> _chem_link_chir.atom_1_comp_id
> _chem_link_chir.atom_id_1
> _chem_link_chir.atom_2_comp_id
> _chem_link_chir.atom_id_2
> _chem_link_chir.atom_3_comp_id
> _chem_link_chir.atom_id_3
> _chem_link_chir.volume_sign
>  XYP-BMA chir_08  1 C1B2 O2 1 C2B1 O5B   both
> #



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Re: [ccp4bb] Unidentified electron density blob

[zaigham mahmood khan]

Hey Uma

Yes, you are right that PFPE is too big for this density. Also, more
experienced scientist in this field has already commented on it.

For the second part of your query, this is how one can generate the
"crystallographic information file" - .cif for the ligand of choice (in
case it is not available):

   1. Using Prodrg server (http://prodrg1.dyndns.org/submit.html)
   2. Phenix Ligands (i usually use eLBOW), but this will require smile
   strings for the molecules not listed in PDB (and hence 3-letter code is not
   available). I use Chemdraw to obtain the Smile Strings..


Best wishes

-Z


Zaigham Mahmood Khan, PhD

Icahn School of Medicine at Mount Sinai
Department of Oncological Sciences
1470 Madison Avenue
New York

On Fri, Jul 6, 2018 at 5:42 AM, Wim Burmeister 
wrote:

> Hello,
> a really molecule should show up also in the 2Fo-Fc type map. This appears
> not to be the case.
> So indeed it is likely that your density corresponds to some alternate
> conformation of the surrounding residues present with low occupancy. The
> glutamic acid sidechain could be modelled, but I have some doubts about the
> rest.
> If the refinement is almost finished, it could simply be noise.
> Best
> Wim
>
>
> On 03/07/2018 04:23, Uma Gabale wrote:
>
> Dear all,
>
> We came across a blob of unidentified electron density in a shallow cavity of
> a bacterial protein structure (pictures attached). It is surrounded by
> residues Asp, Arg, Gln, His, Glu, Thr, and Trp.
>
> The protein was expressed in *E. coli* BL21(DE3) and purified on Ni-NTA
> followed by gel filtration. The purification buffers included Tris,
> crystallization condition had HEPES and PEG3350; perfluoropolyether was
> used as a cryoprotectant.
>
> We would appreciate any help in identifying it.​
>
> Thanks and regards,
>
> Uma.
> --
> Uma Gabale, PhD
> Research Associate
> Molecular and Cellular Biochemistry
> Indiana University Bloomington
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>
>
> --
>
> Wim Burmeister
> Professeur
> Institut de Biologie Structurale (IBS) CIBB
> 71 avenue des Martyrs
> 
> CS 20192
> 38044 Grenoble Cedex 9, FRANCE
> E-mail: wim.burmeis...@ibs.fr
> Tel:+33 (0) 457 42 87 41   Fax: +33 (0) 476 20 94 00
> website
> 
> map
> 
>
>
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>



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Re: [ccp4bb] Please share your experience about "ugly" crystals showing good diffraction

[Peter Keller]

Dear Anirban,

On 05/07/18 22:06, Sanishvili, Ruslan wrote:

Hi Anirban,

It would be great if you could share the compilation of relevant 
responses to your request. I think many others in the community could 
use these examples for educational purposes.


Quite so, and I am sure that a lot of people on this list will agree 
with me that there was no need to apologise for asking this question ;-)


Regards,
Peter.



*From:* CCP4 bulletin board  on behalf of Anirban 
Banerjee 

*Sent:* Thursday, June 28, 2018 7:07 PM
*To:* CCP4BB@JISCMAIL.AC.UK
*Subject:* [ccp4bb] Please share your experience about "ugly" crystals 
showing good diffraction


Dear all,

Apologies for the non-CCP4 related question.

If you have concrete experience about visually unappealing, i.e. ugly 
crystals ( your own take on ugly is fine)  diffracting better than 
comparably similar sized nicer looking crystals of the same protein, 
will you please share here ? Even better if that led to a published 
structure. Might you also have pictures ?


We have all heard anecdotes about not using visual appearance to judge 
the quality of crystals as far as their ability to give good diffraction 
data is concerned but I am trying to gather some concrete pointers here 
to motivate trainees.


Thanks very much for any help.

Best,

Anirban

P.S. I know that there is probably a lot of thought and wisdom  on this 
this specific topic but I am really looking for actual experience.




