Re: [ccp4bb] Different conformation of chains

2021-10-20 Thread Pavel Afonine
Hi,

if I understood your question correctly, then one of 13 scenarios described
here:

http://phenix-online.org/phenixwebsite_static/mainsite/files/newsletter/CCN_2015_07.pdf#page=12

fits your situation and you should be able to handle it in refinement all
right.

For more specific advice please feel free to contact me directly (off list)
with relevant files.

Good luck!
Pavel

On Wed, Oct 20, 2021 at 5:53 PM S  wrote:

> Dear All,
>
> I am working with a protein, the structure of which is already published
> in the PDB (2 chains in asu) The published structure has a break of around
> 20 residues.
>
> I have crystallized the same protein and saw some density near the gap (20
> residues break).
> I could build 3-4 residues in ChainA and 8 residues in ChainB (in the 20
> residue break region). After refinement these showed good density and b
> factor.
> But the issue is that in ChainA, it goes straight. While in ChainB, the 8
> residues converge into a loop and goes to the other side.
>
> The protein is a monomer in solution, is it possible to have different
> conformation in different chains that is completely opposite.
> Also the 8 residues (ChainB) that is build now occupies the site where
> ligand was placed in the published structure. I am not sure how to
> interpret this (since in ChainA that site is unoccupied as contrast to
> ChainB).
>
> Any thoughts/suggestions will be really helpful.
>
> Thanks you
>
>
> --
>
> 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] AI papers in experimental macromolecular structure determination

2021-08-03 Thread Pavel Afonine
One more:

BraggNet: integrating Bragg peaks using neural networks
B. Sullivan, R. Archibald, J. Azadmanesh, V. G. Vandavasi, P. S. Langan, L.
Coates, V. Lynch and P. Langan
J. Appl. Cryst. (2019). 52, 854-863

Pavel

On Tue, Aug 3, 2021 at 4:53 AM Thorn, Dr. Andrea <
andrea.th...@uni-hamburg.de> 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. &
> Si, D. (2019).
>
> - Chojnowski, G., Pereira, J. & Lamzin, V. S. (2019). Acta Cryst D. 75,
> 753–763.
>
>
>
> Crystallization:
>
> - Liu, R., Freund, Y. & Spraggon, G. (2008). Acta Cryst D. 64, 1187–1195.
>
> - (2004). Methods. 34, 390–407.
>
> - Bruno, A. E., Charbonneau, P., Newman, J., Snell, E. H., So, D. R.,
> Vanhoucke, V., Watkins, C. J., Williams, S. & Wilson, J. (2018). PLOS ONE.
> 13, e0198883.
>
>
>
> Crystal centering:
>
> - Ito, S., Ueno, G. & Yamamoto, M. (2019). J Synchrotron Rad. 26,
> 1361–1366.
>
> - Crystal centering using deep learning in X-ray crystallography.
>
> - Elbasir, A., Moovarkumudalvan, B., Kunji, K., Kolatkar, P. R., Mall, R.
> & Bensmail, H. (2019). Bioinformatics. 35, 2216–2225.
>
>
>
> Diffraction image analysis:
>
> - Czyzewski, A., Krawiec, F., Brzezinski, D., Porebski, P. J. & Minor, W.
> (2021). Expert Systems with Applications. 174, 114740.
>
>
>
> Peak search in serial crystallography:
>
> Ke, T.-W., Brewster, A. S., Yu, S. X., Ushizima, D., Yang, C. & Sauter, N.
> K. (2018). J Synchrotron Rad. 25, 655–670.
>
>
>
> Space group assignment from diffraction image (small molecules):
>
> Aguiar, J. A., Gong, M. L., Unocic, R. R., Tasdizen, T. & Miller, B. D.
> (2019). Science Advances. 5, eaaw1949.
>
>
>
> Data quality assessment in MX:
>
> - Vollmar, M., Parkhurst, J. M., Jaques, D., Baslé, A., Murshudov, 

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

2021-08-03 Thread Pavel Afonine
Andrea,

you may want to include this one:

Using support vector machines to improve elemental ion identification in
macromolecular crystal structures. Morshed N, Echols N, Adams PD Acta
Cryst. D71, 1147-58 (2015).

Pavel

On Tue, Aug 3, 2021 at 4:53 AM Thorn, Dr. Andrea <
andrea.th...@uni-hamburg.de> 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. &
> Si, D. (2019).
>
> - Chojnowski, G., Pereira, J. & Lamzin, V. S. (2019). Acta Cryst D. 75,
> 753–763.
>
>
>
> Crystallization:
>
> - Liu, R., Freund, Y. & Spraggon, G. (2008). Acta Cryst D. 64, 1187–1195.
>
> - (2004). Methods. 34, 390–407.
>
> - Bruno, A. E., Charbonneau, P., Newman, J., Snell, E. H., So, D. R.,
> Vanhoucke, V., Watkins, C. J., Williams, S. & Wilson, J. (2018). PLOS ONE.
> 13, e0198883.
>
>
>
> Crystal centering:
>
> - Ito, S., Ueno, G. & Yamamoto, M. (2019). J Synchrotron Rad. 26,
> 1361–1366.
>
> - Crystal centering using deep learning in X-ray crystallography.
>
> - Elbasir, A., Moovarkumudalvan, B., Kunji, K., Kolatkar, P. R., Mall, R.
> & Bensmail, H. (2019). Bioinformatics. 35, 2216–2225.
>
>
>
> Diffraction image analysis:
>
> - Czyzewski, A., Krawiec, F., Brzezinski, D., Porebski, P. J. & Minor, W.
> (2021). Expert Systems with Applications. 174, 114740.
>
>
>
> Peak search in serial crystallography:
>
> Ke, T.-W., Brewster, A. S., Yu, S. X., Ushizima, D., Yang, C. & Sauter, N.
> K. (2018). J Synchrotron Rad. 25, 655–670.
>
>
>
> Space group assignment from diffraction image (small molecules):
>
> Aguiar, J. A., Gong, M. L., Unocic, R. R., Tasdizen, T. & Miller, B. D.
> (2019). Science Advances. 5, eaaw1949.
>
>
>
> Data quality assessment in MX:
>
> - Vollmar, M., Parkhurst, J. M., Jaques, D., Baslé, A., 

Re: [ccp4bb] writing coordinates of full biomol into one (PDB) file

2021-05-25 Thread Pavel Afonine
Hi Frank,

phenix.pdb.biomt_reconstruction command should do it.

Pavel

On Tue, May 25, 2021 at 12:44 PM Frank von Delft <
frank.vonde...@cmd.ox.ac.uk> wrote:

> Hello all - this presumably has a really simple solution:
>
> For a PDB file with a (correct) biomolecular assembly record (REMARK
> 350), what program do I use to generate and write out the coordinates of
> the biomolecular assembly (or one of them).
>
> Thanks
> Frank
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>
> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a
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Re: [ccp4bb] phenix refinement for bent DNA

2021-03-29 Thread Pavel Afonine
Hi Dhiraj,

I have structure with bent DNA. I am trying to refine the structure
> using phenix. do I need to turn off the DNA secondary structure restraints
> during refinement?
>

probably not, unless you have reasons to do so otherwise.

P.S.: There is a Phenix mailing list for Phenix specific questions. This is
CCP4 mailing list!



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Re: [ccp4bb] Student Question--Negative Difference Density in some Histidine side chains in Iron Coordination complex in 2XGF T4 Phage Model Structure

2021-02-22 Thread Pavel Afonine
Hi,

as others pointed out electron rich elements tend to amplify imperfections
visible in Fo-Fc maps. Consider:
- refining occupancy of Fe, the site may be partially occupied;
- refining f' and f'' if data are anomalous;
- surrounding histidines may 'see' this Fe as a nonbonded interaction and
thus repulsion terms may kick in and push Fe from its position. Try
defining weak coordination bonds between Fe and respective nitrogens;
- refining anisotropic ADP of Fe only.

Good luck!
Pavel

On Mon, Feb 22, 2021 at 7:27 AM Patrick Needham 
wrote:

>
> --
>
> 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] increased Rfree after ligand fitting refinement

2021-01-20 Thread Pavel Afonine
Hi Wajahat,

first off, there is a dedicated mailing list for Phenix specific questions (
http://phenix-online.org/).

You need to run more than one refinement cycle before you try making sense
of R factors.

Pavel

On Wed, Jan 20, 2021 at 10:05 AM Wajahat ali khan 
wrote:

> Dear all,
>
>
> I have just started with X-ray diffraction.
> I would appreciate any ideas as to why after one cycle of phenix.refine ,
> the Rfree value increased for my ligand fitted model molecular replacement
> solution model.
>
> Thanks
>
> Wajahat
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>
> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a
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Re: [ccp4bb] Rama-Z, Ramachandran plot validation in PDB-REDO

2021-01-19 Thread Pavel Afonine
Rama-Z is implemented in CCTBX meaning it is available to CCP4 and Phenix.
Also it is reported in validation and refinement in Phenix (you get the
number every time you run real- or reciprocal-space refinement!).
Pavel

On Mon, Jan 18, 2021 at 1:58 PM Boaz Shaanan  wrote:

> Hi,
> Will it be possible to include the rama-z analysis in Coot (perhaps as a
> plugin)?
> Boaz
>
> Boaz Shaanan, Ph.D.
> Department of Life Sciences
> Ben Gurion University of the Negev
> Beer Sheva
> Israel
>
> On Jan 18, 2021 22:47, Robbie Joosten  wrote:
> Dear all,
>
> During the last CCP4 meeting, Oleg presented our collaboration with the
> Phenix team, about the Ramachandran plot Z-score (or Rama-Z). Since then,
> some asked for a convenient way to get this score. You are now welcome to
> use: https://pdb-redo.eu/tortoize
>
> This is a quick and easy way to check you model. Just upload your
> structure model (and restraints if you have non-standard compounds) and
> press "calculate". You get the Ramachandran Z-score with an error margin
> and you get the side-chain equivalent (also known as the Chi-1/Chi-2
> Z-score in WHAT_CHECK) for free.
>
> There are two more ways to get the score, that might be relevant for
> specialized use:
> 1) use the webservice to get the same values and the per-residue values in
> an easy-to-parse JSON file. For example through curl with the command: curl
> -F data=@1cbs_final.pdb -F
> dict=@/zata/ccp4-7.1/lib/data/monomers/a/ALA.cif
> https://pdb-redo.eu/tortoize. Note that the "dict" value is optional. Any
> other POST on https://pdb-redo.eu/tortoize would also work.
>
> 2) to analyse a very large group of models you are encouraged to install
> tortoize locally. It's available on https://github.com/PDB-REDO/tortoize
> with a BSD license.
>
> The scores are also of course available after each PDB-REDO run: the
> Rama-Z is one of the model quality metrics. All  methods take PDB and mmCIF
> formatted files as longs as they are valid, i.e. fit the current format
> specification (mmCIF) or contain at least a CRYST1 record (PDB). As always,
> constructive feedback is appreciated.
>
> If you use Rama-Z, please do cite:
> Sobolev et al. A Global Ramachandran Score Identifies Protein Structures
> with Unlikely Stereochemistry; Structure;
> https://doi.org/10.1016/j.str.2020.08.005
>
> All the best on behalf of Team REDO,
> Robbie
>
> 
>
> 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] how to swap chain IDs

2020-12-07 Thread Pavel Afonine
Hi Christian,

you can do it in Phenix PDBTools: GUI->Model Tools-> load files then
Options->Other modifications look for Rename chain ID.

Pavel

On Mon, Dec 7, 2020 at 9:49 AM Christian GALICIA <
christian.galicia.diaz.sant...@vub.be> wrote:

> Hello,
> I'm trying to swap the chain IDs of a structure. I tried changing the IDs
> in coot and with PDBset, both change labels of the chains but not the atom
> positions nor numbering.Also, after the pdb file is converted to cif for
> deposition it displays in pymol in the original position making chain A not
> to be at the beginning of the sequence. I would appreciate if you would
> suggest a good way to achieve this. The structure is otherwise finished and
> will no go any other rounds of refinement. Thanks
>
> Christian
> --
> *Christian Galicia*
> E-mail: cgali...@vub.be
>
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
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Re: [ccp4bb] Phenix refine distorting a sidechain despite correct density

2020-12-02 Thread Pavel Afonine
Hi Folmer,

I would choose to not do the real space refinement in phenix.refine during
> the last rounds of refinement of a model, when sidechain positions are
> essentially correct.
>

by design it is supposed to place and fit side chains as good as possible,
satisfying both map fit and geometry criteria (such as rotameric states and
NCIs). If it does not perform up to your expectations it is best to report
this to us and I will make sure the issue is taken care of immediately. I
wonder if you wouldn't mind explaining your choice and if possible argue it
with specific examples (preferable all done off mailing list as this gets
way too narrow and specific!). -Thanks!

Pavel



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Re: [ccp4bb] over-fitting? over-refinement?

2020-10-19 Thread Pavel Afonine
Hi Sam,


> Hi, the question may be a bit weird, but how do you define 'over-fitting'
> in the context of structure refinement? From users' perspective the
> practical aspect is to 'fit' the model into the density. So there comes
> this question from our juniors: fit is fit, how is a model over-fit?
>

this is a good question for which there is an answer. I suggest reading
classics on the matter:

https://www.nature.com/articles/355472a0
https://atbweb.stanford.edu/atb_publications/brunger_kleywegt_struct_1996.pdf
https://www.sciencedirect.com/science/article/pii/S0076687997770216
https://pubmed.ncbi.nlm.nih.gov/15299543/
https://journals.iucr.org/d/issues/1998/04/00/ad0030/ad0030.pdf

and numerous references therein. That should set the scene for the next
questions to ask.

Good luck!
Pavel



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Re: [ccp4bb] Tyr pushed out during refinement

2020-10-19 Thread Pavel Afonine
Hi All,

there was a bug at some point that could potentially lead to this.

This all should be fixed in current Phenix nightly builds:
http://phenix-online.org/download/nightly_builds.cgi

If not, get back to us (phenixbb or Phenix help lists or reply directly to
me).

Pavel

On Mon, Oct 19, 2020 at 11:52 AM Boniecki, Michal 
wrote:

> Hello,
> I have a problem during refining with one of the Tyr residues. It is
> constantly pushed out of the position during refinement in all 4 chains in
> ASU.
> I have tried to exclude it from refinement in phenix but it is refined
> anyway out of the position with wrong geometry. Is there a possibility to
> fix it during refinement?
> The closest contact it has, is 2.4A between hydroxyl group and C=O of Pro,
> but Tyr itself is inside hydrophobic cleft (Ile,Pro,Leu)
> Thank You for all help. Stay safe,
> Michal
>
>
>



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Re: [ccp4bb] Protein-DNA covalent bond refinement

2020-07-06 Thread Pavel Afonine
Hi Cristina,

in Phenix it is:

Refinement settings -> Select Atoms -> Custom Geometry Restraints : you can
define bonds, angles, torsions, planes, etc...

Pavel

On Thu, Jul 2, 2020 at 8:11 AM Cristina Machon  wrote:

> Dear all,
>
> I am writing regarding a problem we are facing with the refinement of a
> structure. We would really appreciate it if anybody could suggest how to
> set up geometrical restraints for a protein-DNA covalent bond in Refmac or
> Phenix?
>
> Thanks in advance,
>
> Best wishes,
>
> Cristina
>
>
> --
> Cristina Machón Sobrado, PhD
> Instituto de Biología Molecular Barcelona-CSIC
> Parc Científic de Barcelona
> c/ Baldiri Reixac 10
> 08028 Barcelona
> Spain
>
> Phone: +34934034957
>
> --
>
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Re: [ccp4bb] Heavy atom vs light atoms density

2020-06-12 Thread Pavel Afonine
Hi Vito,

   many of us have probably experienced that, in the
> diffraction of protein ligands containing heavy atoms (cisPt, I3C, etc),
> the overwhelming electron density of the metal can totally flatten that of
> the light atoms around (or rather make it look insignificant).
>

I wonder what FEM map shows in your case (
https://doi.org/10.1107/S1399004714028132)? By design it is supposed to
address exactly this issue.
Pavel



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Re: [ccp4bb] visual mask editor - why

2020-05-29 Thread Pavel Afonine
Hi Bernhard,

"Like comparing these map regions, excluding

intrusion of a solvent mask, etc.":

You didn't say much about the context.. So I'd say Polder map approach
comes to mind first based on these keywords. Next is "map comparison" (
https://doi.org/10.1107/S1399004714016289).

If none of the above: what we (or you) are missing?

Pavel

On Thu, May 28, 2020 at 11:17 AM Bernhard Rupp 
wrote:

> Maybe I should explain an example: Say coot detects an unmodelled blob
> (maybe a ligand). Now, I would like to do
>
> a number of things without biasing towards a model. Like comparing these
> map regions, excluding
>
> intrusion of a solvent mask, etc.
>
>
>
> Now could coot for example just generate a mask around what it already
> knows are blobs?
>
> Possible useful items could be a solvent mask not including that regions,
> or a density map
>
> that includes only features with a certain boundary around that blob.
>
>
>
> I pilfered some kludges together from different sources, but let’s just
> say inelegant would be a compliment.
>
>
>
> Best, BR
>
> 
>
> Brief question: Does something like a visual density mask editor exist?
>
> Thx, BR
>
> --
>
> Bernhard Rupp
>
> http://www.hofkristallamt.org/
>
> b...@hofkristallamt.org
>
> +1 925 209 7429
>
> +43 676 571 0536
>
> --
>
> Many plausible ideas vanish
>
> at the presence of thought
>
> --
>
>
>
> --
>
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Re: [ccp4bb] How to compare between electron density maps?

2020-05-11 Thread Pavel Afonine
phenix.match_maps can overlay model B and map B onto model A and map A. A
and B can be any symmetry and box (unit cell) dimensions. Model A and map A
stay in its original frame of reference. Let me know should you have
questions.

Pavel

On Mon, May 11, 2020 at 3:19 PM Murpholino Peligro 
wrote:

> I want to compare electron density features of map A from protein A and
> map B from protein B...
>
> Because each map has a different rmsd level...
>
> ...what is the best way to compare electron density between maps?
>
> Is there a way to normalize maps or something like that?
>
> Thanks
>
> --
>
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Re: [ccp4bb] [3dem] Which resolution?

2020-03-06 Thread Pavel Afonine
Randy Read's paper in latest Acta D:

Measuring and using information gained by observing diffraction data
http://journals.iucr.org/d/issues/2020/03/00/ba5308/index.html

seems very relevant to this discussion!

