Re: [ccp4bb] criteria to set resolution limit

[Tushar R.]

Along with the paper mentioned by Rajiv, you could look at this paper as
well which discusses a major shift in the understanding of data quality
from I/sig(I) based to CC1/2 based indicators.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4684713/

Hope this helps.

All the best.

Best,
Tushar.



On Sat, 11 Sep 2021, 09:36 Rajiv gandhi.s,  wrote:

> Dear Chang,
> One need to set resolution cut off, to have a meaningful data without
> losing high resolution data and keeping data integrity. Some key quality
> indicators like I/Sigma I,  CC 1/2 and Rpim etc., at outer most shell need
> to be considered.  What was the CC 1/2 value in outer shell ?
>
> Please refer to the below paper.
> How good are my data and what is the resolution
> Assessing and maximizing data quality in macromolecular crystallograph
>
> On Sat, 11 Sep 2021, 9:52 pm Tao-Hsin Chang, 
> wrote:
>
>> Hi Farhan,
>>
>> It looks like that your diffraction data has an anisotropic issue and it
>> leads to the issues of resolution limit, intensity, and completeness. Check
>> The STARANISO Server (
>> https://staraniso.globalphasing.org/cgi-bin/staraniso.cgi). It may be
>> useful for your case.
>>
>> Best wishes,
>> Tao-Hsin
>>
>> On Sep 11, 2021, at 11:55 AM, Syed Farhan Ali 
>> wrote:
>>
>> Dear All,
>>
>> I have query regarding one of my dataset. I am running aimless by keeping
>> highest resolution 1.62 A and getting  I/SigI = 2 but data completeness is
>> around 22 in outermost shell. And if I am increasing the resolution cutoff
>> up to 1.8 A then I/SigI is 6.2 and completeness is 82.4.
>> I have attached the screenshot of the result.
>> What should be the criteria to set the resolution limit?  Should I stick
>> to  I/SigI  or I have to consider about the completeness of data.
>> And if completeness is also a guiding factor than how much minimum
>> completeness I can keep in the higher resolution shell.
>>
>>
>>
>>
>>
>> Regards,
>> Farhan
>>
>>
>>
>>
>> --
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>> 
>>
>>
>>
>> --
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

Re: [ccp4bb] AI papers in experimental macromolecular structure determination

[Tushar R.]

Hi Andrea,

Here is something interesting on the extraction of information on protein
dynamics from cryo-EM data:

https://doi.org/10.1038/s42256-020-00290-y

Best,
Tushar.

On Tue, 3 Aug 2021 at 19:48, Shekhar Mande  wrote:

> In particle picking, you may wish to include the following:
>
> George, B., Assaiya, A., Roy, R.J. *et al.* CASSPER is a semantic
> segmentation-based particle picking algorithm for single-particle
> cryo-electron microscopy. *Commun Biol* 4, 200 (2021).
> https://doi.org/10.1038/s42003-021-01721-1
>
> On Tue, Aug 3, 2021 at 9:17 PM Guillaume Gaullier <
> guillaume.gaull...@icm.uu.se> wrote:
>
>> Hello,
>>
>> In the particle picking section, you may want to include these two:
>>
>> Wagner T, Merino F, Stabrin M, Moriya T, Antoni C, Apelbaum A, Hagel P,
>> Sitsel O, Raisch T, Prumbaum D, et al (2019) SPHIRE-crYOLO is a fast and
>> accurate fully automated particle picker for cryo-EM. Communications
>> Biology 2: 218 https://doi.org/10.1038/s42003-019-0437-z
>>
>> Bepler T, Morin A, Rapp M, Brasch J, Shapiro L, Noble AJ & Berger B
>> (2019) Positive-unlabeled convolutional neural networks for particle
>> picking in cryo-electron micrographs. Nat Methods: 1–8
>> https://doi.org/10.1038/s41592-019-0575-8
>>
>> And this paper on micrograph denoising could go in the "micrograph
>> preparation" section I suppose, or in its own section:
>>
>> Bepler T, Kelley K, Noble AJ & Berger B (2020) Topaz-Denoise: general
>> deep denoising models for cryoEM and cryoET. Nature Communications 11: 5208
>> https://doi.org/10.1038/s41467-020-18952-1
>>
>> I hope this is useful.
>> Cheers,
>>
>> Guillaume
>>
>>
>> On 3 Aug 2021, at 13:43, Thorn, Dr. Andrea 
>> wrote:
>>
>> Dear colleagues,
>> I have compiled a list of papers that cover the application of AI/machine
>> learning methods in single-crystal structure determination (mostly
>> macromolecular crystallography) and single-particle Cryo-EM. The draft list
>> is attached below.
>>
>> If I missed any papers, please let me know. I will send the final list
>> back here, for the benefit of all who are interested in the topic.
>>
>> Best wishes,
>>
>>
>> Andrea.
>>
>>
>> __
>> General:
>> - Gopalakrishnan, V., Livingston, G., Hennessy, D., Buchanan, B. &
>> Rosenberg, J. M. (2004). Acta Cryst D. 60, 1705–1716.
>> - Morris, R. J. (2004). Acta Cryst D. 60, 2133–2143.
>>
>> Micrograph preparation:
>> - (2020). Journal of Structural Biology. 210, 107498.
>>
>> Particle Picking:
>> - Sanchez-Garcia, R., Segura, J., Maluenda, D., Carazo, J. M. & Sorzano,
>> C. O. S. (2018). IUCrJ. 5, 854–865.
>> - Al-Azzawi, A., Ouadou, A., Tanner, J. J. & Cheng, J. (2019). BMC
>> Bioinformatics. 20, 1–26.
>> - George, B., Assaiya, A., Roy, R. J., Kembhavi, A., Chauhan, R., Paul,
>> G., Kumar, J. & Philip, N. S. (2021). Commun Biol. 4, 1–12.
>> - Lata, K. R., Penczek, P. & Frank, J. (1995). Ultramicroscopy. 58,
>> 381–391.
>> - Nguyen, N. P., Ersoy, I., Gotberg, J., Bunyak, F. & White, T. A.
>> (2021). BMC Bioinformatics. 22, 1–28.
>> - Wang, F., Gong, H., Liu, G., Li, M., Yan, C., Xia, T., Li, X. & Zeng,
>> J. (2016). Journal of Structural Biology. 195, 325–336.
>> - Wong, H. C., Chen, J., Mouche, F., Rouiller, I. & Bern, M. (2004).
>> Journal of Structural Biology. 145, 157–167.
>>
>> Motion description in Cryo-EM:
>> - Matsumoto, S., Ishida, S., Araki, M., Kato, T., Terayama, K. & Okuno,
>> Y. (2021). Nat Mach Intell. 3, 153–160.
>> - Zhong, E. D., Bepler, T., Berger, B. & Davis, J. H. (2021). Nat
>> Methods. 18, 176–185.
>>
>> Local resolution:
>> - Avramov, T. K., Vyenielo, D., Gomez-Blanco, J., Adinarayanan, S.,
>> Vargas, J. & Si, D. (2019). Molecules. 24, 1181.
>> - Ramírez-Aportela, E., Mota, J., Conesa, P., Carazo, J. M. & Sorzano, C.
>> O. S. (2019). IUCrJ. 6, 1054–1063.
>> - (2021). QAEmap: A Novel Local Quality Assessment Method for Protein
>> Crystal Structures Using Machine Learning.
>>
>> Map post-processing:
>> - Sanchez-Garcia, R., Gomez-Blanco, J., Cuervo, A., Carazo, J. M.,
>> Sorzano, C. O. S. & Vargas, J. (2020). BioRxiv. 2020.06.12.148296.
>>
>> Secondary structure assignment in map:
>> - Subramaniya, S. R. M. V., Terashi, G. & Kihara, D. (2019). Nat Methods.
>> 16, 911–917.
>> - Li, R., Si, D., Zeng, T., Ji, S. & He, J. (2016). 2016 IEEE
>> International Conference on Bioinformatics and Biomedicine (BIBM), Vol. pp.
>> 41–46.
>> - Si, D., Ji, S., Nasr, K. A. & He, J. (2012). Biopolymers. 97, 698–708.
>> - He, J. & Huang, S.-Y. Brief Bioinform.
>> - Lyu, Z., Wang, Z., Luo, F., Shuai, J. & Huang, Y. (2021). Frontiers in
>> Bioengineering and Biotechnology. 9,.
>> - Mostosi, P., Schindelin, H., Kollmannsberger, P. & Thorn, A. (2020).
>> Angewandte Chemie International Edition.
>>
>> Automatic structure building:
>> - Alnabati, E. & Kihara, D. (2020). Molecules. 25, 82.
>> - Si, D., Moritz, S. A., Pfab, J., Hou, J., Cao, R., Wang, L., Wu, T. &
>> Cheng, J. (2020). Sci Rep. 10, 1–22.
>> - Moritz, S. A., Pfab, J., Wu, T., Hou, J., Cheng, J., Cao, R., Wang, L.
>> 