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--
Peter Keller Tel.: +44 (0)1223 353033
Global Phasing Ltd., Fax.: +44 (0)1223 366889
Sheraton House,
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Re: [ccp4bb] Please share your experience about "ugly" crystals showing good diffraction

[Patrick Shaw Stewart]

Hi All

I have a comment, based on my old supervisor's explanation, which seemed to
make sense.

Crystals usually grow layer by layer.  Once a new layer is formed it
quickly expands to cover the whole surface.  That's why crystals normally
have flat surfaces and sharp edges - the layers/steps expand rapidly until
they get to the edges.

However it doesn't have to be like that.  Sometimes new layers can form
roughly as quickly as the previous layers can spread.  The result is
crystals with curved surfaces - or even just blobs.

Just because the new layers form at a rate that is comparable to the
spreading doesn't mean that the crystals won't be ordered, and won't
diffract well.

Once I understood that I understood what I was seeing better when I checked
my drops.

Best wishes Patrick


On 5 July 2018 at 22:06, Sanishvili, Ruslan  wrote:

> Hi Anirban,
>
> It would be great if you could share the compilation of relevant responses
> to your request. I think many others in the community could use these
> examples for educational purposes.
>
> Best,
>
> Nukri
>
>
> Ruslan Sanishvili (Nukri), Ph.D.
> Macromolecular Crystallographer
> GM/CA@APS
> X-ray Science Division, ANL
> 9700 S. Cass Ave.
> Lemont, IL 60439
>
> Tel: (630)252-0665
> Fax: (630)252-0667
> rsanishv...@anl.gov
>
>
>
> --
> *From:* CCP4 bulletin board  on behalf of Anirban
> Banerjee 
> *Sent:* Thursday, June 28, 2018 7:07 PM
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* [ccp4bb] Please share your experience about "ugly" crystals
> showing good diffraction
>
>
> Dear all,
>
> Apologies for the non-CCP4 related question.
>
> If you have concrete experience about visually unappealing, i.e. ugly
> crystals ( your own take on ugly is fine)  diffracting better than
> comparably similar sized nicer looking crystals of the same protein, will
> you please share here ? Even better if that led to a published structure.
> Might you also have pictures ?
>
> We have all heard anecdotes about not using visual appearance to judge the
> quality of crystals as far as their ability to give good diffraction data
> is concerned but I am trying to gather some concrete pointers here to
> motivate trainees.
>
> Thanks very much for any help.
>
> Best,
>
> Anirban
>
> P.S. I know that there is probably a lot of thought and wisdom  on this
> this specific topic but I am really looking for actual experience.
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>



-- 
 patr...@douglas.co.ukDouglas Instruments Ltd.
 Douglas House, East Garston, Hungerford, Berkshire, RG17 7HD, UK
 Directors: Peter Baldock, Patrick Shaw Stewart

 http://www.douglas.co.uk
 Tel: 44 (0) 148-864-9090US toll-free 1-877-225-2034
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Re: [ccp4bb] Unidentified electron density blob

[Wim Burmeister]

  
  
Hello,
a really molecule should show up also in the 2Fo-Fc type map. This
appears not to be the case.
So indeed it is likely that your density corresponds to some
alternate conformation of the surrounding residues present with low
occupancy. The glutamic acid sidechain could be modelled, but I have
some doubts about the rest.
If the refinement is almost finished, it could simply be noise.
Best
Wim

On 03/07/2018 04:23, Uma Gabale wrote:


  

  

  
  Dear all,
  

  We came across a blob of
  unidentified electron density in a shallow cavity
  of a bacterial protein
  structure (pictures attached). It is surrounded by residues Asp, Arg, Gln, His, Glu, Thr, and Trp.
  

  
The protein was expressed in E. coli BL21(DE3)
  and purified on Ni-NTA followed by gel filtration.
  The purification buffers included Tris,
  crystallization condition had HEPES and PEG3350;
  perfluoropolyether was used as a cryoprotectant.
We would appreciate any help in identifying it.​

Thanks and regards,

Uma.
  

  
--
Uma
Gabale, PhD
  Research
  Associate
  Molecular
and Cellular Biochemistry
  Indiana
University Bloomington


  



  


  

  

  

  

  
  

  

  

  

  

  
  
  
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-- 
  
  
  


  Wim Burmeister
Professeur
  Institut de Biologie Structurale (IBS) CIBB
  71 avenue des Martyrs
  CS
  20192
  38044 Grenoble Cedex 9, FRANCE
  E-mail: wim.burmeis...@ibs.fr
Tel:    +33 (0) 457 42 87 41   Fax: +33 (0) 476 20
94 00
  website
  map
  
  
  

  

  



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