Pavel


On Fri, Mar 6, 2020 at 8:44 AM James Holton  wrote:

> Thank you Kay,
>
> Very good points, as always.  I was thinking there must be a better
> apodization filter than cutoffs and B factors.  I'll have to try a
> CC1/2-based roll-off.  But, I wonder if this could be done better on a
> per-reflection basis?  Taking advantage of the sigmas?  I have tried
> using 1/sigma^2 as a weight in map calculation, and that makes the map
> look really weird.  Your idea makes more sense.
>
> On the other hand, the French-Wilson (F) truncation procedure is
> supposed to come up with the maximum-likelihood Fourier coefficient
> given the observed intensity and sigma(intensity).  So, the "F" values
> we get from truncate or xdsconv should already be "good"?  Maybe the
> problem is that we are sharpening after the F step, rather than
> before?  Or maybe the problem is that F bottoms out around F=sig(F).
> Your proposed weight might finish the job...
>
> As for sigmaA, one thing I do know is that refmac5 now uses experimental
> sigmas by default.  Phenix.refine does not.
>
> One thing is for sure, sharpening the data before refinement is not
> going to become a popular strategy.  This is because pre-sharpened data
> will make Rwork and Rfree higher than they are with the "natural" B
> factor.  You can also make your Rwork Rfree much lower by applying a
> positive B factor to your data before starting refinement.  This comes
> with absolutely no improvement in model quality, so please don't try
> this at home.
>
> -James Holton
> MAD Scientist
>
> On 3/5/2020 9:38 PM, Kay Diederichs wrote:
> > Dear James,
> >
> > important and educational points! This triggers some thoughts ...
> >
> > The one point where I don't quite agree is with "What about filtering
> out the noise?  An ideal noise suppression filter has the same shape as the
> signal (I found that in Numerical Recipes), and the shape of the signal
> from a macromolecule is a Gaussian in reciprocal space (aka straight line
> on a Wilson plot). This is true, by the way, for both a molecule packed
> into a crystal or free in solution.  So, the ideal noise-suppression filter
> is simply applying a B factor.  "
> >
> > I think we can do better than that. We should use the knowledge about
> the actual signal and its noise (which we measure) as a weighting factor,
> rather than that of the theoretical signal (the straight line in the Wilson
> plot), for the purpose of noise suppression. Formula 13.3.6 in Numerical
> Recipes (3rd ed., 2007), which gives the optimal (Wiener) filter to be used
> for weighting, is phi(f) = S(f)^2/(S(f)^2 + N(f)^2)  . But at high
> resolution, this is just CC1/2: see Box 1 of reference (1) - the formula
> CC1/2 = 1/(1 + 2/(I/sigma)^2 can be written as CC1/2 = ^2/(^2 + 2
> ^2) where sigma is the estimate of the noise in I ; don't know right
> now why there is a factor of 2).  This goes to zero at the resolution where
> the signal goes to zero, and is near one in the resolution range in which
> we have good knowledge of the signal.
> > (I only thought about this today, and I also considered CC* as a
> weighting factor, as I understand is suggested by Rosenthal and Henderson,
> J.Mol.Biol. 2003, but I cannot convince myself currently that this is
> right. Anyway, the shape of the CC* curve as a function of resolution
> matches that of CC1/2)
> > In other words, we should be able to suppress the noise by multiplying
> the Fourier coefficients used for map calculation with (a smooth
> resolution-dependent approximation of) CC1/2. This should allow to sharpen,
> with the best noise suppression we can get.
> >
> > Thinking about this, we are already typically using weighted Fourier
> coefficients of the form 2mFobs-DFcalc for map calculation. Aren't these
> already weighted in the correct way? I think not - those m and D weights
> are calculated from estimates of model (in-)accuracy and (in-)completeness,
> but don't properly take the measurement errors into account. Of course,
> since noisy data make the sigmaA values worse, the noise in the data
> influences sigmaA, but not in the functionally correct form. To my
> understanding, the correct way to take account of both model and data
> errors is given by reference (2), which - to my knowledge - is not yet
> implemented except in PHASER.
> >
> > Hope this makes sense!
> >
> > Kay
> >
> > References:
> > (1) Karplus & Diederichs (2015) Assessing and maximizing data quality in
> macromolecular crystallography.
> > Curr. Opin. Struct. Biol. 34, 60-68 . PDF at
> https://www.biologie.uni-konstanz.de/typo3temp/secure_downloads/82815/0/2b10c9e6f9a28129e1b119d21aeeab217c918bb1/Karplus2015_CurrOpinStructBiol.pdf
> > (2) RJ Read, AJ McCoy (2016) A log-likelihood-gain intensity target for
> 

Re: [ccp4bb] Hydrogens in PDB File

2020-03-02 Thread Pavel Afonine
Clearly, it is a good idea to keep hydrogens:

http://phenix-online.org/presentations/hydrogens.pdf

Not sure why this keeps coming up as a topic given how much it was said
about it in the past, all the MolProbity arguments, etc..

Issue of missing side chains and loops is tricker indeed.

Pavel

On Mon, Mar 2, 2020 at 11:33 AM Dale Tronrud  wrote:

> On 3/2/2020 10:12 AM, Alexander Aleshin wrote:
> > Dear Dale,
> > You raised a very important issue that has been overly ignored by the
> crystallographic community. The riding hydrogens are just a tip of an
> iceberg. It is absolutely unclear even to an experienced crystallographer
> how to treat poorly ordered side chains or even whole residues. As a matter
> of fact,  their models are "riding atoms", and consumers have no clue how
> much they can trust our modeling.
>
>Oh no!  Now I've opened up this can of worms.
>
>The matter of describing completely disordered side chains has been
> discussed heavily on this BB, along with the advantages and shortcomings
> of overloading the meaning of "B factor" or "Occupancy" to describe this
> situation.
>
>Using one data item to describe multiple things is never a good idea,
> in my opinion.  The move to mmCIF for model storage does open the
> possibility of adding new tags to uniquely describe model properties.
> Creating such a tag for "place-holder" side chain atoms was one of the
> recommendations in "Outcome of the First wwPDB/CCDC/D3R Ligand
> Validation Workshop" (https://www.ncbi.nlm.nih.gov/pubmed/27050687).  I
> don't know the status of the implementation of any of these
> recommendations.  The wheels of the wwPDB grind exceedingly slowly.
>
>This is just another part of the huge problem of describing the
> nature of the deposited model and the origin of the information
> supporting all of its parts.
>
> 1) Riding Hydrogen atoms vrs free-floating and refined
> 2) Placeholder side chains vrs visible in density
> 3) Placeholder loops vrs visible in density
> 4) TLS anisotropic B's vrs restrained individual atom aniso vrs
> unrestrained individual - The options here are many and multiple types
> may be present in one model
> 5) NCS restraint/constraint - The options here are many and multiple
> types may be present in one model
> 6) Concerted alternative conformation spread over multiple residues
> 7) Sequence heterogeneity
>
> These are just the topics that bother me with almost every model I
> download.  I'm sure there are plenty of other topics that don't come to
> mind at the moment.
>
>With the move to mmCIF we now have the opportunity to create
> descriptions of these model properties w/o just adding more and more
> REMARK cards.
>
>Until that wondrous day arrives we are stuck with trying to create
> models that are useful to the general community and provide minimal
> opportunity for confusion.  We can argue as to where that line is, but
> shouldn't loose sight of the ultimate goal.
>
>Ethan and I disagree over the relative damage caused by the inclusion
> of riding hydrogen atom positions vrs the confusion that results from
> their absence.  I think we agree strongly that all of the list items
> above need to be tackled by the wwPDB and are of extreme importance.  I
> think we need a comprehensive solution, not a piecemeal, special case,
> for each.
>
> Dale Tronrud
>
> > Moreover, some programs (including the version of Pymol that I use), get
> confused when they detect residues with multiple conformations. Like my
> Pymol version fails to build cartoon elements in those areas, and it is not
> obvious for a beginner how to remove the alternative conformations. I
> presume many consumers just ignore such structures and pick up analogues
> that are displayed without problems.
> >
> > Pymol developers, is it so difficult to report a user, when a structure
> is loaded that it has residues with alternative conformations, and one of
> conformers should be hidden for a correct presentation of the secondary
> structure elements?
> >
> > Alex
> >
> >
> >
> > On 3/2/20, 12:57 AM, "CCP4 bulletin board on behalf of Dale Tronrud" <
> CCP4BB@JISCMAIL.AC.UK on behalf of de...@daletronrud.com> wrote:
> >
> > [EXTERNAL EMAIL]
> >
> > Dear Tim,
> >
> >I am in agreement with Ethan and you that a complete description
> of
> > the restraints and constraints applied to the model should be
> included
> > in the deposition.  This is currently a major failing of the wwPDB.
> For
> > hydrogen atoms we, at least, have the "Riding hydrogen atoms were
> added"
> > remark but that simple statement is inadequate to allow anyone (or
> > program) to reproduce what the depositor had on disk before the
> hydrogen
> > atoms were redacted.  We know that shelxl and MolProbity produce
> > hydrogen models that differ, and that shelxl requires additional
> > information about the temperature of the molecule at least.
> >
> >How could someone hope to 

Re: [ccp4bb] [3dem] [ccpem] Which resolution?

2020-02-12 Thread Pavel Afonine
Interesting conversation! I see the 2017 paper is on bioRxiv. I wonder if
it ever made into a peer reviewed journal (couldn't find quickly)?
@Tim Gruene  : have a look at d_model in
https://www.ncbi.nlm.nih.gov/pubmed/30198894 which is sort of along similar
lines of what you are hinting here.
Pavel

On Wed, Feb 12, 2020 at 3:07 PM Marin van Heel <
057a89ab08a1-dmarc-requ...@jiscmail.ac.uk> wrote:

> Hi Tim,
> Good to hear from you!  No longer at PSI??
> See... You are already touching upon one of the logical breaking points in
> the resolutiton story...!  X-ray crystallography resolution criteria like
> R-factors make absolutely no sense outside the field of crystallography and
> of structural biology.  It is the result of a hybrid iterative optimisation
> process between the phases of a model structure and the measured amplitudes
> of a diffraction experiment!  The FRC/FSC resolution criteria, in contrast,
> are universal quality metrics not at all coupled to Cryo-EM or structural
> biology.  Using structural biology arguments like how well I see an alpha
> helix or how well I see the hole in an aromatic ring as an assessment
> criterion of whether a metric is good or not is a waste of time!  (Moreover
> filtering a map can completley change its appearance without changing its
> information contents). Even some my own (ex-)students and (ex-)postdocs
> sometimes completely miss this fundamental point. The FRC and FSC criteria
> are now used as quality metrics in all walks of image science like X-ray
> tomography and super-resolution light microscopy, fields of science where
> atomic coordinates of proteins are not an issue. The FRC / FSC functions
> are universal and very direct metrics that compare both the amplitudes and
> the phases of two independent measurements of images or 3D-densities of the
> same object. For more details, see the 2017 bioRxiv paper and references
> therein (https://www.biorxiv.org/content/10.1101/224402v1) and check my
> #WhyOWhy tweets (@marin_van_heel). See also: van Heel - Unveiling
> ribosomal structures: the final phases - Current opinion in structural
> biology 10 (2000) 259-264.
>
> Cheers,
> Marin
>
>
> On Wed, Feb 12, 2020 at 11:22 AM Tim Gruene 
> wrote:
>
>> Dear Marin,
>>
>> I did not read the enire thread, nor the manuscript you point at -
>> apologize
>> in case this has been discussed before.
>>
>> What about a practical approach to determine the resolution of a cryoEM
>> map:
>> one could take a feature with scales of interest, e.g. an alpha-helix,
>> and
>> shift and/or rotate it in steps of, say, 0.3A in several directions to
>> see, at
>> which magnitude (degree / distance) refinement does not take the helix
>> back to
>> its original position (within error margins).
>>
>> One could also take a Monte-Carlo approach and do an arbitrary number of
>> random re-orientations of such a helix, refine, and calculate the
>> variation in
>> position and rotation.
>>
>> This would reflect my understanding of resolution, much more than any
>> statistical descriptor.
>>
>> Best regards,
>> Tim
>>
>> On Wednesday, February 12, 2020 1:46:48 PM CET Marin van Heel wrote:
>> > Hi Laurence,
>> >
>> > One thing is certain: the 0.143 threshold is RUBBISH and all CC50 etc
>> are
>> > also based on the same SLOPPY STATISTICS  as are all  fixed-valued  FSC
>> > thresholds. This controversy has been ragings for a long long time and
>> the
>> > errors made were extensively described (again) in our most recent paper
>> > (Van Heel & Schatz 2017 BioRxiv:
>> > https://www.biorxiv.org/content/10.1101/224402v1) which has been
>> downloaded
>> > more than 3000 times. Further papers on the issue are in the pipeline.
>> The
>> > math BLUNDER behind this controversy is simple:  the inner product
>> between
>> > a signal vector and a noise vector is NOT zero (but rather proportional
>> to
>> > SQRT(N) where N is the length of the vectors) and cannot be left out of
>> the
>> > equations. This error goes back to a paper published in Nature in 1975
>> and
>> > has since been repeated frequently, including in the first paper
>> promoting
>> > the erroneous 0.143 FSC threshold. The consequences of this blunder in
>> > current processing are serious especially when these erroneous metrics
>> are
>> > used as an optimisation criterion in iterative refinements at
>> resolutions
>> > close to Nyquist.  I get tired of facing this systematic misuse of the
>> FSC
>> > function, which I myself have introduced into the literature in
>> 1982/1986,
>> > and people nevertheless feel they know better (with no scientific
>> arguments
>> > to support!) and they feel justified to use it beyond its definition
>> range,
>> > and to continue to ignore the correct math. To counter this systematic
>> > abuse of my brain child - over decades - I feel the need to use CLEAR
>> > LANGUAGE!
>> > Have fun!
>> > Marin
>>
>> --
>> --
>> Tim Gruene
>> Head of the Centre for X-ray Structure Analysis
>> Faculty of Chemistry
>> 

[ccp4bb] Phenix workshop at ACA 2020 (San Diego)

2020-02-12 Thread Pavel Afonine
Dear Colleagues,

please make a note of upcoming Phenix workshop focusing on crystallography
and Cryo-EM tools for structure solution, August 2nd 2020 in San Diego,
California. This is a day-long satellite workshop prior to ACA meeting. For
schedule and registration see ACA 2020 web site: www.acameeting.com
  (Program -> Workshops).

Looking forward to see you there!
Pavel



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Re: [ccp4bb] refinement of 0.73A data in shelxl

2020-02-03 Thread Pavel Afonine
Hi Matthias,

did you use correct model parameterization and optimal refinement strategy
for the resolution? Such as:
- Add H atoms;
- Refine all but H atoms with anisotropic ADPs;
- Model alternative conformations (that one'd expect many at this
resolution);
- Add solvent (water, crystallization cocktail components if you see any);
- Relax restraints on geometry and ADPs;
 long list!

If not, then what you have in terms of R factors is more or less what I'd
expect.

In the absence of obvious data pathologies, I'd expect Rwork/Rfree in
10-15% range, and the Rfree-Rwork gap around 1-2% or less.

Since you mentioned Phenix refinement, I am happy to help you with details
etc off-list.

Pavel

On Mon, Feb 3, 2020 at 3:08 AM Barone, Matthias 
wrote:

> Dear ccp4 community
>
> Im having some problems solving a 0.73A structure. Spacegroup seems to be
> correct, data are not twinned, 95.5% overall completeness, ISa 25.6. Outer
> shell CC1/2 24% and 90.4% complete.
>
> The model is nearly fully built, there is no remaining unmodelled areas.
> However, Rfact is stuck 27% in phenix, with a very distinct artifact in
> the electron map (see phenix.jpg). You can see difference density on
> various well defined sidechain atoms. Notably, they seem to follow a
> pattern: Nearly all Val CG have difference signal, as well as many backbone
> NH. Hence, I suspected that it might be a problem with the SF, since we
> recorded the DS at 0.86A.
>
>
> Hence I gave shelxl a shot:
>
> I used the refined model from phenix, converted it via pdb2ins and pasted
> the restraints created by prodrg.
>
> The shelxl hkl was produced by xdsconv, using the freeR flagging of the
> mtz used by phenix (no merge, friedel false).
>
> Interestingly, shelxl can bring Rfree down to 16% and almost all of
> the diff-density artifacts seen before are gone (shelxl_noSFAC-CL.jpg).
> Except one: the inhibitor contains a chlorinated phenylring (pdb ligand
> 2L5) which now shows massive difference density for Cl.
>
> I therefore suggested that I might deal with a wrong SF for Cl. Funny
> enough, pdb2ins does not produce a DISP line for Cl if converting the pdb
> that contains the inhibitor. Hence, I used pdb2ins and the pdb from
> PRODRG to produce SFAC for the inhibitor Cloride. I then pasted this line
>
> DISP $CL0.188450.21747   1035.16450
>
> into the .res file and updated the UNIT line. Shelxl runs through, and
> the density looks ok on the Chloride now. However Rfree is back up at 24%
> and the artifacts seen by phenix.refine are back (shelxl_SFAC-CL.jpg):
> now, very distincitvly, backbone carbonyls and NHs show difference density.
>
> Am I right in my assumption, that the SFAC of Cloride is not properly
> calculated at the given wavelenght? And if so, how do I guess it correctly?
>
>
> Thank you very much for your help!
>
> Best, matthias
>
>
>
>
> Dr. Matthias Barone
>
> AG Kuehne, Rational Drug Design
>
> Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)
> Robert-Rössle-Strasse 10
> 13125 Berlin
>
> Germany
> Phone: +49 (0)30 94793-284
>
> --
>
> 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] Examples of EM models at 4.0Å or better with serious modelling errors?

2019-12-10 Thread Pavel Afonine
Dear Gerard,

a possible programmatic approach may be a loop over all (model, map,
resolution) or (model, map, half_map1, half_map2, resolution) from PDB/EMDB
and calling

phenix.validation_cryoem model. emdb_.map resolution=value
> .log
or
phenix.validation_cryoem model. emdb_.map
half_map1.map half_map2.map resolution=value > .log

The log file will have things like overall model counts:

DEVIATIONS FROM IDEAL VALUES.
  BOND  :  0.031   1.220   4166
  ANGLE :  3.271 102.317   5611
  CHIRALITY :  0.085   0.434629
  PLANARITY :  0.018   0.270730
  DIHEDRAL  : 28.082 179.891   1579
  MIN NONBONDED DISTANCE : 1.223

MOLPROBITY STATISTICS.
  ALL-ATOM CLASHSCORE : 20.08
  RAMACHANDRAN PLOT:
OUTLIERS :  3.29 %
ALLOWED  :  9.69 %
FAVORED  : 87.02 %
  ROTAMER OUTLIERS : 24.26 %
  CBETA DEVIATIONS :  0.00 %
  PEPTIDE PLANE:
CIS-PROLINE : 0.00 %
CIS-GENERAL : 1.59 %
TWISTED PROLINE : 0.00 %
TWISTED GENERAL : 1.39 %

and model-to-map fit:

  CC_mask  : 0.8818
  CC_box   : 0.7657

Also it checks the sanity of HELIX/SHEET records.

Then parsing these logs and taking top N entries having the worst metric
you focus on (like clashscore or map-model CC or anything else you choose)
will likely give you some good candidates for your tests. Of course this
won't help you with local modeling issues such as wrong register or similar.

Instead of dealing with text log files you can use pickle=true keyword in
the above commands. Then a Python pickle file will be created that contains
all the information. Once you iterated over all entries, then you can load
these pickle files and harvest information you need.

Also, you may find some examples here (but probably not a lot individual
ones):
http://journals.iucr.org/d/issues/2018/09/00/kw5139/index.html

I can help more with details, if needed.

Good luck!
Pavel

On Tue, Dec 10, 2019 at 5:26 AM Gerard DVD Kleywegt 
wrote:

> Dear colleagues,
>
> We are developing a new validation method that takes EM maps and models
> into
> account. In order to understand the potential, the applicability and the
> limitations of the method we are looking for good test cases, which turn
> out
> to be surprisingly hard to find.
>
> What we are looking for are EM structures with serious modelling errors,
> e.g.
> register errors (model sequence out-of-register with the map),
> connectivity
> errors (between (non-)adjacent secondary structure elements),
> directionality
> errors (e.g., a helix built backwards), substantial stretches of mistraced
> residues, etc.
>
> The structures should be publicly available in PDB (model) and EMDB (map),
> they should be at 4.0Å resolution or better, and ideally there should be a
> higher resolution improved structure (EM or X-ray).
>
> If the modelling errors have been confirmed and discussed in the
> literature
> that is ideal, but we are also interested if this is not the case.
>
> Feel free to reply either in confidence to me (mailto:ger...@ebi.ac.uk),
> or to
> the entire list.
>
> Many thanks in advance for any examples you can think of!
>
> PS: apologies for cross-posting to two other mailing lists.
>
> --Gerard
>
> ---
> Gerard J. Kleywegt, EMBL-EBI, Hinxton, UK
> Head of Molecular and  Cellular Structure
> ger...@ebi.ac.uk pdbe.org emdb-empiar.org
> PA: Roisin Dunloppdbe_ad...@ebi.ac.uk
>
> 
>
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Re: [ccp4bb] TLS parameters

2019-11-19 Thread Pavel Afonine
Dear Eleanor,

Phenix reads and writes TLS records, both PDB and mmCIF format. It can also
read (but not write) TLS records in REFMAC and BUSTER format.