Re: [ccp4bb] Does anyone know of a "CHARMM bulletin board" ?

[Tushar R.]

Hi Fred,

Since you're using CHARMM forcefield, another option is to use swissparam.ch
.
I don't know which system you're working on but I've recently used
swissparam for multiple protein-ligand simulations.

Best,
Tushar.


On Sat, 22 May 2021, 21:13 Murpholino Peligro, 
wrote:

> Hi Fred..
> As an alternative, not mentioned yet, you can use NAMD (
> https://www.ks.uiuc.edu/Research/namd/). If I remember correctly it
> accepts the charmm force fields.
> I think the documentation is way better...
> they also have a mailing list ...
> As a plus... you can download a 'full' version without problems.
>
> El vie, 21 de may. de 2021 a la(s) 06:50, Fred Vellieux (
> frederic.velli...@lf1.cuni.cz) escribió:
>
>> Hi folks,
>>
>> Sorry about the non-ccp4 question. I don't know where to ask.
>>
>> I have to perform MD simulations but I am totally on my own here. The
>> one program that appears to be free (in terms of license) seems to be
>> CHARMM. GROMACS (testing with the examples found in the internet) did
>> not work in my hands so I forget about that.
>>
>> Charmm somehow looks similar to a program I used to work with, X-PLOR.
>> However I haven't found a manual similar to the old XPLOR manual nor a
>> web site that can generate the input files as was the case for X-PLOR.
>> Neither did I find anywhere a flow chart allowing me to know which steps
>> to be performed and in what order.
>>
>> Hence: does anyone know of an X-PLOR to CHARMM dictionary ? Or a CHARMM
>> bulletin board similar to CCP4BB ?
>>
>> Just to give an example using the CHARMM setup.inp file for a protein
>> that has an "ACE" cap at the N-terminus: fails. It complains about the
>> ACE cap. Removing the cap solves that problem but then CHARMM fails
>> because of "HIS". If CHARMM fails because it doesn't like any
>> amino-acids then I don't know how I can use the program. But still I'd
>> like to use it because I have to.
>>
>> Thanks,
>>
>> Fred.
>>
>> --
>> MedChem, 1st F. Medicine, Charles University
>> BIOCEV, Vestec, Czech Republic
>>
>> 
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>>
>> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a
>> mailing list hosted by www.jiscmail.ac.uk, terms & conditions are
>> available at https://www.jiscmail.ac.uk/policyandsecurity/
>>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

Re: [ccp4bb] positive density near asparagine

[Tushar R.]

