Re: [ccp4bb] PDB validation - oligosacchides

Natalie If you send me the model file off-list I can help. BTW, there is a Phenix specific BB that can help with all things Phenix. Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235

Re: [ccp4bb] Automated refinement convergence

I, too, love the smell of cooking (or cooked?) jobs in the morning. Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Email : nwmoria...@lbl.gov Web : CCI.LBL.gov ORCID :

Re: [ccp4bb] problem with phenix in macos sonoma 14.1

Debipreeta There is a fix with instructions on the download page and it is also here on the Phenix bulletin board ( https://phenix-online.org/pipermail/phenixbb/2023-October/025579.html). Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging

Re: [ccp4bb] How to fix ARG planarity outliers?

Vladyslav I would be very interested in seeing the PDB report that you received. If you wish to share, please send it directly to me. Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA

Re: [ccp4bb] O-glycans in coot and phenix/refmac

To the point of refining in Phenix, once you have the glycans in place it should be automatic except for the first link of the tree. Send me the model and I can provide the necessary files for refinement. Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated

Re: [ccp4bb] eLBOW aromatic restraints

Henry There is a PhenixBB that is more relevant to eLBOW questions but if you send me (directly) the inputs you used and tried, I can help you. Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA

Re: [ccp4bb] Issue about cif file of ligand

Ning Can you send the SMILES and the output directly to me? Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Email : nwmoria...@lbl.gov Web : CCI.LBL.gov ORCID :

Re: [ccp4bb] Refinement of ligand with alternate chemical structure

Stuart The sum of occ in these three is 1.3 and it looks like you put the occ in the B-factor column. Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Email : nwmoria...@lbl.gov Web

Re: [ccp4bb] Refinement of ligand with alternate chemical structure

One may need to set a preference in Coot to allow such a situation to be viewed. Paul helped me but I can't find the email. Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Email :

[ccp4bb] Computational Crystallography Newsletter (CCN) submissions

Folks The deadline for submissions to the Computational Crystallography Newsletter (CCN) is 11 JAN 2023. Please consider writing an article of general interest to the community. The Computational Crystallography Newsletter (CCN) is an electronic newsletter for structural biologists, and is

Re: [ccp4bb] Missing double bonds in the ligand

orcid.org/-0001-8857-9464 On Thu, Jul 7, 2022 at 3:06 PM Joel Tyndall wrote: > Does the Schrodinger software read a .cif file? The bond order should be > embedded in there. > > > > *From:* CCP4 bulletin board *On Behalf Of *Nigel > Moriarty > *Sent:* Friday,

Re: [ccp4bb] Missing double bonds in the ligand

Further reading https://en.wikipedia.org/wiki/The_Treachery_of_Images https://phenix-online.org/phenixwebsite_static/mainsite/files/newsletter/CCN_2016_01.pdf#page=10 Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National

Re: [ccp4bb] Easy/Silly question

Yes, MAL was obsoleted about 2 years ago. 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 :

Re: [ccp4bb] CCPBioSim Industry Talk

-5709 Email : nwmoria...@lbl.gov Fax : 510-486-5909 Web : CCI.LBL.gov ORCID : orcid.org/-0001-8857-9464 On Thu, Jun 30, 2022 at 6:10 AM Nigel Moriarty wrote: > Is this meeting still proceeding? My link doesn't work. > > Cheers > > Nigel > > --- > Nigel W. Mor

Re: [ccp4bb] CCPBioSim Industry Talk

Is this meeting still proceeding? My link doesn't work. 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

Re: [ccp4bb] PDB file secondary structure annotations

Neno Can you tell me what version of Phenix you are using? and send me the file in question? Off-list.\ NB. Any files sent to me will be held in strictest confidence. Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National

Re: [ccp4bb] Computational Crystallography Newsletter (CCN) submissions

Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : nwmoria...@lbl.gov Fax : 510-486-5909 Web : CCI.LBL.gov ORCID : orcid.org/-0001-8857-9464 On Tue, Apr 13, 2021 at 1:49 PM Nigel Moriarty wrote: > Folks > > The deadline for submissions to the Comp