In ATOM records Phenix outputs complete B factors, which includes both
individual and TLS components (this is why they have ANISOU).

Phenix won't re-define (or define from scratch) TLS groups automatically
unless it is asked to do so.

Pavel

On Tue, Nov 19, 2019 at 7:36 AM Eleanor Dodson <
176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote:

> And what about PHENIX?
> E
>
> On Tue, 19 Nov 2019 at 15:33, Pierre Rizkallah 
> wrote:
>
>> I can vouch for TLS blocks being used by REFMAC and the PDB validation
>> servers, after some frustration I had with a deposition recently:
>> Towards the end of a refinement, I renamed some chains, to make oligomers
>> in the a.u. contiguous in real space. Validation told me the centre of
>> gravity as declared in the header is not the same as that produced from the
>> coordinates. I edited the input TLS file, but it still produced the same
>> outcome. I eventually realised that REFMAC reads the TLS blocks from the
>> input PDB after reading all the other input instructions for the refinement
>> run. This happening last, it overrides the declarations in the input TLS
>> definitions file. In order to get the coordinates and the definitions to
>> match, I had to remove the TLS blocks, produced by an earlier run of
>> REFMAC, from the pdb input file, so that the new definitions can be
>> followed, and appropriate TLS blocks produced. REFMAC would use
>> pre-existing TLS blocks if they are in the PDB file.
>>
>> The mismatch notwithstanding, REFMAC still worked correctly, although the
>> shifts from the group origins would have looked strange if one tries to
>> analyse the TLS motions with TLSANL. I admit, I don't view them. Moral of
>> the story is, be careful when you rename chains at the end of the
>> refinement!
>>
>> Pierre Rizkallah
>> ***
>> Dr Pierre Rizkallah, Senior Lecturer Structural Biology
>> Institute of Infection & Immunology, Sir Geraint Evans Building,
>> School of Medicine, Heath Campus, Cardiff, CF14 4XN
>> email: rizkall...@cardiff.ac.ukphone: +44 29 2074 2248
>> http://www.cardiff.ac.uk/people/view/126690-rizkallah-pierre
>>
>> -Original Message-
>> From: CCP4 bulletin board  On Behalf Of Robbie
>> Joosten
>> Sent: 19 November 2019 15:14
>> To: CCP4BB@JISCMAIL.AC.UK
>> Subject: Re: [ccp4bb] TLS parameters
>>
>> Hi Eleanor,
>>
>> The blocks are reliably recorded in PDB entries but in some cases the
>> renumbering of residues was not pushed through to TLS groups. Certain
>> selections cannot be captured in the PDB format, for instance the split in
>> main chain and side chain that Refmac allows. Fortunately that feature is
>> hardly used.
>> Parsing TLS records is not straightforward, particularly the sets from
>> Buster suffered a lot from inconsistent manual editing in the early days of
>> TLS refinement. PDB-REDO's extractor does a decent job in getting
>> selections and changing those into Refmac format, but there are definitely
>> cases that it cannot do. We also have a tool that does this for mmCIF files
>> which is not written by me and (therefore) much more sophisticated in
>> handling more complicated cases.
>>
>> Cheers,
>> Robbie
>>
>> > -Original Message-
>> > From: CCP4 bulletin board  On Behalf Of Eleanor
>> > Dodson
>> > Sent: Tuesday, November 19, 2019 3:59 PM
>> > To: CCP4BB@JISCMAIL.AC.UK
>> > Subject: [ccp4bb] TLS parameters
>> >
>> > Does anyone know how reliably the different programs record and use
>> > these blocks from the PDB file?
>> >
>> > Eleanor
>> >
>> > 
>> >
>> >
>> > To unsubscribe from the CCP4BB list, click the following link:
>> > https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.
>> > jiscmail.ac.uk%2Fcgi-bin%2Fwebadmin%3FSUBED1%3DCCP4BB%26A%3D1data
>> > =01%7C01%7Crizkallahp%40CARDIFF.AC.UK%7Cf2a9834dd919481f28d508d76d030e
>> > 63%7Cbdb74b3095684856bdbf06759778fcbc%7C1sdata=BMwtQsLcQzHTeZcKqC
>> > Yg5W7MLDM7Phk0MUx8ohylApI%3Dreserved=0
>>
>>
>> 
>>
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>>
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>
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>
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> 

Re: [ccp4bb] Calculating RMSD of a loop

2019-09-17 Thread Pavel Afonine
Yet another way is:

phenix.superpose_pdbs fixed.pdb moving.pdb selection_fixed="chain A and and
resseq 1:10 and name CA" selection_moving="chain B and resseq 1:10 and name
CA"

or using the GUI.
Pavel

On Tue, Sep 17, 2019 at 8:06 AM Folmer Fredslund  wrote:

> Dear Kyle,
>
> As other non-CCP4 solutions have also been suggested, perhaps I can
> suggest using PyMOL?
> https://pymolwiki.org/index.php/Align
> Here's a nice wiki article about what you can do with the align command.
>
>
> If you're already familiar with scripting languages it's quite easy, and
> you can load your already superimposed structures and calculate on the
> selection you want.
>
>
> Hope this helps,
> Folmer Fredslund
>
>
> tir. 17. sep. 2019 15.42 skrev Kyle Gregory <
> 3632e92fcc15-dmarc-requ...@jiscmail.ac.uk>:
>
>> Hi all,
>>
>> What is the best/easiest way to calculate RMSD of a loop for 2 c-alpha
>> aligned structures?
>> Thought I could do this in Coot but I only see this if I align the
>> specific loops, which I don't want to do.
>>
>> Thanks,
>>
>> Kyle
>>
>> --
>>
>> 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
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Re: [ccp4bb] I am doing phenix refinement now. Is it a problem if the r-work and r-free values are equal?

2019-08-30 Thread Pavel Afonine
Thanks for sharing log file. The answer is -- there are no valid free r
flags in your data file:

Number of work/free reflections by resolution:
 work  free  %free
  bin  1: 52.1844 -  3.0380 [4249/4297]  4249 0   0.0%
  bin  2:  3.0380 -  2.4114 [3632/4074]  3632 0   0.0%
  bin  3:  2.4114 -  2.1065 [3304/4043]  3304 0   0.0%
  bin  4:  2.1065 -  1.9139 [2664/3989]  2664 0   0.0%
  bin  5:  1.9139 -  1.7767 [1763/3961]  1763 0   0.0%
  bin  6:  1.7767 -  1.6720 [1304/3975]  1304 0   0.0%
  bin  7:  1.6720 -  1.5882 [ 891/3947]   891 0   0.0%
  bin  8:  1.5882 -  1.5191 [ 571/3912]   571 0   0.0%
  bin  9:  1.5191 -  1.4606 [ 293/3936]   293 0   0.0%
  bin 10:  1.4606 -  1.4102 [ 130/3913]   130 0   0.0%
overall 18801 0   0.0%

That's what log file is for: to check for obvious issues like this one!
Pavel

On Fri, Aug 30, 2019 at 7:59 AM Pavel Afonine  wrote:

> Please send me log file off-list and that may be a start. -Thanks!
> Pavel
>
> On Fri, Aug 30, 2019 at 6:48 AM Tung Thanh Dinh  wrote:
>
>> After phasing with phenix, i clicked on the phenix.refine ribbon. Since
>> then for every macrocycle of refinement, r-work and r-free values are
>> always the same. Is this a problem that I need to fix?
>>
>>
>> Kindest regards,
>> Tung Dinh
>>
>> PhD student
>> The University of Georgia
>> Department of Chemistry
>>
>> --
>>
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Re: [ccp4bb] I am doing phenix refinement now. Is it a problem if the r-work and r-free values are equal?

2019-08-30 Thread Pavel Afonine
Please send me log file off-list and that may be a start. -Thanks!
Pavel

On Fri, Aug 30, 2019 at 6:48 AM Tung Thanh Dinh  wrote:

> After phasing with phenix, i clicked on the phenix.refine ribbon. Since
> then for every macrocycle of refinement, r-work and r-free values are
> always the same. Is this a problem that I need to fix?
>
>
> Kindest regards,
> Tung Dinh
>
> PhD student
> The University of Georgia
> Department of Chemistry
>
> --
>
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Re: [ccp4bb] How to include in refinement high resolution shells with VERY low completeness ?

2019-08-07 Thread Pavel Afonine
Hi Ivan,


> My conclusion is that  "no fill-in" option might be tried at some
> stages, but with caution, especially for datasets with poor low res
> completeness.
>

I'm guessing you really meant *high*, not low. More or less repeating what
others said already.. Correcting for low res completeness doesn't add
high-res details and so has lesser risk of introducing model bias at atomic
level. Contrary, filling in high-res terms is likely to noticeably bias the
map at atomic level of detail.

Here is one of my favorite examples of what missing low-res data can do to
your map:
http://cci.lbl.gov/~afonine/tmp/1nh2.pdf

Pavel



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Re: [ccp4bb] How to include in refinement high resolution shells with VERY low completeness ?

2019-08-06 Thread Pavel Afonine
For the record, phenix.refine always produces two versions of 2mFo-DFc
maps, with and without filling in missing Fobs. The one that opens in Coot
by default is the "filled" map, but you can always load the other one for
comparisons.

Pavel

On Tue, Aug 6, 2019 at 8:34 AM Ivan Shabalin 
wrote:

> Dear Clemens,
>
> Thanks!
>
> It sounds like a good test to do on the output .mtz and see if there are
> any significant changes in maps after these "filled in" coefficients are
> removed.
>
> Ivan
>
> With best regards,
> Ivan Shabalin, Ph.D.
> Research Scientist,
> Department of Molecular Physiology and Biological Physics,
> University of Virginia,
> 1340 Jefferson Park Avenue, Pinn Hall,Room 4223,
> Charlottesville, VA 22908
> https://www.linkedin.com/in/shabalinig/
> https://minorlab.org/person/ivan_s/
>
> On 8/6/19 08:59, Clemens Vonrhein wrote:
> > Dear Ivan,
> >
> > On Mon, Aug 05, 2019 at 05:44:56PM -0400, Ivan Shabalin wrote:
> >> Dear Kay,
> >>
> >> Thanks a lot for your answers!
> >>
> >> To my best understanding, REFMAC does not have an option of for
> restoring
> >> reflections only in certain resolution shells.
> >
> > Remember that you can always do some simple (but powerfull) operations
> > within SFTOOLS (*). So using something like
> >
> >read refmac.mtz
> >CALC col resol = 0.5 stol /
> >select col FP = absent
> >absent col FWT  if col resol < 3.0
> >absent col PHWT if col resol < 3.0
> >delete col resol
> >select all
> >write refmac_new.mtz
> >
> > might/should do the trick: setting all filled-in FWT/PHWT values to a
> > MNF (missing-number-flag) for reflections with resolution higher than
> > 3A. So you should only have filled-in 2mFo-DFc valeus for the low-res
> > data (3A and lower).
> >
> > But check those commands above (typed from memory)
> >
> > Cheers
> >
> > Clemens
> >
> > (*) there is very little one can't do with SFTOOLS
> >
>
> 
>
> 
>
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Re: [ccp4bb] Fo-Fc density close to cysteine residue

2019-07-09 Thread Pavel Afonine
Hard to see from a static image, but could it be an alternative
conformation?
Pavel

On Tue, Jul 9, 2019 at 2:32 AM Lumbini Yadav  wrote:

> Dear all,
>
>
>
> We have found a huge Fo-Fc density close to cysteine residue (see attached
> image) in the structure with resolution of 1.2A. In the crystallization
> condition, we have PEG 3350, Potassium phosphate monobasic, glycerol and
> protein was in Tris and NaCl. Before freezing the crystals were soaked in
> mother liquor containing sodium dithionite.
>
>
>
> I have tried different modified cysteine (CSX, CSO, OCS, CME, CSS, SNC, CSD,
> CXM, SCH, CSU) from the library and also SO3, SO2 and peroxide. But in
> all the screenings we do see some part of Fo-Fc density unaddressed at 3
> sigma.
>
>
>
> Does anyone have an idea about what this density could be? Covalent
> modification?
>
>
>
> Thanks.
>
>
>
> Kind regards,
>
> Lumbini
>
> --
>
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Re: [ccp4bb] resolution

2019-07-04 Thread Pavel Afonine
Hi Sam Tang,

Sorry for a naive question. Is there any circumstances where one may wish
> to refine to a lower resolution? For example if one has a dataset processed
> to 2 A, is there any good reasons for he/she to refine to only, say 2.5 A?
>

yes, certainly. For example, when information content in the data can
justify it.. Randy Read can comment on this more! Also instead of a hard
cutoff using a smooth weight based attenuation may be even better. AFAIK,
no refinement program can do this smartly currently.
Pavel



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Re: [ccp4bb] Phenix / Coot neutron queries.

2019-06-22 Thread Pavel Afonine
Hi Jonathan,

send me files off list and I will have a look. From your description it
isn't clear to me what the problem is. You need to add H or D or H and D
only once (and phenix.ready_set is the right tool to do it!), then just do
refinement and all should work. Coot indeed may not play well with some of
exotic scenarios but so far that hasn't been a huge issue as phenix.refine
can handle this mostly automatically.

Pavel

On Thu, Jun 20, 2019 at 5:44 PM Jonathan Cooper <
0c2488af9525-dmarc-requ...@jiscmail.ac.uk> wrote:

> I am trying to refine a neutron structure for someone and I have come
> across a couple of things which I need help with.
>
> I am struggling to get the occupancy refinement of the
> hydrogens/deuteriums on the N-terminal nitrogens to behave right. Some of
> them get deleted by readyset but the trick seems to be to call them
> hydrogen in the atom name field yet say they are D in the element symbol
> field. Is that the best way?  Also, readyset seems to delete the D's in D2O?
>
> I would appreciate any tips on what is the best 'strategy' for refining
> with neutron data i.e. reciprocal- versus real-space or both, etc, because
> my R-free just seems to go up.
>
> Also, if I do a real-space refine on a D2O molecule (DOD) in Coot it
> stretches the O-D bond length from around 1 to 1.3 Angstrom and the bond
> angle from ~110 to about 120 degrees so it seems to be picking-up wrong
> geometry info from somewhere.
>
> --
>
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Re: [ccp4bb] Disulphide occupancies.

2019-05-26 Thread Pavel Afonine
Hi Jonathan,

this may also be a result of too strong SS bond restraints or/and
inaccurate SS bond restraints parameters or/and disorder (in some fraction
of unit cells there is no SS bond). More on the topic:

"Disulfide bond restraints" here:
http://phenix-online.org/newsletter/CCN_2015_01.pdf#page=13

Pavel

On Mon, May 27, 2019 at 6:20 AM Jonathan Cooper <
0c2488af9525-dmarc-requ...@jiscmail.ac.uk> wrote:

> When you refine structures with disulphide bridges you often get negative
> difference density for the sulphurs, presumably due to the well-known
> radiation damage effects. The negative difference density often won't
> disappear with usual B-factor refinement. However, it seems to go away if
> you refine the occupancy of the affected sulphur atoms e.g. to 0.9 or
> thereabouts. Would it be acceptable to publish/deposit structures where the
> sulphur occupancy is less than one, given a suitable REMARK in the pdb
> file? Thank you.
>
> --
>
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Re: [ccp4bb] On estimating Unit Structure Factor distribution

2019-05-15 Thread Pavel Afonine
Hi Andre,

here is the link to cctbx-based code that computes Uhkl according to your
formula below, using model mean B and F000 that accounts for atomic model
and bulk-solvent:

https://www.dropbox.com/sh/g7sp7pqxst4ldj0/AAD1whlVD2mvAGoRa5jOF-fla?dl=0

I leave it up to you to read and understand the script, as well as ensuring
it works as you expect (bug-free!). I hope it exemplifies enough for you to
pick up from there and modify it the way you wish. The only test I did is I
made sure it runs and outputs and MTZ file!

Good luck,
Pavel

On Wed, May 15, 2019 at 3:20 PM Andre LB Ambrosio  wrote:

> Dear all,
>
> We seek to calculate the distribution of Unitary Structure Factors, Uhkl,
> from a few datasets (at different maximum resolutions) for which the
> corresponding atomic models are already available at the PDB; this
> according to the formula (6.4), in the 2nd edition of Jan Drenth´s book:
>
> Uhkl = exp[B*(sin^2(theta)/lambda^2)] x FOBShkl / F(000)
>
> Hence, the following questions:
>
> - Is there any macromolecular crystallography software that can compute
> Uhkl as above, or equivalent?
>
> - If not, would it be more correct to use the Wilson-B or the mean B from
> the final model?
>
> - How can F(000) be best estimated from the final model, which is not
> necessarily always the most complete or best refined? Should we simply add
> together the number of electrons for all the atoms refined in the
> asymmetric unit (protein + ligands + solvent)?
>
> Many thanks in advance and best wishes,
>
> --
> Andre LB Ambrosio
>
> --
>
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Re: [ccp4bb] On estimating Unit Structure Factor distribution

2019-05-15 Thread Pavel Afonine
Hi Andre,


> - Is there any macromolecular crystallography software that can compute
> Uhkl as above, or equivalent?
>

I estimate this can take about 10 minutes to script in CCTBX. I can write a
script for you, if interested, and send off list.


> - If not, would it be more correct to use the Wilson-B or the mean B from
> the final model?
>

I'd guess mean B from the model is a better estimate.

- How can F(000) be best estimated from the final model, which is not
> necessarily always the most complete or best refined? Should we simply add
> together the number of electrons for all the atoms refined in the
> asymmetric unit (protein + ligands + solvent)?
>

See my previous email.