Hi,

What is the highest resolution for your data?
Depending on the resolution, do you see positive Fo-Fc peak which resembles
the indole ring of Trp even if you have to lower the contour level of your
Fo-Fc map a bit? What are the B-factors of the atoms of Trp for which there
is a possibility of double conformation?
Same for Asn.
Even at 1 sig., the sidechain of Asn doesn't really seem to fit into the
2Fo-Fc map. Also, the positive peak near Asn seems to be very prominent and
I am not sure if a misplaced sidechain can give to such a prominent
positive peak. This is again subject to the resolution of your data and the
degree of disorder for the Asn sidechain.
Also, what are the components of your crystallization and cryoorotectant
solutions?
It might be possible to give more detailed comments if you can share your
structure factor data and co ordinates.

Best,
Tushar.


On 19 August 2017 at 04:50, Napoleão  wrote:

> Hi Zach,
>
> It is hard to judge from one screen shot, maybe a double conformation of
> the Asn and the Trp immediately before it?
>
> Regards,
>
> Napo
>
>
>
> Em 2017-08-18 18:17, Maben, Zachary escreveu:
>
> Hello,
>
>
> I am refining a few datasets of my protein of interest (ERAP1) bound to
> various inhibitors, and I repeatedly observe a positive density peak near
> an asparagine.  I first thought this might be a glycan, but this site does
> not fit the canonical N-linked glycosylation motif (this site sequence is
> NKL).  Previous crystal structures of this protein do not identify any
> ligand at this position.
>
>
> https://www.dropbox.com/sh/2wdax5uqlb1f4m3/AABQlGK2_mgibtqnm61E-7o0a?dl=0
> 
>
> Asn833 positive density
> 
> www.dropbox.com
> Shared with Dropbox
>
>
> I would appreciate any suggestions of what this density might be.  Thank
> you for your help.
>
>
> Best,
>
> Zach Maben
>
> Stern Lab
>
> Pathology Department
>
> University of Massachusetts Medical School
>
>
>
>


-- 
Tushar B. Raskar
Graduate student,
49A/106, Pearson Lab,
Centre for Free electron Laser Science (CFEL),
Deutsches Elektronen-Synchrotron (DESY),
Notkestrasse 85, 22607 Hamburg.

Re: [ccp4bb] visible side-chains but breaks in main-chain

[Tushar R.]

Dear Veronica
The map doesn't look good. What is the contour level for these maps?
As Tim suggested, you should try rebuilding the model.
Besides using the softwares which are listed by Tim, you can use
AutoRickshaw server for structure determination.
Do the rest of the regions (excluding the ones you've shown in the image)
look the same as those in these images?
If yes, then probably you should consider reprocessing the data in
different space group.
Best,
Tushar.

On Thu, Dec 1, 2016 at 7:48 PM, Tim Gruene  wrote:

> Dear V,
>
> your map still looks quite poor and disconnected. Maybe you could improve
> your
> overall model before you worry about such detailed questions like main
> chain
> vs. side chain density.
>
> If your resolution is not too poor, you could try rebuilding your model
> with
> shelxe, or buccanner, or phenix, or ...
>
> Regards,
> Tim
>
> On Thursday, December 01, 2016 02:35:21 PM Veronica Fiorentino wrote:
> > Dear bb-ers,
> > Is it uncommon to see side-chains for PHE/ARG visible in density but the
> > main-chain density breaking (say within a beta-strand)? I have attached
> > 1.FEM (map) 2&3. Experimental phase map. If I refine the model as
> Poly-ala,
> > the side-chains appear green in difference map. I therefore assume that
> my
> > sequence assignments are correct(?). Is this symptomatic of some big
> > mistake?
> >
> > R/Rfree are around 27/32 % respectively. The phase problem was solved by
> > SeMet phasing.
> >
> > Many thanks
> > V[image: Inline images 1]
> >
> > [image: Inline images 2]
> >
> > [image: Inline images 3]
> --
> --
> Paul Scherrer Institut
> Dr. Tim Gruene
> - persoenlich -
> Principal Investigator
> Biology and Chemistry
> OFLC/102
> CH-5232 Villigen PSI
>
> Phone: +41 (0)56 310 5297
>
> GPG Key ID = A46BEE1A
>
>


-- 
Tushar B. Raskar
Project JRF (DBT),
Protein Crystallography Lab,
Department of Biosciences and Bioengineering,
Indian Institute of Technology - Bombay.