[ccp4bb] Computational Crystallography Newsletter (CCN) submissions

Folks The deadline for submissions to the Computational Crystallography Newsletter (CCN) is 11 JUN 2021. Please consider writing an article of general interest to the community. The Computational Crystallography Newsletter (CCN) is an electronic newsletter for structural biologists, and is

Re: [ccp4bb] Fwd: Please register - Phenix Workshops - April 7 & 14

cult for us to be available at > that time > > Kindly let us know if that is a possibility from your end. > > Kind regards, > Rini Chaturvedi > Molecular Medicine > ICGEB, New Delhi > > > On Mon, Apr 5, 2021 at 10:45 PM Nigel Moriarty wrote: > >> Forward in case it

Re: [ccp4bb] Omit maps in phenix and ccp4

Hari I'm happy to take a closer look if you send me the files directly. Phenix has an omit map known as the Polder map that takes care of the solvent masking. Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National

[ccp4bb] Fwd: Thank you for registering - Phenix Workshops - April 7 & 14

-- Forwarded message - From: Ashley Dawn Date: Mon, Apr 5, 2021 at 9:56 AM Subject: Thank you for registering - Phenix Workshops - April 7 & 14 To: Ashley Dawn Cc: Nigel Moriarty , Christopher Schlicksup < cjschlick...@lbl.gov>, phenixdev Good morning,

[ccp4bb] Fwd: Please register - Phenix Workshops - April 7 & 14

-5909 Web : CCI.LBL.gov ORCID : orcid.org/-0001-8857-9464 -- Forwarded message - From: Paul Adams Date: Wed, Mar 31, 2021 at 2:08 PM Subject: Please register - Phenix Workshops - April 7 & 14 To: PHENIX user mailing list Cc: Nigel Moriarty , Ashley Dawn , CC

[ccp4bb] Computational Crystallography Newsletter – Jan. 2021

Folks The latest issue of the CCN is available on the website. Please consider contributing to future issues. The Computational Crystallography Newsletter (CCN) is an electronic newsletter for structural biologists, and is published online every 6 months. Feature articles, meeting announcements

Re: [ccp4bb] Phenix refine distorting a sidechain despite correct density

Igor There is a Phenix BB for your Phenix related questions. You can subscribe here. http://www.phenix-online.org/mailman/listinfo/phenixbb In the meantime, please send the Phenix version and OS to myself and Pavel privately and I'm sure we can help. We may also need the inputs (privately, of

[ccp4bb] Computational Crystallography Newsletter (CCN) submissions

Folks The deadline for submissions to the Computational Crystallography Newsletter (CCN) is 15 DEC 2020. Please consider writing an article of general interest to the community. The Computational Crystallography Newsletter (CCN) is an electronic newsletter for structural biologists, and is

Re: [ccp4bb] Omega angles with molprobity

Joana The developers of molprobity.omegalyze have tried to make their tool easy to use and understand by providing lots of help if you type the command without inputs. This is a common technique that command line tools employ to provide documentation. > molprobity.omegalyze usage:

[ccp4bb] Submissions to the Computational Crystallography Newsletter – 30 NOV 19

Folks Calling for articles and short communications of interest to structural biologists. The deadline for submission for the January 2020 issue is 30 November 2019. The Computational Crystallography Newsletter (CCN) is an electronic newsletter for structural biologists, and is published online

[ccp4bb] Submissions to the Computational Crystallography Newsletter – 15 NOV 19

Folks Calling for articles and short communications of interest to structural biologists. The deadline for submission for the January 202-0 issue is 15 November 2019. The Computational Crystallography Newsletter (CCN) is an electronic newsletter for structural biologists, and is published online

Re: [ccp4bb] [OT] Structure-related pun needed urgently

Everybody enjoys me modelling a protein, but not when I'm modelling shorts! Or Crocs. Nice legs! :-) 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

[ccp4bb] Computational Crystallography Newsletter (CCN) submissions

Folks Calling for articles and short communications of interest to structural biologists. The deadline for submission for the July 2019 issue is 20 May 2019. The previous issue is available http://phenix-online.org/newsletter/ and contains the following. January 2019