Pavel



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Re: [ccp4bb] On estimating Unit Structure Factor distribution

2019-05-15 Thread Pavel Afonine
Hi Andre,

- How can F(000) be best estimated from the final model, which is not
> necessarily always the most complete or best refined? Should we simply add
> together the number of electrons for all the atoms refined in the
> asymmetric unit (protein + ligands + solvent)?
>

the text here explains how to do this:

"On the analysis of residual density distributions on an absolute scale"
http://phenix-online.org/newsletter/CCN_2012_07.pdf

Also, there is a Phenix tool to do this:

phenix.f000

Good luck,
Pavel



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Re: [ccp4bb] “Bound ligand” versus “modified residue”

2019-04-24 Thread Pavel Afonine
Hi Ian,
perhaps there are as many answers to this as many subscribers to this list,
but personally "Cysteine with attachment" seems more logic and clear to me
than calling the whole thing a different name. Although I would also
understand arguments like if it is a CYS with an attachment it is not
really CYS any more and perhaps should be called a unique name. From
refinement viewpoint both a fine.
Pavel

On Wed, Apr 24, 2019 at 8:59 AM Ian Clifton 
wrote:

> Hello everyone,
>
> PDB structure 4qdu contains a “modified residue”, 30V. This is joined
> into the rest of the main chain by means of LINK records. In 5kwj, a
> similar type of modification is described as a cysteine with a
> side‐chain LINK to its “bound ligand”, 6Y3 . (These structures are just
> two clear examples we found to illustrate the question.)
>
> Is there any reason to prefer one of these approaches over the other?
> Does it just depend on what ligands are already in the PDB?
>
> Thanks,
> --
> Ian Clifton ⚗ ℡: +44 1865 275677
> Chemistry Research Laboratory ℻: +44 1865 285002
> Oxford University : ian.clif...@chem.ox.ac.uk
> Mansfield Road   Oxford OX1 3TA   UK
>
>
> 
>
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Re: [ccp4bb] High Rfree in last Shell

2019-04-18 Thread Pavel Afonine
Also, values in parentheses (high-res shell) depend on how you (the program
you use) do binning. Different programs do it differently and so these
values can vary quite substantially. With a little of trial-and-error
effort choosing the binning one can make these values farther or closer to
overall R. To me this is a hint that these numbers are not very useful. A
plot R (completeness, ..) vs resolution is much more useful than the values
for an arbitrarily defined resolution bin!
Pavel

On Wed, Apr 17, 2019 at 12:57 AM Jan van Agthoven  wrote:

> Hi everyone,
> I’m trying to publish two structures at 3.1Å resolution with the following
> refinement statistics:
>
> Resolution range (Å)   49.2-3.1
> 49.3-3.1
> *R*factor (%)24.0 (32.4)
> 23.4 (32.0)
> *R*free (%)  26.6 (29.2)
> 26.3 (31.6)
>
> *Data collection*
>
> Completeness  100 (100)
> 100 (100)
>
> Redundancy6.9 (7.0)
> 6.2 (6.3)
>
> Molecules in asymmetric unit  1
> 1
>
> Average* I*/σ 14.1 (1.7)
> 15.3 (2.0)
>
> *Rmerge *(%)  14.9 (100)
>  12.7 (100)
>
> *Rmeas* (%)16.2 (100)
>13.9 (100)
>
> *Rsym* (%)   6.2 (68.6)
>5.5 (57.1)
> Wilson *B*-factor 65.6
> 62.7
>
> I’ve been told that the Rfree factor in the* last shell* are too high.
> Does anyone know how I can improve these Rfree factors other then cutting
> the resolution, which already is rather low?
>
> --
>
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Re: [ccp4bb] Question about the electron density maps (.ccp4) in PDBe

2019-03-05 Thread Pavel Afonine
P.S.: while on the topic, it might be helpful to you to have a look at this
article ("On the analysis of residual density distributions on an absolute
scale", page 43) available here:

http://phenix-online.org/newsletter/CCN_2012_07.pdf

Pavel

On Tue, Mar 5, 2019 at 10:02 AM Pavel Afonine  wrote:

> Hi Sen,
>
> As Pavel mentioned, phenix.f000 will give you F(0,0,0) value, but I don't
>> see that information stored and easily calculated from .ccp4 data.
>>
>
>  phenix.f000 requires atomic model (PDB or mmCIF file) as input, not a
> map. If you want bulk-solvent to be added, then you need to give it mean
> solvent density.
>
> Pavel
>
>>



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Re: [ccp4bb] Question about the electron density maps (.ccp4) in PDBe

2019-03-05 Thread Pavel Afonine
Hi Sen,

As Pavel mentioned, phenix.f000 will give you F(0,0,0) value, but I don't
> see that information stored and easily calculated from .ccp4 data.
>

 phenix.f000 requires atomic model (PDB or mmCIF file) as input, not a map.
If you want bulk-solvent to be added, then you need to give it mean solvent
density.

Pavel

>



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Re: [ccp4bb] Question about the electron density maps (.ccp4) in PDBe

2019-03-04 Thread Pavel Afonine
Hi,


> Unfortunately not all structure
> factor programs will give you that F000.
>

phenix.f000 will give you F(0,0,0) value based on atomic model alone or
atomic model plus bulk-solvent.

Pavel



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Re: [ccp4bb] Electron scattering factors for SHELXL

2019-03-04 Thread Pavel Afonine
Hi,


> Or, alternatively, if anyone has used a different program to refine small
> molecule structures determined by ED, we would be happy to hear about that
> program too.
>

phenix.refine has an option to use electron scattering factors. I can
provide further assistance off-list or on phenix mailing list, if needed.

Pavel



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Re: [ccp4bb] Turning off the bulk solvent modelling in Refmac5 to generate Polder maps?

2019-02-08 Thread Pavel Afonine
Hi,
this is why Polder map tool also includes analysis of the map in question
to determine whether it looks like bulk-solvent or something else, as
described in paragraph 5 here:
http://journals.iucr.org/d/issues/2017/02/00/ba5254/ba5254.pdf
This analysis tells you in plain English what you are likely to look at.
Otherwise I agree that making sense of maps in solvent-excluded regions are
very tricky.
Pavel

On Fri, Feb 8, 2019 at 2:32 AM Bernhard Rupp 
wrote:

> Hi Fellows,
>
> I'd really like to emphasize the point in the Buster instructions "be
> careful when
> examining fo-fc at low levels" when solvent is excluded. If the solvent
> contribution
> is omitted where you suspect the ligand (e.g. occupancy 0.02 in Refmac),
> there
> will be a fo contribution there from the solvent that is there.
> Particularly if that solvent is a
> dense solution, that fo component will show up nicely and at not so low
> difference
> map levels, and in the shape of that 'excluded' ligand.
>
> Figure 2 in link illustrates that.
> https://febs.onlinelibrary.wiley.com/doi/epdf/10./febs.14320
>
> If you start to fill that void with multiple ligands of various low
> occupancies, you
> are effectively modelling disordered solvent. This is particularly tempting
> because
> I found multiple cases where the classical RSR and RSCC measures give
> acceptable stats for such models. The hunt for low occupancy ligands then
> quickly
> becomes murky density fishing business...
>
> Best, BR
>
>
> -Original Message-
> From: CCP4 bulletin board  On Behalf Of Clemens
> Vonrhein
> Sent: Friday, February 8, 2019 09:53
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Turning off the bulk solvent modelling in Refmac5 to
> generate Polder maps?
>
> Dear Samuel,
>
> On Mon, Feb 04, 2019 at 11:39:58AM +, Samuel Davis (PG Research) wrote:
> > I'm wondering if anyone knows if it is possible to turn off the bulk
> > solvent modelling in Refmac5, for the purpose of generating Polder
> > maps? I know that an option for Polder maps is directly implemented in
> > Phenix, but we ideally want to use Refmac5, as we have used it for the
> > rest of our refinement and want to keep it consistent if possible.
>
> And if you want to try the original implementation of the underlying idea
> as
> an alternative, have a look at the ligand detection mode and maps [1]
> produced by BUSTER [2]. See also [3] and some early examples of their
> usefulness [4-5].
>
> Cheers
>
> Clemens
>
> [1]
> https://www.globalphasing.com/buster/wiki/index.cgi?LigandDetectionModes
> [2] https://www.globalphasing.com/buster/
> [3] Vonrhein, C., & Bricogne, G. (2005). "Automated Structure
> Refinement for High-throughput Ligand Detection with
> BUSTER-TNT". Acta Crysta A61, C248.
> [4] Thoma, Ralf, et al. "Insight into steroid scaffold formation from
> the structure of human oxidosqualene cyclase." Nature 432.7013
> (2004): 118.
> [5] Ekroos, Marika, and Tove Sjogren. "Structural basis for ligand
> promiscuity in cytochrome P450 3A4." Proceedings of the National
> Academy of Sciences 103.37 (2006): 13682-13687.
>
> --
>
> *--
> * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com
> * Global Phasing Ltd., Sheraton House, Castle Park
> * Cambridge CB3 0AX, UK   www.globalphasing.com
> *--
>
> 
>
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>
> 
>
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Re: [ccp4bb] [offtopic for ccp4bb] Real space vs reciprocal refinement

2019-02-05 Thread Pavel Afonine
Hi Mahesh,

In the current version of phenix.refine contains the separate option for
> refinement: xyz (reciprocal space) and xyz (real space ).  What does it
> mean and how it differs from the previous versions which had xyz and real
> space instead.
>

All the same, different name. One refines model against Fobs, the other one
against 2mFo-DFc map (whole model and side chain rotamer fitting using grid
searches, if it is a protein).


> Can we run both of them simultaneously?
>

Both are enabled by default, so apparently the answer is yes.


> Is it advisable to do both refinement for DNA ?
>

Sure, why not?

Good luck!
Pavel



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Re: [ccp4bb] Experimental phasing vs molecular replacement

2018-12-06 Thread Pavel Afonine
Hi,


> Any time you do a thought experiment you make a fake-data data set, the
> "true" phases and "true" amplitudes become the ones you put into the
> simulation process.  This is by definition.  Is there potential for
> circular reasoning?  Of course!  But you can do controls:
>

this is so much true! This is what I've been doing for development and
testing all the time since started working for Phenix! Fully controlled
thought/numerical experiments done this way are super-helpful (but
obviously have limitations!).


>If you start with an ordinary single-conformer coordinate model and
> flat bulk solvent from refmac to make your Ftrue, then what you will
> find is that even after adding all plausible experimental errors to the
> data the final Rwork/Rfree invariably drop to small-molecule levels of
> 3-4%.  This is true even if you prune the structure back, shake it, and
> rebuild it in various ways.  The difference features always guide you
> back to Rwork/Rfree = 3/4%. However, if you refine with phenix.refine,
> you will find Rwork/Rfree stall at around 10-11%.  This is because Ftrue
> came from refmac and refmac and phenix.refine have somewhat different
> bulk solvent models.  If Ftrue comes from phenix and you refine with
> refmac you get similar "high" R values.  High for a small molecule
> anyway. And, of course, if you get Ftrue from phenix and refine with
> phenix you also get final Rwork/Rfree = 3/4%. If you do more things that
> automated building doesn't do, like multi-headed side chains, or get the
> bulk solvent from an MD simulation, then you can get "realistic"
> Rwork/Rfree in the 20%s.  All of this is the main conclusion from this
> paper: https://dx.doi.org/10./febs.12922


Even within Phenix alone this is true if you switch between different
scaling/bulk-solvent models or play with automation levels (such as
ignoring reflection otliers, etc).

Pavel



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Re: [ccp4bb] Polder or FEM

2018-11-26 Thread Pavel Afonine
Hi Markus,

I can only guess without seeing files (and link to files seems to be
broken).. So my guess is that the ligand density is weak enough so FEM
treats it as "near noise" and it wipes it. Polder decides it is likely
ligand because it uses correlations, and so even of two maps are weak but
similar the CC is going to be high. I can have a closer look if you send me
files (off mailing list!).

Pavel

On Fri, Nov 23, 2018 at 11:39 PM Markus Heckmann 
wrote:

> Dear Pavel,
>
> By coincidence today I was looking at a soak-dataset and got totally
> confused with FEM (map) and Polder now.
>
> I am working on a dataset that processed it at 2.7A (in summer with
> XDS) and there was weak density for (OCA-Octanoic acid) when looked
> with FEM. This week, I retried it with DIALS and got about 2.6A (for
> CC_half 0.5).  I ran FEM, and there was*no* density at all at OCA.
> After seeing this CCP4 answer, I ran Polder maps and it shows clear
> density for OCA. Now I am really confused why and what should I infer?
> Polder run also states "The polder map is likely to show the ligand."
> CC(1,2): 0.5639
> CC(1,3): 0.8722
> CC(2,3): 0.6193
>
>
> https://imagebin.ca/v/4NbuaSRUbc5t
> FEM in violet and Polder in Green
>
> Any guidance appreciated.
> Markus
>
> 
>
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Re: [ccp4bb] high SOLVENT content low RESOLUTION and a LIGAND to be found

2018-11-21 Thread Pavel Afonine
Hi Almudena,

I wonder to which extent I can trust the positive blobs or polder maps that
> I am generating...
>

the answer to this question is given in corresponding paper that describes
Polder map:
http://journals.iucr.org/d/issues/2017/02/00/ba5254/ba5254.pdf

Based on the analysis described in this paper the program states the
verdict in plain English (as opposed to a bunch of numbers).

For a lazy option you can watch the video tutorial

https://www.youtube.com/watch?v=TcTuMJayh5c=youtu.be

For even lazier option you can fast-forward to minute 4 of the video where
Dorothee shows what to watch for.


> Anybody that can make other suggestions concerning how to validate the
> ligand binding site and/or generate other maps that could be more helpful?
>

If you have another data set collected from the crystal without the ligand
and crystals are reasonably isomorphous, you can calculate Fobs-Fobs map.

Good luck,
Pavel



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Re: [ccp4bb] VERY old mtz file..

2018-11-09 Thread Pavel Afonine
Now I see the value of storing data in plain text files even more (mind
Shelx or X-plor formats, for example) -;)



On Fri, Nov 9, 2018 at 9:47 PM Clemens Vonrhein 
wrote:

> Hi Eleanor,
>
> You could try running the oldest MTZ2VARIOUS binary you can find -
> e.g.
>
>   wget ftp://ftp.ccp4.ac.uk/ccp4/4.2/binaries/ccp4-4.2_Linux.tar.gz
>   tar -xvf ccp4-4.2_Linux.tar.gz bin/mtz2various
>
>   bin/mtz2various hklin ...
>
> Any older binaries (ftp://ftp.ccp4.ac.uk/ccp4/4.0.1/) will require an
> SGI or Dec/Alpha machine ;-)
>
> If that doesn't help I would first check that it is actually a correct
> MTZ file: does the ASCII header (trailer) show up with
>
>   strings your.mtz
>
> towards the end?
>
> Cheers
>
> Clemens
>
> On Fri, Nov 09, 2018 at 12:47:09PM +, Eleanor Dodson wrote:
> > Anyone any idea what to do about this?? Created in 1992!!
> > Seems unreadable..
> >
> > No CTYP lines input for file:  1
> > Indices output even if all data items flagged "missing"
> >  Warning, NOT all LABOUT data lines given
> > Warning: Machine stamp corrupted? Assuming native format.
> > >> CCP4 library signal library_file:End of File (Error)
> >
> > 
> >
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> --
>
> *--
> * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com
> * Global Phasing Ltd., Sheraton House, Castle Park
> * Cambridge CB3 0AX, UK   www.globalphasing.com
> *--
>
> 
>
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Re: [ccp4bb] transform NMR ensemble with pdbset

2018-11-08 Thread Pavel Afonine
Perhaps

phenix.pdbtools model.pdb rotate=... translate=...

which should work with any PDB or mmCIF file.

Pavel

On Thu, Nov 8, 2018 at 11:36 PM Tim Gruene  wrote:

> Dear Kaushik,
>
> you could try moleman2 from the Uppsala Software Factory,
> http://xray.bmc.uu.se/usf/moleman2_man.html - maybe it keeps those cards
> in the PDB file.
>
> Best,
> Tim
>
> On 11/8/18 4:23 PM, KAUSHIK H.S. wrote:
> > Hello,
> >
> > I want to transform (rotate+translate) structures determined by NMR.  I
> > tried using pdbset from the commandline.  The program seems to remove
> > "MODEL" and "TER" lines from the coordinate file.  Is there a way to
> > make pdbset retain these lines? or am I missing something obvious?
> >
> > I could split the ensemble into individual coordinate files, apply
> > transformation and merge them back.  However, is there an easier way out?
> >
> > Best wishes,
> > Kaushik
> >
> > 
> >
> > To unsubscribe from the CCP4BB list, click the following link:
> > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
> >
>
> --
> --
> Paul Scherrer Institut
> Tim Gruene
> - persoenlich -
> OSUA/204
> Forschungsstrasse 111
> CH-5232 Villigen PSI
> phone: +41 (0)56 310 5297
>
> GPG Key ID = A46BEE1A
>
>
> 
>
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Re: [ccp4bb] CC work / free

2018-11-08 Thread Pavel Afonine
Clément,
I'm guessing this is because it isn't clear what CCwork/CCfree can tell you
that Rwork/Rfree can not. Needless to say we all more or less have a good
idea about what the ok values for Rwork, Rfree and Rfree-Rwork (as function
of resolution) while it is much less clear (to me at least) when it comes
to CCwork/CCfree.
I think phenix.refine used to report CCwork/CCfree in some releases but I
removed it as useless.
All the best,
Pavel

On Thu, Nov 8, 2018 at 8:16 PM Clement Degut <
26de0a160250-dmarc-requ...@jiscmail.ac.uk> wrote:

> Hi all,
>
> This probably have already be discussed, but can't find trace of it :
> Is there any reason I am not aware of that refinement software (thinking
> of both phenix and refmac) do not output CC work / free ?
> We all accepted CC 1/2 for resolution cut (whether it's 30 or 10 %) which
> tend to lead to high Rfree ( last shells having very poor phases), at least
> high overall R free in regard to the majority same resolution structures as
> they been refined with I/sig > 3.
> Which in return push people to cut resolution AFTER refinement which
> obviously drastically decrease the R free and catapult your structure from
> worst of the PDB to best of the PDB. It should never be done but it is
> nonetheless.
> How to blame a "non expert"  to do that when changing the resolution from
> 1.49 to 1.5 change your Rfree by 2% (yes it exaggerated but you get the
> idea).
> Now it seems to me -but I may be very wrong as I am far from expert in the
> arcane math of these- that CC work and free would be more agnostic to this
> resolution cut off problem, as we compare it to the CC* value anyway ?
> thought it will never start to be used if refinement software don't output
> it as a standard (not talking about completely replacing Rfree here as it
> is obviously useful).
> Would CC work/free be a bad appreciation of the refinement process ?
>
> Thanks
>
> Clément
>
> --
>
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Re: [ccp4bb] Issue with high Rfree (0.25) for a high-resolution dataset (1.05 Ang)

2018-10-10 Thread Pavel Afonine
Hi Tony,

I always feel some people are too "greedy" with the resolution they want to
> achieve. I mostly find that extremely high density is a pain to work with
> as it's usually accompanied by many dual, triple conformers, a lot of noise
> in the solvent phase that is often difficult to interpret, etc... Often you
> spend more time on a high resolution structure that clearly shows your
> protein, as opposed to a low resolution structure where it's difficult to
> interpret parts of the map. Also, in most cases you REALLY don't need a 1
> Ang map to clearly show the overall structure of your protein, ligands,
> first shell of solvent molecules on the surface of your protein, etc...
>

higher resolution typically means you have a chance to obtain a more
accurate atomic model of a crystal structure, which in turn may lead to a
more accurate interpretation of this model. I fully agree that high
resolution requires more modeling effort. There is still a great room for
software developers to provide more automation.


> Your completeness is 90% in your high resolution shell, which is fine, but
> have you checked you can clearly see most reflections for h, k and l? Maybe
> you're missing many reflections for one of them. I would at least
> try cutting your data back to 1.1 or 1.2 Ang, as it might dramatically
> improve your R factors and still show everything you want to show.
>
>
> Also, did you try TLS refinement?
>

At resolutions like 1.2A or better one normally models ADPs as anisotropic
for all atoms (except H), so no need to use TLS.

Pavel



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Re: [ccp4bb] structure with missing density

2018-10-10 Thread Pavel Afonine
Hi Deepanshu,

how complete the data set? What's completeness across resolution zones?
Systematically missing reflections can have systematic impact in real space
(maps). I've seen entire ligands or domains disappear due to missing
low-resolution data.

Just another check-point to consider..