Re: [ccp4bb] Density for an unknown ligand

[Tushar R.]

Dear Wei,
I am not sure which molecule this density corresponds to but I think you
should also consider the possibility of a molecule that can be fitted in
the density but is in fact at a special position meaning that the axis of
symmetry passes through the center of the molecule leading to presence
symmetry related molecule also in the same position. However, this would
obviously mean that the atoms of these two molecules would have partial
occupancies.

Best,
Tushar.

On Mon, Nov 28, 2016 at 5:27 PM, Bythell-Douglas, Rohan R <
r.bythell-doug...@imperial.ac.uk> wrote:

> Dear Wei,
>
> I think Prem’s suggestion that the molecule is on a symmetry axis is
> right. There are 2 images in those that you have sent that show a two fold
> rotation axis within the missing density, so I think the density
> corresponds to two molecules. - possibly something like PMSF? Did you
> happen to use PMSF during your purification?
>
> Regards,
> Rohan
>
> On 28 Nov 2016, at 11:36, Prem Prakash  wrote:
>
> Dear Wei,
> I am not sure but is it possible that the crystallization condition you
> have used has already this compound (may be as an impurity) rather than
> expecting this as an extract from E. coli. If that can be searched it may
> be useful.
>
> Good luck
> Have a nice day
>
> On Mon, Nov 28, 2016 at 3:51 PM, LiuWei  wrote:
>
>> Hi Prem,
>>
>> Thanks for your response. The compound really looks to be a two-fold
>> symmetry related molecule, but I am very sure that it is not located at a
>> symmetry axis. It looks like a compound with 3 or 4 terminal ring, could-be
>> two molecules of biphenyl enter. Such a compound, however, is almost
>> insoluble, and I wonder if it can be copurified with a protein.
>>
>> Regards
>> Wei
>>
>> 2016年11月28日 下午02:50，Prem Prakash  写道：
>>
>> Hi Wei,
>> Is the electron density of this compound lie at the symmetry axis ? It
>> seems to me that two planar rings with one connecting oxygen. And the
>> compound is more looks like a diphenyl ether to me with its symmetry
>> related molecule.
>>
>> Hope others will give some more idea about it.
>>
>> Cheers
>> P.P
>>
>> On Sun, Nov 27, 2016 at 4:03 PM, Wei Liu  wrote:
>>
>>> Dear all,
>>>
>>> We have recently crystallized a recombinant protein produce from E.
>>> coli, and determined the structure at 1.9 Å. The asymmetric unit contains
>>> two protein monomers. Beyond our expectation, strong Fo - Fc density is
>>> present at a cleft of one subunit, but not in the other. Density maps are
>>> given in the snapshots attached to this email. We tried to model Tris or
>>> Bis-tris propane that were used as the purification and crystallization
>>> buffers, but apparently either of them poorly fitted in this density.  The
>>> molecule that can be modeled here seems more likely to be a ligand
>>> comprising 3 or 4 rings with good planarity, however we did not add any
>>> additives in our crystallization trials. So we think it should be something
>>> from E. coli, which has high affinity to our protein. I wonder if anybody
>>> can figure out which molecule well fits to the electron density.
>>>
>>> Best wishes
>>> Wei Liu
>>>
>>>
>>>   
>>> 
>>>
>>
>>
>
> Rohan Bythell-Douglas
> rbyth...@ic.ac.uk
> Section of Structural Biology,
> Dept. Medicine,
> Imperial College
> London SW7 2AZ
>
>
>
>


-- 
Tushar B. Raskar
Project JRF (DBT),
Protein Crystallography Lab,
Department of Biosciences and Bioengineering,
Indian Institute of Technology - Bombay.