Good luck!
Pavel

On Wed, Oct 10, 2018 at 10:59 AM Deepanshu Choudhary <
deepanshui...@gmail.com> wrote:

> Dear all,
> I am working on a protein complex. After many efforts, I obtained crystals
> from one of the refinement screen (which took few weeks to grow) and I got
> a 3 Å dataset at synchrotron. I scaled the dataset in P21 spacegroup (which
> is also confirmed by Zanuda and Pointless). There is no twinning detected.
> I solved the phase using molecular replacement with a model of over 90%
> sequence identity. After several rounds of refinement with Refmac, the
> Rfree is 0.307 and Rfactor of 0.23.
> The density looks good and I can see everything that's important. But one
> of the proteins has missing density in 2 of its beta strands (corresponding
> to ~15%) and its not appearing upon several rounds of refinement. Also, the
> B factors are higher for this protein. The missing beta strands are not at
> the interface of the complex.
> I ran some crystals on the gel and did silver staining to find both the
> proteins and no degradation products. I doubt that there is any proteolytic
> cleavage because the protein is unlikely to remain folded if those beta
> strands are chopped out.
> I want to ask if such a structure with missing density and high B-factors
> (>100) can be deposited. Is it possible that some parts of the lattice
> don't have this protein with missing density which is resulting in high B
> factors?
> I would appreciate your efforts if someone can send me few references
> describing such type of structures. I would also welcome any other
> suggestions and recommendations.
>
> Thanks and regards,
> Deepanshu
>
> --
>
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Re: [ccp4bb] collective term for hydrogen bonds and salt bridges

2018-09-17 Thread Pavel Afonine
Nonbonded interactions? (if you approach this from classic geometry
restraints used in refinement programs)

Pavel

On Mon, Sep 17, 2018 at 2:09 PM Joel Tyndall 
wrote:

> Hi,
>
>
>
> Polar interactions seems to make the most sense. This is what Pymol uses
> as I don’t  think it differentiates
>
>
>
> J
>
>
>
> *From:* CCP4 bulletin board  *On Behalf Of *Sheila
> Boreiko
> *Sent:* Tuesday, 18 September 2018 8:06 AM
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* [ccp4bb] collective term for hydrogen bonds and salt bridges
>
>
>
> Dear all,
>
>  I had some literature search, but could not find clearly. Would there
> be an appropriate term to call the sum of hydrogen bonds (HB) and salt
> bridges (SB)? What about "hydrophilic interactions" or "polar
> interactions"? I am analyzing the different number of theses interactions
> in different monomers of my protein, as a totality I wanted to cite
> (compare) the number of HB + SB, yet I think to specify them separately
> could take out some focus of the discussion.
>
>  Thank you,
>
>
> Sheila
>
>
> --
>
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>
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>
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Re: [ccp4bb] Electron density maps for Cryo-EM structures.

2018-09-09 Thread Pavel Afonine
P.S.: all questions are welcome of course, no labeling. It's just some of
them are so orthogonal to common sense that answers my be such as well.
Best,
Pavel

On Sun, Sep 9, 2018 at 9:38 PM Pavel Afonine  wrote:

> Hi,
>
> Is there any sever available to create electron density maps for cryo-em
>> structures?
>>
>
> The questions are nonsensical. Here is why:
>
> 1) In cryo-EM maps are not electron density maps but surfaces representing
> electric potential.
>
> 2) Creating such a map is essentially carrying on from cryo-EM experiment
> and obtaining the 3D reconstruction.
>
> Are you really sure about what you are asking for?
>
>
>> Or, we should create the maps from mmCIF.
>>
>
> mmCIF is a file format. It may contain representations of rabbits,
> boysenberries or some diffraction data. So.. how you think it may be
> related to cryo-EM, in your particular case?
>
>
>> I am particularly interested in those cryo-em structures with high
>> resolution, like 2.6~2.8A.
>>
>
> Sure, all are excited about high-res cryo-EM!!!
>
>
>> Please give me an education.
>>
>
> Sure. One of available universities can do this.
>
> Cheers,
> Pavel
>
>



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Re: [ccp4bb] Electron density maps for Cryo-EM structures.

2018-09-09 Thread Pavel Afonine
Hi,

Is there any sever available to create electron density maps for cryo-em
> structures?
>

The questions are nonsensical. Here is why:

1) In cryo-EM maps are not electron density maps but surfaces representing
electric potential.

2) Creating such a map is essentially carrying on from cryo-EM experiment
and obtaining the 3D reconstruction.

Are you really sure about what you are asking for?


> Or, we should create the maps from mmCIF.
>

mmCIF is a file format. It may contain representations of rabbits,
boysenberries or some diffraction data. So.. how you think it may be
related to cryo-EM, in your particular case?


> I am particularly interested in those cryo-em structures with high
> resolution, like 2.6~2.8A.
>

Sure, all are excited about high-res cryo-EM!!!


> Please give me an education.
>

Sure. One of available universities can do this.

Cheers,
Pavel



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Re: [ccp4bb] cryo-EM

2018-08-31 Thread Pavel Afonine
Hi Xavier,

> is there some kind of general trend if not consensus as how to refine
> cryo-EM structures?
>
Not really consensus, but my clearly biased contribution to the topic:

I'd say basic common sense for refinement applies:

- optimally sharpen the map (
https://journals.iucr.org/d/issues/2018/06/00/ic5102/);

- refine against the map using refinement parameterization appropriate for
the data (map) quality (resolution) (
https://journals.iucr.org/d/issues/2018/06/00/ic5103/);

- make sure to validate data (map), model, and model-to-map fit (
https://doi.org/10.1101/279844).

> What do people do for maps in the 3-4Å range,
>
3-4A may require secondary structure and rotamer restraints. Use "NCS" if
available. If map is symmetrized, then use "NCS" constraints, otherwise
restraints should be just fine. Typically, data at this resolution range
does not allow to confirm geometry validation outliers, so your aim is no
outleirs. Etc, etc. And again, validate the model and model-to-map fit,
locally (at atom/residue level) and globally (standard "Table 1" metrics,
discussed here https://doi.org/10.1101/279844 , for example).

> pure RSR against the untouched map and that's it?
>
Good idea, in my opinion.

> Reciprocal space refinement against the backtransformed structure factors
> from the map but without touching the map?
>
Personally don't like this idea.

> I've even heard that some people "dare" to calculate 2mFo-DFc-maps
>
Not a good idea, I'm pretty sure. Cryo-EM map is not biased by atomic model
(normally, unless a model was used in reconstruction). 2mFo-DFc map is
model biased by definition. Also needless to say that absence of "Fobs" in
cryo-EM is a good hint that this map isn't what you want -;)

All the best,
Pavel



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Re: [ccp4bb] Can H-clashes be ignored ?

2018-08-22 Thread Pavel Afonine
Hi,

also, it helps to keep in mind that some clashes may actually be valid
interactions that are labeled as 'clashes' by validation software that is
simply not sophisticated enough to distinguish between bad steric clashes
and chemically/physically favorable valid interactions. For an example,
please refer to results we show in our full quantum refinement of a small
structure done as part of quantum refinement project (www.qrefine.com):

http://scripts.iucr.org/cgi-bin/paper?S2059798317016746

All the best,
Pavel

On Fri, Aug 17, 2018 at 6:27 PM, Firdous Tarique  wrote:

> Hello everyone.
>
> I have a basic question. When a validation report of a coordinate is
> generated we often come across a term known as "Too-Close Contacts".
> First of all can somebody please explain me what is the shortest
> interatomic distance between the two atoms which is permissible ?
>  Next, in this list there are Non-H and H columns list, their Interatomic
> distance and Clash overlap. I could see  two types of clashes in my
> validation report. One in which interatomic distance between the two atom
> (one is always a modeled  H) ranges from 1.7-2.4A, and clash overlap from
> 04-1.0. The other in which the interatomic distance between two atom is
> greater than 2.2A and the clash overlap is between 0.4-0.6 (always between
> two non H-atoms).
>
> So my question is that out of so many clashes shown in the list which are
> one which actually need to be fixed and can't be ignored specially because
> one of my ligand is an amino acid which is showing lots of these H clashes
> (interatomic distance less than 1.5A).
>
> Regards
>
> Kahkashan
>
>
>
> --
>
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Re: [ccp4bb] Normalization of B-factors

2018-08-09 Thread Pavel Afonine
> I (personally) think the best answer from these was to look at the
> TLS-subtracted residuals (ie. total B-factor - TLS component) — can’t
> remember who sent it, off the top of my head.
>

TLS is just an approximation, sometimes good and sometimes not. If TLS
parameters are refined along with individual ADPs ("residual") the latter
tend to compensate for eventual inadequacy of TLS model.

Pavel



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Re: [ccp4bb] identifying bound ions

2018-07-31 Thread Pavel Afonine
There is an option in phenix.refine to do this, described here:

Automated identification of elemental ions in macromolecular crystal
structures. Echols N, Morshed N, Afonine PV, McCoy AJ, Miller MD, Read RJ,
Richardson JS, Terwilliger TC, Adams PD Acta Cryst. D70, 1104-1114 (2014).

Pavel

On Tue, Jul 31, 2018 at 5:39 AM,  wrote:

> Dear BB,
>
>
>
> I know it has been discussed some time ago, but a google search did not
> come up with anything useful.
>
>
>
> I need a program which analyzes the bound waters and suggests whether a
> particular water might be a chloride, calcium, sulfate, sodium or something
> else. Preferably a program that can be run off-line (not a web server), but
> if there is no choice, we will use a webserver as well.
>
>
>
> Thank you for your suggestions!
>
> Herman
>
>
>
>
>
>
>
> --
>
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Re: [ccp4bb] wwpdb validation

2018-07-27 Thread Pavel Afonine
Phenix has its own way to do it which is "Comprehensive validation"
available from the GUI. This includes validation of model, data and
model-to-data fit. It is data-specific: there is one for crystallography
(X-ray or neutron) and one for Cryo-EM. For best results, you need the
latest version from nightly builds. Hope "wwpdb validation pipeline" is
something along the same lines, or close at least.
All the best,
Pavel

On Fri, Jul 27, 2018 at 9:24 AM, wtempel  wrote:

> Hi,
> did I hear correctly that the wwpdb validation pipeline can be accessed
> from within ccp4 and/or phenix? If so, how does one access that
> functionality in either software suite?
> Many thanks.
> Wolfram Tempel
>
> --
>
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Re: [ccp4bb] Help with omit map

2018-07-24 Thread Pavel Afonine
As others suggested, you can use Polder map:

- how-to video tutorial can be found here:

http://www.phenix-online.org/documentation/reference/tutorial_channel.html

- background is described here:

http://journals.iucr.org/d/issues/2017/02/00/ba5254/ba5254.pdf

Pavel


On Tue, Jul 24, 2018 at 3:26 PM, Vikram Dalal 
wrote:

> Hi everyone,
>
>
> I have to generate the omit map of metal and coordinating residues of
> protein structure for the figure.
>
> Which program can be used to generate the omit map for my requirement.
>
>
>
> Thanks & Regards,
>
>
>
>
>
>
>
>
> --
>
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Re: [ccp4bb] R-flag choose

2018-07-10 Thread Pavel Afonine
It's important to remember that free-R reflections are not only used to
calculate Rfree, but also are used in calculation of m and D scales in
2mFo-DFc and mFo-DFc maps, as well as in likelihood-based refinement
targets. The fact is that you need to have a sufficient amount of free-R
reflections in each relatively thin resolution bin. Some authors estimate
this number as at lest 50 reflections per bin. In Phenix binning is defined
such that each sufficiently thin bin gets no less than 150 reflections.
Bernhard pointed out about "precision or significance of Rfee". Also, I
would add that too few free-R reflections can affect refinement progress
(not only robustness of Rfree value) (I've done relevant tests to convince
myself more than a decade ago)! Thus I favor having 10% just to be on a
safer side.

Pavel


On Tue, Jul 10, 2018 at 1:02 AM, 张士军 <21620150150...@stu.xmu.edu.cn> wrote:

> Dear all
>
> I am confusing the choose of free R-flags recently. Rfactor
> means calculatted from reflection not used in refinement,so what's big the
> difference between different percentage of R-flags,like it's about 5% in ccp4
> -refmac, while it is 10% in phenix-refinement,what'
> s the difference between them and how they affect the
> Rwork and Rfree values when do refinement. Thanks a lot !
>
> best regards
>
> shijun
>
> --
>
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Re: [ccp4bb] Clear segid

2018-07-06 Thread 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
>
> --
>
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Re: [ccp4bb] disulfate bond ?

2018-07-04 Thread Pavel Afonine
More re disulfide bonds:
http://www.phenix-online.org/newsletter/CCN_2015_01.pdf#page=13

Pavel

On Tue, Jul 3, 2018 at 11:26 PM, 张士军 <21620150150...@stu.xmu.edu.cn> wrote:

> Hi all
>
> I got a structure which has COA in it, and the SH in the tail of COA
> is very close to the SH side chain of Cys in the structure. I don't know
> whether it is disulfate bond or not? I remember they
> should link together if they are disulfate bond,am I right?
>  so what could this be? Thanks a lot!!!
>
> best regards
>
> shijun
>
>
>
> --
>
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Re: [ccp4bb] B-factor standardization

2018-04-05 Thread Pavel Afonine
> If I am not wrong, I remember that someone proposed to standardize
> B-factors of protein atoms as “BS = B - Bave”, where Bave is the average
> B-factor of the protein.


This will make some of BS negative (if B

Re: [ccp4bb] (arcane) How to generate complete set of indices at low res

2018-04-05 Thread Pavel Afonine
Just in case you find it helpful, you can get 100% complete set of
reflections (Fcalc) in specified resolution range using

phenix.fmodel model.pdb high_res=2.5 low_res=15

or if you leave out low_res it will go all the way up to theoretical limit
of low resolution.

If you have/use cctbx then I can show to do this at lower (Python) level.

Pavel

On Thu, Apr 5, 2018 at 3:52 AM, Frank von Delft  wrote:

> Hello - can anybody shed light on this mystery:
>
> We need (for PanDDA analysis) a lot of datasets each to have the complete
> set of low resolution indices, whether measured or not.  (Refmac adds the
> estimates as DFc, which is crucial when comparing maps.)
>
> In ccp4, there are two obvious ways to get these indices complete:
>
>- uniqueify
>- CAD using the keyword "RESOLUTION FILE 1 999 "  (999 is the
>low resolution limit).
>
> Mystifyingly, in ~1% of datasets, one or the other route misses one or two
> indices.  Our work-around is to go belt-and-braces and run both for each
> dataset.
>
>
> It does however remain a bug.  Does anybody have any idea what's
> happening?  We can send example datasets to any volunteers who want to
> fiddle with it.
>
> phx
>
>
>


Re: [ccp4bb] Looking at an EM map..

2018-03-15 Thread Pavel Afonine
This is discussed, for example, here:
http://www.pnas.org/content/114/12/3103

Also, here I calculated the distribution of map values (scaled in r.m.s.)
for four groups of atoms: main-chain atoms, side-chain oxygen atoms of ASP
and GLU (negatively charged OD1, OD2, OE1, OE2), side chain atoms of ARG
and LYS (positively charged NH1, NH2, NZ), and all other side-chain atoms.
Clearly side-chain oxygen atoms of ASP and GLU have indeed systematically
weaker density:

http://cci.lbl.gov/~afonine/tmp/fig.png

First picture: all maps from EMDB of resolution 3A or better. Second
picture: all maps from EMDB of resolution 3-4A.

All the best,
Pavel

On Thu, Mar 15, 2018 at 7:17 AM, Eleanor Dodson <
176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote:

> I am pig-ignorant about these ,, but this example has negative values as
> well as positive..
>
> What does this mean? I thought a well phased map would be pretty well all
> positive..
>
>  Eleanor
>


Re: [ccp4bb] building into EM map

2018-01-23 Thread Pavel Afonine
> I am new to building into an EM map, and I wonder if I could get a
> recommendation for some standard routine for programs to use. I tried "find
> helixes and strands" tool in phenix, it found some secondary structure
> elements, however, it seems that there is more that could be done
> automatically. Is there any standard set of tools to use for automatic
> building in EM map of about 4A resolution?
>


phenix.map_to_model may be able to do more:
https://www.phenix-online.org/documentation/reference/map_to_model.html

Pavel


Re: [ccp4bb] new ContaMiner features

2017-11-23 Thread Pavel Afonine
It's amusing how a seemingly innocent ad for a new tool can ignite a rather
prickly thread.. I see two keys to this.

Firstly, for those who are not familiar with the issue the add could be
better structured by providing a clearer statement of what the problem is
or why it is important (with appropriate citations as examples) and then
addressing how this is solved using the tool being advertised (ContaMiner).

Second, I can't agree more with with Gerard: "a word of warning" (concerns
about Staraniso use) is best to discuss with respective developers first
before going public. (A nuance though is: not all developers are keen to
open-access source code or even allow their software for benchmarking by
others in some instances. So this may be tricky sometimes.)

Radu's assessment is harsh to my taste.. I guess others commented on this
enough to explain the validity of effort. Plus, I find wording "on the
bizarre ContaMiner" isn't helpful.

All in all, intentionally or not, this made enough of advertisement for
ContaMiner and Staraniso! Win-win, I think!

All the best,
Pavel


On Thu, Nov 23, 2017 at 10:33 PM, Graeme Winter  wrote:

> Dear All,
>
> As someone who is both a user of external software and supports internally
> developed software to external users, I am quite familiar with both sides
> of this argument. From time to time someone will notice a "weird feature"
> in software - sometimes this is a bug, sometimes misuse (which is still by
> and large a bug, but in documentation) and sometimes a change in
> circumstances i.e. reasonable assumptions made in developing a package
> (e.g. background always over 1 count / all data sets have some reflections
> with I/sigI > 3 etc) become problematic.
>
> As an individual developing software, and a member of a team doing so, it
> is always more comfortable if a user comes back with a collegiate "quiet
> word" that the software did something odd. However, I suspect it would be
> for the greater good that a more public approach was taken in general,
> since the less attentive user may miss this odd feature and take the
> results as gospel - if the knowledge of the bug / feature whatever was not
> in the public domain. Despite appearances people do not like to contact
> authors of software packages to complain.
>
> To make a note that "this version of package xyz has been found to be
> sometimes unpredictable with version 123 of the pipeline" does not blame
> the package, or the pipeline, but says that you should be warned with this
> combination. Ideally the authors of package xyz and the pipeline would be
> alerted, by the other developers or users, but it is better (IMHO) to be
> open. Public bug trackers are a good example of this.
>
> I suspect this matter of anisotropy correction is a similar one. Here we
> have a change in circumstances - the actual intensity measurements are
> modified - and passed in as if they are the originals. It is reasonable
> that this may affect the outcome of subsequent analysis and it is hoped
> that this does change the outcome but in a positive manner. This does not
> appear to be the case here.
>
> I have been asked on several occasions to incorporate the anisotropy
> correction into xia2 as it 'always makes things better', and have resisted
> on the grounds that the purpose of the package is to faithfully analyse the
> data as provided and provide uncorrected intensities as output. The
> corrections should ideally be performed within the downstream software,
> since they then know exactly what has happened to the measurements and will
> make fewer (ideally no) incorrect assumptions.
>
> It's already routine to write out multiple versions of e.g. phases,
> weights, sigma values etc based on different assumptions and flag then
> accordingly - perhaps we should be doing the same with modified
> intensities, so that packages which require the unmodified values could
> ignore the corrected ones. That would avoid the need for any health
> warnings and ensure changes in the wider environment do not invalidate
> assumptions...
>
> Obviously, all of the above is my humble opinion and other opinions are
> equally valid.
>
> Best wishes Graeme
>
>
> --
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> damage which you may sustain as a result of software viruses which may be
> transmitted in or with the 

Re: [ccp4bb] [Off-topic] Comparison of the same structure built by many people

2017-11-21 Thread Pavel Afonine
Perhaps this can be automated:

https://www.phenix-online.org/papers/wd5073_reprint.pdf

Software doesn't get tired or bored, and thus potentially can try more and
produce more plausible interretations. Then one can hire a number of people
of various expertise to choose "best" result according to their subjective
interpretations.

Pavel

On Mon, Nov 20, 2017 at 12:25 PM, Shintaro Aibara  wrote:

> Dear All,
>
> Apologies for the slightly off-topic, but I was wondering if anybody knew
> of a paper/textbook where a protein model was built by multiple people
> (ranging from novice to experienced builders) and compared. I believe the
> conclusion was that while the overall trace was broadly correct,
> experienced builders maintained better geometry compared to beginners.
>
> I distinctly remember reading it a couple of years ago but cannot seem to
> find the figure. If anybody knows of this figure/paper/textbook it would be
> much appreciated if you could point me in the direction.
>
> Yours faithfully,
> Shintaro
>


Re: [ccp4bb] High R/Rfree

2017-11-13 Thread Pavel Afonine
Hi Radhika,

R-factor value is almost useless unless you know the resolution (which you
did not tell us): 26% is ok for 3A resolution and is nonsense for 1A, for
example. The Rfree-Rwork gap is obviously large, suggesting sub-optimal
refinement strategy. Try optimizing weights, let program update
(add/remove/refine) water. You can send me model and data files for further
diagnostics.

Pavel

On Mon, Nov 13, 2017 at 3:45 PM, Radhika Singh  wrote:

> Hello All,
>
> I am currently working on the structure of a DNA protein complex.  The
> data has been processed in space group P1 (53.042   59.527   78.526 105.24
> 98.03 106.99 P 1, Rpim 11.7%).  At this stage I have almost 85% model is
> complete but my R/Rfree is stuck as 26%/34%.
>
> I have some concerns and questions:
> * Xtriage says there are a large number of outliers; however no
> pseudotranslational symmetry is detected by the program.  What are the
> other reasons for outliers?
>
> * I am trying phenix.refine for refinement with the default settings. Is
> there any special setting that can help me?
>
> I would like to have some suggestions about my problem.
>
> Thanks in advance
>
> Radhika
>
>


Re: [ccp4bb] question about resolution bins in deposition

2017-11-06 Thread Pavel Afonine
See Table 1 and corresponding discussion here:

http://journals.iucr.org/d/issues/2013/04/00/dz5273/dz5273.pdf

Hope that hints you the answer. If not get back to me with questions.

All the best,
Pavel


On Mon, Nov 6, 2017 at 7:18 PM, Eze Chivi  wrote:

> Hi, my PDB file lists only 4 resolution bins (full range: 1.6-19.1A). This
> is the first time I noted this behavior (It's used to be 20 bins). It is OK
> for deposition? It is need to rearrange statistics? How I can do that?
> Thank you very much. (I did my refinements in phenix, oops!, but the ccp4bb
> people is so kind...)
>


Re: [ccp4bb] another unknown density problem

2017-11-03 Thread Pavel Afonine
If by "it was truncated at 5A for clarity" you really mean you truncated
all low-resolution data from 5A and lower then I am not surprised you see
funny densities all over or don't see density where it is expected. Why?
Consult a textbook for the answer.

All the best,
Pavel

On Fri, Nov 3, 2017 at 3:10 AM, Abhishek Anan 
wrote:

> Dear Prof Schreuder
>
> Here are another couple of perspectives from coot. The density is too far
> and isolated from the peptide chain to be an alternate conformation or
> conformational change. The density of the peptide chain does not look good
> because it was truncated at 5A for clarity.
>
> Best regards
> Abhishek
>
> On Fri, Nov 3, 2017 at 9:33 AM,  wrote:
>
>> Dear Abhishek,
>>
>>
>>
>> To me, it looks like an alternative conformation of the peptide chain or
>> maybe even a conformational change with respect to the starting model. The
>> peptide chain does not look too well defined, despite high resolution
>> electron density.
>>
>>
>>
>> Best,
>>
>> Herman
>>
>>
>>
>> *Von:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *Im Auftrag
>> von *Abhishek Anan
>> *Gesendet:* Freitag, 3. November 2017 09:26
>> *An:* CCP4BB@JISCMAIL.AC.UK
>> *Betreff:* [EXTERNAL] [ccp4bb] another unknown density problem
>>
>>
>>
>> Hi all,
>>
>> I have an "unknown" density in the map. I have tried to fit it to PEG but
>> it doesn't fit very well. I was wondering if there are other PEG-related or
>> other molecules I could try.
>>
>> The crystal grew in TRIS-HCl and PEG MME 2K.
>>
>> Thank you
>>
>> Abhishek
>>
>
>


Re: [ccp4bb] efresol download?

2017-10-26 Thread Pavel Afonine
Johan,

core functionality described in that paper is implemented in cctbx. Re the
stand-alone program -- I'm cc'ing to the author.

Pavel

On Thu, Oct 26, 2017 at 8:39 AM, Hattne, Johan 
wrote:

> Dear all;
>
> Would anybody know where I can find efresol (as detailed in
> http://dx.doi.org/10.1107/S0907444913016673) these days?  Googling lead
> me to a 2014 post (https://www.jiscmail.ac.uk/
> cgi-bin/webadmin?A2=ind1406=ccp4bb===155751), but those links
> result in 403 Forbidden as of right now.
>
> // Best wishes; Johan
>
>
>   Research Specialist @ Gonen Lab
> 
> Janelia Research Campus * 19700 Helix Drive
> Ashburn, VA 20147 * +1 (571) 209-4000 extension 3376
>


Re: [ccp4bb] model bias

2017-10-11 Thread Pavel Afonine
A round of refinement with simulated annealing followed by minimization
should address your concern.
Pavel

On Wed, Oct 11, 2017 at 4:48 PM, Karsten Dreifus 
wrote:

> Dear all,
> I have a 120 aa protein. Matthews coefficient indicates 3 mol in asu.
> Molrep (template with 70 % seq identity)  finds three NCS molecules
> (the template model has only 1 chain as it is in different space
> group). Now, REFMAC refines it to 25/30 % R/RFREE. I was just worried
> about model bias, so I just deleted chain C and re-ran the refinement.
> I observe that in the place of chain C, the DELFWT map in Coot shows
> negative density (red colour). Shouldnt the deleted regions show
> POSITIVE density (green colour)? The 2fo-fc map in the deleted region
> shows usual blue colour. I shook the 2chain model with Phenix simple
> dynamics and then ran refinement with same results.
>
> How do I verify the model is correct?
> Karsten
>


Re: [ccp4bb] How to deal with the bad omega angles?

2017-10-10 Thread Pavel Afonine
And I should add this works just great! (given we are on the same page
defining 'great').

I used this for Cryo-EM model challenge; Nigel added this functionality at
that time to make this possible.

Pavel

On Wed, Oct 11, 2017 at 2:17 AM, Nigel Moriarty  wrote:

> Since you are using phenix.real_space_refine, there is a rather brutal
> parameter
>
> peptide_link.apply_all_trans=True
>
> that will restrains all peptide links to be trans. It can help with moving
> all cis to trans but you should check them as best you can at 4.3A.
>
> Cheers
>
> Nigel
>
> ---
> Nigel W. Moriarty
> Building 33R0349, Molecular Biophysics and Integrated Bioimaging
> Lawrence Berkeley National Laboratory
> Berkeley, CA 94720-8235
> Phone : 510-486-5709 Email : nwmoria...@lbl.gov
> Fax   : 510-486-5909   Web  : CCI.LBL.gov
>
> On Tue, Oct 10, 2017 at 9:03 AM, Gert Vriend 
> wrote:
>
>> Look at http://swift.cmbi.ru.nl/servers/html/index.html under "structure
>> validation" you will find a server that predicts which peptide planes most
>> likely need to be flipped. This server is the implementation of:
>>
>> Detection of trans-cis flips and peptide-plane flips in protein
>> structures. 
>>
>> *Touw* WG, *Joosten* RP, *Vriend* G.
>>
>> Acta Crystallogr D Biol Crystallogr. 2015 Aug;71(Pt 8):1604-14. doi:
>> 10.1107/S1399004715008263. Epub 2015 Jul 28.
>>
>>
>> Good luck,
>>
>> Gert
>>
>> On 10-10-2017 15:28, Yang Shi wrote:
>>
>> Hi, Tristan Croll,
>>
>> Thanks for your suggestion.I will consider to rebuild these first.
>>
>> Yang
>>
>>
>> 在 2017年10月10日,下午9:18,Tristan Croll   写道:
>>
>> Relying on refinement to fix cis peptide bonds for you is unlikely to end 
>> well. It looks to me like you really need to spend some time investigating 
>> and manually rebuilding these first.
>>
>> On 2017-10-10 13:52, 师扬 wrote:
>>
>> Dear all,
>> I am refining a model based on a 4.3A EM density map,and there are
>> some cis-peptides in the beginning model.
>> By using phenix.real_space_refine with a very low cis-peptide
>> threshold (0), all the cis-peptide become to the twisted.
>> The start Omega angle:
>> cis-proline: 31.63 %
>> twisted proline: 0.00 %
>> cis-general: 11.11 %
>> twisted-general: 0.05 %
>> The final Omega angle:
>> cis-proline: 0.00 %
>> twisted proline: 27.55 %
>> cis-general: 0.00 %
>> twisted-general: 6.04 %
>> My questions are:
>> 1) What is the twisted peptide?
>> 2) Is the amount acceptable at the current resolution?
>> 2) How to refine it?
>> Thanks in advance!
>> Yang Shi
>> 【网易自营|30天无忧退货】仅售同款价1/4!MUJI制造商“2017秋冬舒适家居拖鞋系列”限时仅34.9元>>
>> [1]
>> Links:
>> --
>> [1] http://you.163.com/item/detail?id=1165011=web_gg_mail_jiaobiao_9
>>
>>
>>
>


Re: [ccp4bb] RMSD between superposed structures without moving

2017-08-28 Thread Pavel Afonine
Or using cctbx:


from scitbx.array_family import flex
import iotbx.pdb

def run():
  xyz_1 = iotbx.pdb.input(file_name="file_1.pdb").atoms().extract_xyz()
  xyz_2 = iotbx.pdb.input(file_name="file_2.pdb").atoms().extract_xyz()
  print flex.mean(flex.sqrt((xyz_1 - xyz_2).dot()))

if (__name__ == "__main__"):
  run()


Pavel


On Mon, Aug 28, 2017 at 9:46 AM, Tristan Croll  wrote:

> I should learn not to post while distracted. That last line was both
> over-engineered, and wrong. What you want is:
>
> rmsd = sum(numpy.linalg.norm(xyz1-xyz2, axis=1))/len(xyz1)
>
>
> On 2017-08-28 14:32, Tristan Croll wrote:
>
>> In this case calculating the rmsd is easy:
>>
>> - get the coordinates of each structure as n x 3 numpy arrays. The
>> Pymol commands for this should look like:
>>
>> xyz1 = cmd.get_coords('sele1', 1)
>> xyz2 = cmd.get_coords('sele2', 1)
>>
>> Then,
>>
>> rmsd = numpy.linalg.norm(numpy.sqrt((xyz1-xyz2)**2), axis=1)
>>
>> Tristan Croll
>> Research Fellow
>> Cambridge Institute for Medical Research
>> University of Cambridge CB2 0XY
>>
>> On 28 Aug 2017, at 10:04, Johannes Sommerkamp
>> <155b9e78396e-dmarc-requ...@jiscmail.ac.uk> wrote:
>>
>> Thanks a lot for your answers and the PyMOL mailing list hint. I
>>> didnt had in mind this list.
>>>
>>> I read the Pymol Wiki. The commands
>>>
>>> align moving, target, cycles=0, transform=0
>>>
>>> align moving, target, cycles=0
>>>
>>> give identical values for RMSD. So, the only difference is, that
>>> the moving structure is not moved in the graphical output.
>>> Additionally the RMSD with the argument cycles=0 can't be the RMSD
>>> before any movement because the values differ for the super and the
>>> align command. I think its just without refinement.
>>> Since the two structure I want to compare are already aligned based
>>> on the central beta sheet CA atoms, I want to calculate the RMSD
>>> without any movement.
>>>
>>> Regards
>>> Johannes
>>>
>>> On 27/08/17 19:18, Folmer Fredslund wrote:
>>> Hi Johannes,
>>>
>>> Did you read the PymoWIKI entry on the align command?
>>>
>>> https://pymolwiki.org/index.php/Align#RMSD [1]
>>>
>>> I think this should give you what you want within PyMOL.
>>>
>>> Btw, there is a nice dedicated PyMOL mailing list
>>> https://pymolwiki.org/index.php/PyMOL_mailing_list [2]
>>> It is rather low traffic, but the replies are generally from the
>>> developers or very knowledgeable users.
>>>
>>> Hope this helps,
>>> Folmer Fredslund
>>>
>>> On 2017-08-27 13:09, Johannes Sommerkamp wrote:
>>> Hello everybody,
>>> I have superposed two structures based on the central beta-sheet CA
>>> atoms with the "super" command in Pymol.
>>> Now, I want to calculate the RMSD between ALL atoms or ALL CA atoms
>>> without moving the structures again. The rms_cur command in Pymol
>>> would do that, but only works if all atom identifiers match. Adding
>>> "transform=0" to the super, oder align command still does the
>>> alignment and moves the structure but does not show the movement.
>>>
>>> Is there an easy way to just calculate the all atom RMSD between
>>> two already superposed structures in pymol or any other programm?
>>>
>>> Thanks in advance!
>>> Johannes
>>>
>>
>> --
>> Johannes Sommerkamp
>> Ruhr-Universität Bochum
>> AG Röntgenstrukturanalyse an Proteinen, LS Biophysik, ND04/396
>> Universitätsstraße 150
>> 44801 Bochum
>> Tel: +49-(0)234/32-25754
>>
>>
>> Links:
>> --
>> [1] https://pymolwiki.org/index.php/Align#RMSD
>> [2] https://pymolwiki.org/index.php/PyMOL_mailing_list
>>
>


Re: [ccp4bb] normalization of B-factor values from different crystal structures

2017-08-02 Thread Pavel Afonine
Hi,

also keep in mind that the total model structure factor used in refinement
and anywhere where model-to-data agreement needs to be evaluated (such as
maps or R factors) is:

Fmodel = ktotal * (Fcalc_atoms + F_bulk_solvent + F_something_else)

where ktotal ~ scale * exp(-h*Uoverall*h_transpose) .

This makes it obvious that B factor is arbitrarily shared between Uoverall
matrix and atomic B factor.
phenix.refine subtracts as much as possible from the trace of Uoverall and
adds that to atomic B; however, sometimes it is only possible to add a part
of what can be removed from Uoverall.

With this in mind and as James pointed out, atomic B factors are likely
defined up to a constant.

Pavel


On Wed, Aug 2, 2017 at 5:54 PM, James Holton 
wrote:

> Woops, sorry.  There was a typo in my response.  here it is again without
> the typo.
>
> B factors are 78.96x the value of the mean square variation in an atom's
> position.  The square is the important part of how you scale them.  Lets
> say you have static disorder in the crystal lattice, and that gives every
> atom an rms variation of 0.5 A relative to their ideal lattice positions,
> then that static disorder imparts a B factor of 78.96*(0.5)^2 = 19.7 to all
> atoms.  If in addition to lattice disorder you have a side chain flapping
> in the breeze by another rms 1.0 A, that is B = 79, but the combination of
> the two things is an rms fluctuation of sqrt(0.5^2 + 1.0^2) = 1.118 rms A,
> and the total B factor resulting from that is 98.7.  It is not a
> coincidence that 98.7 is the sum of 19.7 and 79.  That is, independent
> sources of disorder _add_ when it comes to the B factors they produce.
>
> So, if you want to "normalize" B factors from one structure to another,
> the best thing to do is subtract a constant.  This is mathematically
> equivalent to "deconvoluting" one source of overall variation from the
> site-to-site differences.  What should the constant be?  Well, the
> structure-wide atomic B factor average isn't a bad choice.  The caveat is
> that a B factor change of 5 in the context of an overall B of 15 is
> probably significant, but in a low resolution structure with an overall B
> factor of 100, it might be nothing more than a random fluctuation.  It's
> like looking at the width of bands on a gel.  A small change in a sharp
> band is significant, but that same change in position for a fat band is
> more dubious.
> Now, crystallographically, all a B factor is is the rate of falloff of the
> contribution of an atom to the diffraction pattern with increasing
> resolution.  So, the overall B factor can be quite well known, but the B
> factor of a single atom in the context of tens of thousands of others can
> be harder to determine.  Refinement programs do their best finding the best
> fit, but in the end you are trying to reconcile a lot of different possible
> contributors to the fall-off of data with resolution.  Because of phases, a
> small change in one B factor can cancel a small change in another.  This is
> why B factor refinement at low resolution is dangerous.
>
> If you want to compare B factors I'd recommend putting "error bars" on
> them.  That is, re-refine the structures of interest after jiggling the
> coordinates and setting all the B factors to a constant.  See how
> reproducible the final B factors are.  This will give you an idea of how
> big a change can happen by pure random chance, even with the same data.
>
> Hope that helps!
>
> -James  Holton
> MAD Scientist
>
> On 8/2/2017 12:09 PM, Asmita wrote:
>
> Hi,
>
> This might look as a very fundamental question. I have a dataset of
> crystal structures better than 3.5Ang resolution. For a qualitative
> analysis, I want to compare the residue-wise B-factors in these structures,
> but due to different procedures adopted in refinement and scaling, I
> understand that these values cannot be compared in a raw manner.
>
> Can someone suggest appropriate normalization methods that could be used
> for scaling these B-factors for a relevant and meaningful comparison? All
> the files have isotropic B-factor values and there are no ANISOU entries in
> any of the files.
>
> Thanks
>
> Asmita
>
>
>


Re: [ccp4bb] refmac output

2017-08-02 Thread Pavel Afonine
Hi Ed,

your suggestion makes perfect sense to me, and it's trivial to add an
option to do what you want. This will be available in next Phenix nightly
build (clearly not tomorrow given today's power outage).

Command line: use "write_map_coefficients_only=True" (by default is is
False).

Refinement GUI: Configure -> Output -> Other options -> tick "Write map
coefficients only" box.

Pavel

On Wed, Aug 2, 2017 at 1:12 PM, Edwin Pozharski 
wrote:

>
> Just to clarify, how do you use the extra columns in this scenario?  My
> suggestion was to have the output file that includes only the map
> coefficient columns, so you still can look at the map.  IIRC, FP/SIGFP
> columns from refmac output are actually modified from the input (scaled
> with Boverall), so it was not recommended to use refmac output as input of
> any kind.
>
> Also, to provide context, my comment resulted from dealing with a large
> chunk of data that included ~200 output mtz files - which is Gb-sized
> tarball that had to be uploaded/downloaded.  Not the end of the world, but
> cutting it in half seemed like a good idea at the time. :)  Not hard to
> script that, of course.
>
> I am not necessarily advocating for skinny files to be the default, but as
> it stands, refmac/buster/phenix do not even provide the option of doing it
> (It's entirely possible that I am wrong here on specifics and will get
> corrected by Garib, Gerard and Pavel).
>
> Cheers,
>
> Ed.
>
> Edwin Pozharski, PhD, Assistant Professor
> University of Maryland, Baltimore
> --
> When the Way is forgotten duty and justice appear;
> Then knowledge and wisdom are born along with hypocrisy.
> When harmonious relationships dissolve then respect and devotion arise;
> When a nation falls to chaos then loyalty and patriotism are born.
> -- / Lao Tse /
>
>


Re: [ccp4bb] refmac output

2017-07-31 Thread Pavel Afonine
>
> I know space is cheap these days, but is there a reason for Refmac to
> generate all those extra columns in the output mtz file?  Refmac (as well
> as phenix.refine and buster-tnt) output mtz file is almost always used for
> only one purpose - look at the map in coot.  You only need 4 columns for
> that, not 14.  Other columns are useful for testing, but why not make them
> optional?
>

a phenix.refine run creates an MTZ file with four kinds of data:

1) Copy of input data. Why? For convenience and consistency. Inputs may not
necessarily be in MTZ format and may be spread across multiple files of
different format.

2) Data that were actually used in refinement. Why? A user has options to
cut resolution from both ends, as well as apply cutting by sigma. Plus,
phenix.refine may choose not to use a handful of reflections as outliers
(Read, 1999). So it may be good to have set of reflections that were used
in given refinement run.

3) Model in reciprocal space: Fmodel. Why? This is a reciprocal space
representation of what's in PDB file except that it is richer because
contains not only atomic model (Fcalc) but also solvent contributions (bulk
and non-uniform) as well as all scales. Fmodel taken from this array and
Fobs from "2)" are expected to reproduce reported R-factor exactly.

4) Fourier map coefficients (2mFobs-DFmodel, mFobs-DFmodel, anomalous map
if applicable).

"1)" and "3)" can be optional:
- with trivial scripting one can obtain Fmodel using data from "2)" and
"4)".
- "1)" duplicates inputs. It's not unreasonable to assume they are
still available by the time you finalize your structure.
But.. as you pointed out space is cheap and personally I find it much
easier to have relevant arrays of data centralized in one place (file)
rather than scattered across hard drive.

All the best,
Pavel


Re: [ccp4bb] resolution limits

2017-07-26 Thread Pavel Afonine
Andrew,

phenix.refine may not use reflection-outliers (Read, R. J. (1999). Acta
Cryst. D55, 1759–1764.). Typically this is just a few reflections. If you
have a good reason to disable this, then use
xray_data.outliers_rejection=false.

P.S.: There is Phenix mailing list for Phenix-related questions.

Pavel

On Wed, Jul 26, 2017 at 12:36 AM, Andrew Marshall <
andrew.c.marsh...@adelaide.edu.au> wrote:

> Dear crystallographers,
>
> I have two datasets that were merged/scaled using ccp4's aimless, with
> resolution ranges of 52-1.7 and 57-1.9. However, upon refinement, the
> resolution range used by phenix.refine is 36-1.7 for one and 104-1.9 for
> the other. 1) Why does phenix.refine change the low resolution limits of my
> processed data? 2) How can I prevent this?
>
> Thanks,
>
> Andrew
>


Re: [ccp4bb] Chain ID number limit!

2017-07-24 Thread Pavel Afonine
Hi Lijun,

it's not a problem if you use mmCIF or PDB with two-letter chain ID (both
supported in Phenix).

Pavel

On Mon, Jul 24, 2017 at 5:09 PM, Lijun Liu  wrote:

> Hi:  this must be an old problem but I would like to know if there are
> other ideas to make things easier.
>
> I solved a structure that contains 240 helices of identical sequences in
> the asymmetric unit.  Handling so many chains is really a headache as pdb
> contains only a single column for chain ID (currently support up to 61
> chains).  I had to combine some (say a tetramer) as a single chain for a
> trick, which made me use just enough letters/numbers (A-Z,1-9,a-z).
> However this will need further manual dealing with OXTs (currently I cheat
> with single N of a residue) and raise new problems (like restraints).  Some
> softwares does even not recognize chain IDs like a-z.  SegID might be
> another trick however nowadays many softwares won't take that part, so a
> down-to-chain rigid body / TLS refinement could be impossible, without the
> combination trick.
>
> With tricks I am ok to make things going?  But is there a solution really
> solve the many-chain problem with PDB?
>
> Best,
>
> Lijun
>
>
>
> Sent from my iPhone


Re: [ccp4bb] Total occupancy of two conformations of one nucleotide is over 1.0? Need help!

2017-07-21 Thread Pavel Afonine
Hi Wei,

thanks for sharing the data (off-list). I did some detective work and yes,
Clemens is correct: what you see is the effect of bulk-solvent. After
adjusting the solvent contribution (mask) in regions occupied by altlocs A
and B the positive density mostly disappears.

Pavel

On Fri, Jul 21, 2017 at 12:26 AM, Clemens Vonrhein <
vonrh...@globalphasing.com> wrote:

> Dear Wei,
>
> remember that you might have "something else" in the location occupied
> by each alternate conformation when it is not occupied by that
> particular conformation. If you only model two alternate conformations
> you are saying something like
>
>  that space A is occupied 50% of the time by this A conformation and
>  50% it is vacuum
>
>  that space B is occupied 50% of the time by this B conformation and
>  50% it is vacuum
>
> It is more likely that you will have space A occupied N% by altConf A
> and (100-N)% e.g. by water/solvent. And for B you have (100-N)%
> altConf B and N% e.g. water/solvent. So you will need to model
> everything marked as N% as altConf A and everything marked (100-N)% as
> altConf B - including water/solvent.
>
> Because this is not yet done, the occupancy refinement might try to
> explain the non-vacuum density (water/solvent) by increasing the
> occupancy of each conformation so they sum up to larger than 1.
>
> Does that make sense?
>
> Cheers
>
> Clemens
>
> PS: in BUSTER (http://www.globalphasing.com/buster/) you can restrain
> the summed occupancy to one, which can help clarifying how to
> model the water/solvent region underneath each conformation
> ... depending on data quality/resolution of course. I'm sure other
> refinement programs have a similar feature.
>
> PPS: it can be sometimes useful to start refinement once from
> A=0.1/B=0.9 and a second run with A=0.9/B=0.1. Refinement should
> reach very similar final values in both cases - which is also a
> good way of providing confidence in the final results, I think.
>
>
> On Fri, Jul 21, 2017 at 01:10:15AM +, Wang, Wei wrote:
> > Hi Everyone,
> >
> >
> > One quick question:
> >
> >
> > When I do phenix refinement, I see continuous omitted map at one RNA
> chain 3'-end (Fig1).
> >
> > There is no possibility of next nucleotide because I have built
> full-length RNA sequence, which is well fitted into density.
> >
> > Hence two conformations is most possible for the last nucleotide. And
> our biochemical data also supported the result of two conformations.
> >
> > However, I found the occupancy is always > 1.0 (fig2 and fig3), when I
> did refinement of occupancy using phenix refinement,.
> >
> > I also think about the possibility of small molecules in the crystal
> buffer. But in most structures of this protein, there is always no small
> molecule here.
> >
> >
> > Any suggestions for occupancy refinement? I will appreciate your great
> help.
> >
> >
> > Best,
> >
> > Wei
> >
> >
> >
> > [cid:2b30f1a8-2a3a-4483-ac12-310f4bbed70b]
> >
> >
> >
> >
> >
> >
>
>
>
> --
>
> *--
> * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com
> * Global Phasing Ltd., Sheraton House, Castle Park
> * Cambridge CB3 0AX, UK   www.globalphasing.com
> *--
>


Re: [ccp4bb] Questionable Data collection and refinement statistics for 5XQL

2017-06-29 Thread Pavel Afonine
I agree with Dominika, I can't see major problems with this entry (I also
did some quick refinement and briefly looked at maps). Reported R factors
match re-calculated values using data from PDB, which is good.

Smaller issues I see are:
- no solvent (water) in the model, while density suggests some;
- maps don't look like 2.5A resolution, which is perfectly expectable given
data completeness (overall 81%):

  ResolutionCompl
35.051-13.721   89.38
13.660-11.061   95.19
11.024-8.85898.41
 8.848-7.119   100.00
 7.115-5.723   100.00
 5.714-4.596   100.00
 4.595-3.692   100.00
 3.692-2.96795.92
 2.966-2.49456.98

and effective resolution along axes a,b,c:  2.453  2.453  3.167 A.

- model contains 4% of rotamer outliers, some of them can be trivially
fixed.
- Xtriage shows three yellow "traffic lights".

I'm sure many PDB entries (especially older ones) would have something that
you could do better or fix using modern tools.

Pavel

On Thu, Jun 29, 2017 at 10:48 AM, Dominika Borek 
wrote:

> Dear C-Daddy,
>
> Did you look at the maps? Do you see any astonishing misinterpretations
> there?
> Do you think that the completeness in the last resolution shell would
> affect the maps and the model? If so, why?
>
> There are many possible reasons for the discrepancy you pointed out. In
> I422 a=b, alpha=90.00, so typos in the table are the most probable reason.
> I did look at the maps after running a quick refinement. Both the structure
> and the ligand are fine. I would probably add solvent molecules myself, but
> some conservative crystallographers prefer not to do it, even at 2.5 A.
>
> In other words, there is nothing wrong with this deposit. I would even say
> that the level of sloppiness is below the average for this one.
>
> D.
>
>
>
>
> On 2017-06-29 11:07 AM, CDaddy wrote:
>
>> Dear colleagues,
>>
>> I am really astonished by a recently released structure 5XQL. This
>> structure was just published in BBRC with a super fast process
>> (accepted overnight). Significant inconsistences were observed when I
>> compared the Data collection and refinement statistics in the paper
>> and at PDB website. The paper shows the crystal belong to  I 4 2 2
>> with  a=135.77, b=136.11, c=95.13 (Å) ; α=90.01. The resolution is
>> 2.5Å with  completeness of 99.7 (99.1). However when I checked the
>> released structure I got  a= b=135.94, c=95.13 (Å) ; α=90.0. The
>> resolution is 2.5Å with  completeness of 81.5 (44.0). The
>> completeness of the highest resolution shell is so low that 2.5Å
>> seems unreasonable. At first I thought that the authors could be
>> rookies in structural biology. But the molecular replacement in this
>> paper could be very difficult due to very low sequence identity
>> between the search model and the final structure. It was unlikely that
>> two new hands could solve it easily. Is there anyone who has this kind
>> of experience and know why?
>>
>> With best wishes,
>> Richard
>>
>
> --
> Dominika Borek, Ph.D. *** UT Southwestern Medical Center
> 5323 Harry Hines Blvd. *** Dallas, TX 75390-8816
> 214-645-9577 (phone) *** 214-645-6353 (fax)
>


Re: [ccp4bb] Problem with Mg2+ binding site refinement

2017-06-15 Thread Pavel Afonine
Hi Mubinur,

try without "metal restraints" and see if that helps. As others suggested,
make sure 2+ is present in rightmost column of PDB file. The side may be
partially occupied, so refining occupancy of Mg2+ is not a bad idea.

Pavel

On Wed, Jun 14, 2017 at 2:44 PM, Mohammad Rahman 
wrote:

> Dear All,
>
> I am trying to refine a tetrameric enzyme structure that was determined at
> 2.7 Å. The structure contains a Mg2+  binding site in each monomer.  After
> refinement,   in Mg2+ binding site  negative density (red) has been found
> as in pictures. I am using Phenix refine, and during refinement, metal
> restrains were used. Herewith I have attached the refinement statistics.
>
> please help me to overcome this problem.
>
> Thank you
>
> -Mubinur
>
>


[ccp4bb]

2017-05-19 Thread Pavel Afonine
Yes, that is what I have been doing. Build one subunit and assemble into
> tetramer before realspace refinement (with "ncs" constraints). I used
> tetramer for refinement because I want the distances between the inter
> subunits interaction partners to be considered. The problem is, whenever I
> want to make some manual adjustments of the model afterwards, I have to
> break it into monomer and repeat the whole process again. I assume if the
> map is in P4 spacegroup, I only need to modify one subunit of this protein
> and changes will be automatically applied to the other subunits. Am I
> right?
>

So you have 4 copies and NCS group consisting of one master (or reference)
copy and three related by NCS symmetry. Then you make changes in master
copy and when you run refinement with NCS constraints the changes will be
propagated onto the related copies by applying NCS constraints. This is how
this works in phenix.real_space_refine. So no need to make identical
changes in all 4 copies or go to P4.



> Another question is, when I tried to refine my model using phenix
> realspace refinement (energy minimization and adp), the statistics
> generally become better (map CC, rotamer outlier etc), however, the
> ramachandron statistics become worse, with increase number of outliers
> (from below 1% to around 5%) and allowed (from several percent to 10-20%).
> Do you know what could be the cause? I know I am asking the right person...
>

This is not expected (about worsening Ramachandran plot outliers). I'm sure
we can solve this problem if you send me model and map files (and
resolution) off list (if files too large to send by email please use
Dropbox or similar file sharing tools).

Pavel


[ccp4bb]

2017-05-18 Thread Pavel Afonine
Just use P1 and "ncs" constraints. What's the problem? Or just keep entire
map and have only symmetry independent copy to work with until finishes,
then make the whole molecule. For real-space refinement it's totally
irrelevant whether you have whole molecule or 1/Nth of it. So.. it isn't
clear what the problem is..
Pavel

On Thu, May 18, 2017 at 10:06 PM, Qingfeng Chen  wrote:

> Hi,
>
> I have an EM map of a tetrameric protein. It was painful to work with this
> map since it is in P1 spacegroup, although 4-fold symmetry was already
> applied during map reconstruction.
>
> I noticed that people used MAPMAN to transform spacegroup, however, it
> seems not working for me. The map remained in P1 spacegroup afterwards.
>
> I used mtz file converted from .mrc and the tetrameric protein model as
> input and choose "run fft to generate simple map". I also specified "output
> map in ccp4 format to cover all atoms in pdb". In "infrequently used
> options", I input P4 in "generate map in spacegroup". Everything else was
> left as default.
>
> Any suggestions will be appreciated.
>
> Thanks!
>


Re: [ccp4bb] Using Coot and CCP4 program for cryoEM data

2017-05-17 Thread Pavel Afonine
Hi,

2. How do I convert cryoEM map file to MTZ file?
>

While technically you can do it, normally there is absolutely no need to do
it. In cryo-EM the map is your data, not reflection data (structure
factors!). So no need to 'massage' your data (the map) by converting it
into "Fobs" and storing as reflection data in MTZ file.


> 3. Can I also use Phenix for this purpose?
>

Yes. Some relevant information:
http://phenix-online.org/presentations/latest/real_space_refine_web.pdf
http://phenix-online.org/documentation/


 Pavel

P.S.: there is Phenix mailing list for Phenix-specific questions (which
applies to your question #3 above).


Re: [ccp4bb] very high B-factor

2017-05-04 Thread Pavel Afonine
Hi,


I'm working on a crystal structure with resolution of 2.2A. At the final
> step, I use different strategies to refine the structure, they are:
> no4: strategy=individual_sites+individual_adp+tls / set_b_iso=20
> results: Rwork/free=0.2052/0.2658  b-factor=11.4/136.8/48(min/max/average)
>
> no5: strategy=individual_sites+individual_adp+tls / set_b_iso=10 /
> optimize_xyz/adp_weight=true
> results: Rwork/free=0.2161/0.2639  b-factor=11.3/135.2/48.4(min/
> max/average)
>


make sense to me, both - the strategy and results. Getting the same results
using different starting B is also a good sign.



> no6: strategy=individual_sites+individual_adp / anisotropic for all
> residues and isotropic for water /
>  set_b_iso=10 / optimize_xyz/adp_weight=true
> results: Rwork/free=0.2183/0.2706  b-factor=10.9/144.6/45.7
> (min/max/average)
> PS: the results is read from pdb file
>

This does not make sense: 2.2A isn't good enough to refine all residues
with anisotropic ADP.



> The results showed that the strategy of no5 is the best one.
>


Both, no4 and no5 looks same to me.



> And my questions are:
> 1. Which strategy should I choose to refine my structure? Or any other
> suggestions to refine the structure at 2.2A resolution?
>


Your no4 and no5 look fine. Make sure you let phenix.refine to add water
automatically as part of refinement run. Check manually at the very final
stage.



> 2. Does it possible that some residues have very high B-factor in "B
> factor variance Graphs", while in the pdb file, the b-factor of
> corresponding residues are relatively low? For example, one residue have
> B-factors of 417 in "B factor variance Graphs", but in PDB file the b
> factor is 76. Does the two factor mean the same thing?
>


I don't know how that analysis works. Perhaps it's looking at variance of
local Bs not the absolute value.



> 3. If i want to set the weight manually, which parameter should i set,
> wxc/wxc_scale? or others?
>

wxc_scale for coordinates, wxu_scale for ADP. Normally, though, you are not
expected to do this if you let the program to optimize weights.

Pavel


Re: [ccp4bb] peroxy-glutamate?

2017-05-03 Thread Pavel Afonine
Dear Gerard,

I am sure others
> are certain to propose a cooler name for that very same type of map
> some day ;-) .
>

a free tip: how about DDM (Decarboxylation Detector Map)?

All the best,
Pavel


Re: [ccp4bb] CH-bond length discrepancies

2017-04-29 Thread Pavel Afonine
Also, see figure 4 here:
http://phenix-online.org/papers/dz5209_reprint.pdf
that illustrates the difference.
Pavel

On Fri, Apr 28, 2017 at 10:33 AM, Bernhard Rupp 
wrote:

> Dear Fellows of the Bond,
>
>
>
> when validating a QM refined homology model with Molprobity, I noticed
> various 8 sigma deviations in the carbon-hydrogen bond distances.
>
> Out of curiosity, I then used refmac to calculate riding Hs for the same
> model, and at least in one instance (N-H backbone) there are
>
> significant differences between Molprobity and Refmac H bond distances
> (differences to the QM distances in other
>
> instances I find interesting, but less relevant for us).
>
>
>
> The riding H vs Molprobity presumably should be consistent, because if we
> use them in VDW restraints but
>
> they differ from the validation target, systematic bias will occur. I have
> no feel how significant that effect
>
> might be – maybe someone more erudite can comment.
>
>
>
> Examples
>
>
>
> distance  MP   REF QM
>
> backbone N-H   0.861.011.00
>
> phenyl C-H 0.930.931.09
>
>
>
> Best, BR
>
>
>
> PS: If someone has accurate experimental values for CH distances I’d
> appreciate a link.
>
> No access to CSD.
>
>
>
> --
>
> Bernhard Rupp
>
> Crystallographiae Vindicis Militum Ordo
>
> http://www.hofkristallamt.org/
>
> b...@hofkristallamt.org
>
> +1 925 209 7429 <(925)%20209-7429>
>
> +43 767 571 0536 <+43%207675%20710536>
>
> --
>
> Many plausible ideas vanish
>
> at the presence of thought
>
> --
>
>
>


Re: [ccp4bb] CH-bond length discrepancies

2017-04-28 Thread Pavel Afonine
Note, Molprobity has an option to use longer (neutron) X-H distances.
Pavel

On Fri, Apr 28, 2017 at 11:46 AM, Tristan Croll  wrote:

> I believe the reason for the discrepancy here is that MolProbity by
> default places the hydrogens according to the centroid of the electron
> cloud (most relevant to x-ray crystallographic data) rather than the
> nuclear position. In a polar bond like N-H the difference can be quite
> substantial.
>
> Cheers,
>
> Tristan
>
>
>
> Tristan Croll
> Research Fellow
> Cambridge Institute for Medical Research
> University of Cambridge CB2 0XY
>
>
>
>
> On 28 Apr 2017, at 18:33, Bernhard Rupp  wrote:
>
> Dear Fellows of the Bond,
>
>
>
> when validating a QM refined homology model with Molprobity, I noticed
> various 8 sigma deviations in the carbon-hydrogen bond distances.
>
> Out of curiosity, I then used refmac to calculate riding Hs for the same
> model, and at least in one instance (N-H backbone) there are
>
> significant differences between Molprobity and Refmac H bond distances
> (differences to the QM distances in other
>
> instances I find interesting, but less relevant for us).
>
>
>
> The riding H vs Molprobity presumably should be consistent, because if we
> use them in VDW restraints but
>
> they differ from the validation target, systematic bias will occur. I have
> no feel how significant that effect
>
> might be – maybe someone more erudite can comment.
>
>
>
> Examples
>
>
>
> distance  MP   REF QM
>
> backbone N-H   0.861.011.00
>
> phenyl C-H 0.930.931.09
>
>
>
> Best, BR
>
>
>
> PS: If someone has accurate experimental values for CH distances I’d
> appreciate a link.
>
> No access to CSD.
>
>
>
> --
>
> Bernhard Rupp
>
> Crystallographiae Vindicis Militum Ordo
>
> http://www.hofkristallamt.org/
>
> b...@hofkristallamt.org
>
> +1 925 209 7429 <(925)%20209-7429>
>
> +43 767 571 0536 <+43%207675%20710536>
>
> --
>
> Many plausible ideas vanish
>
> at the presence of thought
>
> --
>
>
>
>


Re: [ccp4bb] NCS difference

2017-04-24 Thread Pavel Afonine
I suspect most (if not all) refinement software now have a nice way to deal
with NCS in refinement locally. Technically, this means you can use NCS
restraints at any resolution and software should be able to be careful and
not wipe out local differences between NCS copies. In phenix.refine this is
done by parameterizing NCS restraints in torsion angle space and using
top-out potential as restraint target, all described here in great details:

http://journals.iucr.org/d/issues/2014/05/00/rr5054/rr5054.pdf

Pavel

On Mon, Apr 24, 2017 at 5:42 AM, Clemens Vonrhein <
vonrh...@globalphasing.com> wrote:

> Dear all,
>
> On Mon, Apr 24, 2017 at 08:15:57AM +, Bert Van-Den-Berg wrote:
> > Not quite sure what you mean but I suppose you refined with NCS
> > restraints and the red bar means that your chains in those regions
> > are not identical. I would turn NCS restraints off during
> > refinement, with your resolution there is no real good reason to
> > include them.
>
> While that might have been understandable advice in the days when we
> used purely superposition/rmsd-based NCS restraints/constraints (and
> true differences between NCS-related copies became a nightmare to
> define/model), this should no longer be true for the majority of
> refinement programs out there.
>
> We now use much "softer" NCS restraints that allow for local
> similarity - which at the same time allows for large differences like
> domain/loop movements etc. Most programs will at the same time detect
> local outliers and prune those. See e.g. [1] for such an
> implementation in BUSTER [2] (-autoncs flag) ... I'm sure other
> programs use similar approaches.
>
> Anyway, the traditional recommendation to drop NCS restraints at later
> stages of refinement was nearly always based on procedural
> complexities and should no longer hold true: there is no reason to
> drop NCS restraints at any (within reason) resolution I think. Of
> course, the real differences need to be taken care of by exclusion
> (what we call 'pruning', mostly done automatically anyway).
>
> Cheers
>
> Clemens
>
> [1] Smart, O. et al (2012). Acta Cryst. D68, 368-380.
> [2] http://www.globalphasing.com/buster/
>


Re: [ccp4bb] NCS difference

2017-04-24 Thread Pavel Afonine
Minimizing a red bar may be tricky.. Have you tried to make it less red
(blue or may be green)? Otherwise Rw/Rf~20/25 is just fine at 2.2A
resolution. What exactly your worry is about?
Pavel

On Mon, Apr 24, 2017 at 12:48 AM, Vipul Panchal 
wrote:

> Hi all,
>
> I am solving structure of one of the acyltransferse protein. We have
> collected data at 2.16A resolution. Currently the Rfree is 0.2508 and
> Rwork is 0.2042.
>
> *My query is regarding NCS difference.* Under validation tool of coot
> while looking for NCS differene, i can find some residues with red bar. *Can
> some one suggest me how may i minimize it if i am expected to do it?*
>
>
> --
> Vipul Panchal
> Senior Research Fellow,
> Respiratory disease and biology,
> CSIR-IGIB
> (M)-9540113372
>


Re: [ccp4bb] software or tool for Individual residue in a Ramachandran plot graph?

2017-03-25 Thread Pavel Afonine
Except that Procheck is now ages behind the standard, with Molprobity being
the standard. I'm not sure even if Coot uses the latest libraries. Those I
quoted in example below come from latest Molprobity (Phenix that is) and
are the latest.

Pavel


On Fri, Mar 24, 2017 at 2:55 PM, Edward A. Berry  wrote:

> On 03/23/2017 11:39 PM, Alex Lee wrote:
>
>> Dear All,
>>
>> Is there a tool or software which can give Ramachandran information of
>> individual residues in a plot?
>>
>> I used Coot to check for Ramachandran plots, but it shows all the
>> residues in a coordinate I put in Coot, not individual one. I also use
>> "residue info" in coot, it tells Ramachandran "phi psi" angles of
>> individual residue, but it does not show it in a plot, only numbers.
>>
>> Thanks ahead for any input.
>>
>> Well, you can always AWK out 3 residues and run procheck on them,
> something like:
>
>   awk '$1~/ATOM/ && $5~/B/ && $6~/^6[567]/' /a/pdb/pdb2h88.ent >w.pdb
>   procheck w.pdb 1.8
> followed by:
>   gs w_01.ps
> or:
>   ps2pdf w_01.ps
>   acroread !$
>
> (The AWK command will have to be tweaked if fields run together in the
>   pdb due to large numbers or alt. conformations for these three residues)
>
> I agree such a feature would be useful in coot. Sometimes you want to
> know if an outlier is just outside or way outside, or if it is halfway
> between two allowed regions, and with large, low-quality structures it is
>  hard to find the residue in the crowded rama plot.
> Clickable points in the R plot fills the bill going one way, now
> highlighting
> points corresponding to selected residue would be the other half.
> eab
>


Re: [ccp4bb] software or tool for Individual residue in a Ramachandran plot graph?

2017-03-24 Thread Pavel Afonine
May be not exactly what you want, but should be close:

phenix.secondary_structure_restraints 1yjp.pdb

then here you have options

- for output format:

format = *phenix phenix_refine phenix_bonds pymol pdb refmac kinemage

- for search  (annotation method):

search_method = *ksdssp mmtbx_dssp from_ca cablam
I suggest you please with them and see which one suits you most.

Pavel



On Fri, Mar 24, 2017 at 1:18 PM, Xiao Lei <xiaolei...@gmail.com> wrote:

> Thanks Pavel,  is there a command that can tell secondary structure
> assignment based on Rama plot of each residue beside phi and psi? for
> example :
>  A   2  ASN:56.93:-60.58:141.19:Favored:General   alpha helix
>  A   3  ASN:48.44:-119.25:125.15:Favored:General  alpha helix
>
> On Fri, Mar 24, 2017 at 1:09 PM, Pavel Afonine <pafon...@gmail.com> wrote:
>
>> Trivial using command line. Example:
>>
>> - get a file from PDB:
>>
>> phenix.fetch_pdb 1yjp
>>
>> - get all phi/psi for all residues:
>>
>> phenix.ramalyze 1yjp.pdb
>> residue:score%:phi:psi:evaluation:type
>>  A   2  ASN:56.93:-60.58:141.19:Favored:General
>>  A   3  ASN:48.44:-119.25:125.15:Favored:General
>>  A   4  GLN:16.23:-126.16:112.81:Favored:General
>>  A   5  GLN:55.13:-114.98:126.76:Favored:General
>>  A   6  ASN:6.17:-116.42:97.69:Favored:General
>> SUMMARY: 5 Favored, 0 Allowed, 0 Outlier out of 5 residues (altloc A
>> where applicable)
>> SUMMARY: 0.00% outliers (Goal: < 0.2%)
>> SUMMARY: 100.00% favored (Goal: > 98%)
>>
>> Pavel
>>
>>
>> On Fri, Mar 24, 2017 at 10:37 AM, Nigel Moriarty <nwmoria...@lbl.gov>
>> wrote:
>>
>>> Alex
>>>
>>> It seems that nobody has answered your question. I'm not sure what you
>>> can do in CCP4, but if I understand your question correctly, you can
>>> perform a comprehensive validation in Phenix complete with Ramachandran
>>> plot including clickable points relating to your residues which allow you
>>> to see the residues in Coot.
>>>
>>> Happen to help further on the PHENIXBB or off-line.
>>>
>>> Cheers
>>>
>>> Nigel
>>>
>>> ---
>>> Nigel W. Moriarty
>>> Building 33R0349, Molecular Biophysics and Integrated Bioimaging
>>> Lawrence Berkeley National Laboratory
>>> Berkeley, CA 94720-8235
>>> Phone : 510-486-5709 <(510)%20486-5709> Email : nwmoria...@lbl.gov
>>> Fax   : 510-486-5909 <(510)%20486-5909>   Web  : CCI.LBL.gov
>>>
>>> On Thu, Mar 23, 2017 at 8:39 PM, Alex Lee <alexlee198...@gmail.com>
>>> wrote:
>>>
>>>> Dear All,
>>>>
>>>> Is there a tool or software which can give Ramachandran information of
>>>> individual residues in a plot?
>>>>
>>>> I used Coot to check for Ramachandran plots, but it shows all the
>>>> residues in a coordinate I put in Coot, not individual one. I also use
>>>> "residue info" in coot, it tells Ramachandran "phi psi" angles of
>>>> individual residue, but it does not show it in a plot, only numbers.
>>>>
>>>> Thanks ahead for any input.
>>>>
>>>>
>>>
>>
>


Re: [ccp4bb] Ramachandran statistics and referee responsibility

2017-03-08 Thread Pavel Afonine
Hi Evette,


(1) best practices in refining against  lower resolution data (~4 angstrom)
> to achieve the best model,
>


obtain a model that fits data best under requirement that it has zero
geometry violations (Ramachandran, Cbeta deviations, rotamers, CABLAM,
etc..).

Note, a geometry outlier (Ramachandran plot outlier, for instance) does not
necessarily mean wrong. Example of a valid outlier: page 21 here:
http://phenix-online.org/presentations/latest/pavel_validation.pdf

However, low-resolution data is unlikely to justify outliers, that's why
zero is the goal (unless there is no other strong reasons to support the
outlier).


> One might encounter a hypothetical situation where standard refinement
> approaches gave a model with poor Ramachandran statistics.  Imposing
> Ramachandran restraints gave a model with improved Ramachandran statistics
> but at the expense of higher Rfree.
>

This is likely a software issue or incorrect use by the user. Contact
refinement software developers to resolve the issue.

Pavel


Re: [ccp4bb] Removing TLS component of B factor of deposited PDB files to input to refmac

2017-03-08 Thread Pavel Afonine
Normally, these days at least, a model that is result of TLS refinement
contains total B factor in ANISOU records and its TLS component in TLS
records (REMARK3), with Btotal = Btls+Bresidual.

If TLS matrices are available, it's trivial to calculate Btls from TLS
matrices in REMARK3 and subtract it from Btotal (ANISOU), which will give
you Bresidual.

Some of older PDB files are likely to have Bresidual in ATOM records and
TLS component in REMARK3 as TLS matrices. In this case, to get total
Btotal, you need to compute Btls from TLS and add to Bresidual.

I guess TLSANAL is the CCP4 tool to do this, and phenix.tls will do
conversion both ways as well.

Pavel

On Wed, Mar 8, 2017 at 6:34 AM, Eleanor Dodson 
wrote:

> Actually I think it is pretty dangerous to trust the TLS stuff in the PDB
> header - there is a muddle between B_residual and B_merged and no adequate
> description in the header.
>
> Unless you are planning on doing many many repeats I would re-refine
> before checking the map...
> eleanor
>
> On 8 March 2017 at 14:16, Eleanor Dodson 
> wrote:
>
>> TLSANL?
>> Eleanor
>>
>> On 8 March 2017 at 14:08, Nicholas Keep 
>> wrote:
>>
>>> It would be nice to be able to run zero cycles of refmac to get a map
>>> etc direct from a PDB file.
>>>
>>> However due the PDB requiring the TLS component of B factor to be
>>> included this does not work.
>>>
>>> Is there software to remove the TLS component so a zero cycle of refmac
>>> can be run.
>>>
>>> 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
>>>
>>
>>
>


Re: [ccp4bb] Estimating the amount of missing electron density for a model

2017-02-22 Thread Pavel Afonine
Hi,

Is there a straight-forward way to estimate the amount of missing electron
> density that a particular protein structure is missing based on the
> difference between Fo and Fc?
>

Any refinement or map calculation software that uses likelihood-based
approach does this routinely. In phenix.refine and phenix.maps I coded this
approach : Acta Cryst. (2002). A58, 270-282. Here it calculates alpha/beta
parameters by comparing Fo and Fc taken from free set. alpha is a function
of model error, and beta is proportional to amount of missing scattering.
If you look up the formulas it should be possible to convert alpha into
error in coordinates (in A) and beta into number of missing atoms (of some
general type). ML based estimate of error in model that phenix.refine
reports is actually done this way.

Pavel


Re: [ccp4bb] Composit omit map vs. ligand

2017-02-16 Thread Pavel Afonine
Dear Gerard,
Thank you so much for letting us know of the reference and details about
your long-standing BUSTER method for ligand density maps which we now see
is very similar to our recent polder map method.  We apologize for not
being aware of the early reference and we will be very sure to cite it in
future publications.
Very best regards,
Pavel


On Thu, Feb 16, 2017 at 5:35 AM, Gerard Bricogne <g...@globalphasing.com>
wrote:

> Dear Pavel,
>
>  As much as I would have wished to, I was unable to contribute to
> this thread for the past week because of more pressing matters. I hope
> it hasn't entirely gone cold in the minds of CCP4BB readers.
>
>  I want to congratulate the Phenix developers for having come up
> with such a catchy name for a method that was first conceived, and
> implemented in autoBUSTER, by Clemens Vonrhein over 12 years ago, and
> has been abundantly exercised and appreciated for its usefulness by
> its users (especially, drug discovery companies) ever since.
>
>  You do mention BUSTER:
>
>   The program BUSTER (Bricogne et al., 2016) allows the exclusion of
>   regions from bulk solvent by processing an additional file which
>   describes the binding site (without resembling the putative ligand).
>   Furthermore, statistical treatment of non-uniformity of bulk solvent
>   or as yet unmodeled regions has been discussed ... [with two more
>   BUSTER-related references dated 2000 and 2004]
>
> but the 2016 date (which is the one we recommend that users cite for
> the latest version of the program) rather obliterates any sense of
> chronology when it comes to the specific underlying idea of "Polder
> maps" and of its prior implementation mentioned above.
>
>  We (here) can certainly not claim to be champions when it comes
> to publicizing our work through the usual channel of polished academic
> publications, as our lives as developers are driven and dominated by
> rather different imperatives. However there happens to be an official
> record of the origins of that method in
>
>  http://journals.iucr.org/a/issues/2005/a1/00/a32958/a32958.pdf
>
> or (for a prettier format)
>
>  http://dx.doi.org/10.1107/S0108767305089415
>
>  To complete that record: this development was released to our
> Consortium members in November 2003, and to academic users at large in
> July 2009. It is described in quite explicit terms in the online
> documentation we later wrote for academic users and posted on our
> external Wiki, e.g.
>
> http://web.archive.org/web/20121216164211/http://www.
> globalphasing.com/buster/manual/autobuster/manual/autoBUSTER5.html
>
>  In spite of the lack of a standard academic reference, this
> feature has therefore been an open secret for a very long time under
> the name of "the -L option" in autoBUSTER, where L stands for "ligand
> chasing".
>
>
>  So, again, congratulations for finding such a good name for the
> method and for publishing a collection of nicely illustrated examples
> of its usefulness. Your presentation, however, might be seen as rather
> economical in its acknowledgment of "prior art" - a notion that surely
> has to be recognised as existing outside the confines of standard,
> neatly packaged, immediately quotable Acta D publications :-) .
>
>
>  With best wishes,
>
>   Gerard.
>
> --
> On Thu, Feb 09, 2017 at 03:45:22PM -0800, Pavel Afonine wrote:
> > In addition to excellent Kay's reply..
> >
> > Also make sure to check refined B factors. Note, if the ligand is not
> there
> > then that volume is likely filled with bulk-solvent. Now low occupancy in
> > combination with very large B factors may approximate bulk-solvent quite
> > well. The Polder map along with three CC values that its calculation
> > procedure reports should give you the answer whether the ligand is there
> or
> > not.
> >
> > Pavel
> >
> > On Wed, Feb 8, 2017 at 2:43 AM, Kay Diederichs <
> > kay.diederi...@uni-konstanz.de> wrote:
> >
> > > Dear Petr,
> > >
> > > if I understand correcty, the mFo-DFc density (1)  shows almost
> nothing,
> > > but the 2mFo-DFc  (2) as well as the composite omit map (3) show the
> ligand?
> > >
> > > As you say, the apparent contradiction between (1) versus (2)&(3) is
> > > unexpected. One explanation could be that the Fc are simply too bad,
> i.e.
> > > the model not good enough to result in useful signal in the difference
> > > map.  OTOH, that you see the ligand in (2) may be simply model bias,
> so is
> > > not meaningful. (3) is hopeful since there is n

Re: [ccp4bb] Composit omit map vs. ligand

2017-02-09 Thread Pavel Afonine
In addition to excellent Kay's reply..

Also make sure to check refined B factors. Note, if the ligand is not there
then that volume is likely filled with bulk-solvent. Now low occupancy in
combination with very large B factors may approximate bulk-solvent quite
well. The Polder map along with three CC values that its calculation
procedure reports should give you the answer whether the ligand is there or
not.

Pavel

On Wed, Feb 8, 2017 at 2:43 AM, Kay Diederichs <
kay.diederi...@uni-konstanz.de> wrote:

> Dear Petr,
>
> if I understand correcty, the mFo-DFc density (1)  shows almost nothing,
> but the 2mFo-DFc  (2) as well as the composite omit map (3) show the ligand?
>
> As you say, the apparent contradiction between (1) versus (2)&(3) is
> unexpected. One explanation could be that the Fc are simply too bad, i.e.
> the model not good enough to result in useful signal in the difference
> map.  OTOH, that you see the ligand in (2) may be simply model bias, so is
> not meaningful. (3) is hopeful since there is no model bias.
>
> I would suggest to
> - refine the occupancy, to find out why the density is so weak
> - calculate a  (Fo,soak - Fo,native) (4) map with phases from a model
> unbiased by the ligand
> - try a Polder map (5)
>
> - If the occupancy is around 0.5 or higher, that would be a good sign.
> - but if you don't see density in (4) and (5), then your ligand is
> probably not there in any useful amount
>
> I consider (4) as the most sensible method to show presence of the ligand,
> and it should convince reviewers.
>
> HTH,
>
> Kay
>
>
>
> On Wed, 8 Feb 2017 09:05:50 +0100, Petr Kolenko 
> wrote:
>
> >Dear colleagues,
> >
> >we have a dataset with potential enzyme:ligand complex at 2.2 AA
> >resolution. The ligand is very good substrate for the enzyme, we used
> >soaking. We do not see the ligand in the regular difference electron
> >density, only five out of twenty atoms. However, the ligand placed at
> >the active site (model used from structure of a mutant variant) is
> >refined well, giving no negative peaks in difference electron density
> >map and nice observed electron density. I have calculated composit omit
> >map with annealing in Phenix (input model did not contain the ligand)
> >and the electron density for the ligand is there.
> >
> >I have my own opinion, but we are desperate to obtain such data (more
> >than 40 crystals already tested). My question is, would this be proof of
> >presence of the ligand with reduced occupancy? Will this map convince
> >the reviewers? Is there any other way to validate presence of the ligand?
> >
> >Best regards,
> >Petr
>


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