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

The "CYS with" means that the main chain is restrained and treated the same as "normal" CYS. However, I'm not sure how the sequence should be handled in the file especially mmCIF. Maybe John Berrisford can comment. Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and

[ccp4bb] Computational Crystallography Newsletter (CCN) submissions

Folks Calling for articles and short communications of interest to structural biologists. The deadline for submission for the January 2019 issue is 20 January 2019. The Computational Crystallography Newsletter (CCN) is an electronic newsletter for structural biologists, and is published online

[ccp4bb] CCN resend

Folks It seems that 50% of people got an email that was 50% greek. I have tried to remove this by removing formatting. Hope this helps. The second 2018 issue of the CCN is now available at http://phenix-online.org/newsletter/ Articles include · Fitting tips #16 – Vicinal disulfides: Have

[ccp4bb] Computational Crystallography Newsletter

Folks The second 2018 issue of the CCN is now available at http://phenix-online.org/newsletter/ Articles include · Fitting tips #16 – Vicinal disulfides: Have you seen one of these strange gems? · CaBLAM: A C-Alpha Based Low-resolution Annotation Method for secondary structure and

[ccp4bb] Computational Crystallography Newsletter (CCN) submissions

Folks Calling for articles and short communications of interest to structural biologists. The initial deadline for submission for the July 2018 issue is 22 June 2018. The Computational Crystallography Newsletter (CCN) is an electronic newsletter for structural biologists, and is published online

Re: [ccp4bb] phenix refinement about cis-proline

Shijun You can ask all the questions you like about Phenix on PhenixBB. However, to answer your question, you can set all peptides to trans using apply_all_trans=True or more specific control using apply_cis_trans_specification { cis_trans_mod = cis *trans residue_selection = None

Re: [ccp4bb] Computational Crystallography Newsletter, Volume 9, Number 1

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 Wed, Feb 7, 2018 at 12:46 PM, Nigel Moriarty <nwmoria...@lbl.gov> wrote: > I am pleased to announce the publication of t

[ccp4bb] Computational Crystallography Newsletter, Volume 9, Number 1

I am pleased to announce the publication of the latest issue of the Computational Crystallography Newsletter: http://www.phenix-online.org/newsletter/ A listing of the articles and short communications is given below. Please note that the newsletter accepts articles of a general nature of

Re: [ccp4bb] covalent bond

Gerado John is correct that you can modify the restraints model to include a covalent bond. Also in more recent version of Phenix, if the input geometry is approximately correct, the bond can be automatically linked. If you send me the input file, I'll take a closer look. Cheers Nigel ---

[ccp4bb] Computational Crystallography Newsletter (CCN) submissions

Folks Calling for articles and short communications of interest to structural biologists. The initial deadline for submission for the January 2018 issue is 20 December 2017. The Computational Crystallography Newsletter (CCN) is an electronic newsletter for structural biologists, and is published

[ccp4bb] Announcing the release of CryoFIT

Dear colleagues, We are excited to announce the release of CryoFIT, a program for fitting atomistic models to cryo-EM maps. The current version is designed for fitting lower resolution maps but this does not preclude use with higher resolution maps. The CryoFIT modules is built on Gromacs and

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

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

[ccp4bb] Comput. Cryst. Newsl. (2017) 2

The latest Computational Crystallography Newsletter is available for download. Below is the clickable table of contents. July 2017 Short Communications - phenix.mtriage: a tool for analysis and validation of cryo-EM 3D reconstructions

[ccp4bb] Lab Evac

Folks The Grizzly Fire (the media loves a interesting name) is more than 50% contained and the lab is now open. The servers are, once again, available for downloading the latest version of Phenix, 1.12. Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated

[ccp4bb] Computational Crystallography Newsletter (CCN) submissions

Folks Calling for articles and short communications of interest to structural biologists. The initial deadline for submission for the July 2017 issue is 30 June 2017. The Computational Crystallography Newsletter (CCN) is an electronic newsletter for structural biologists, and is published online

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

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

[ccp4bb] Computational Crystallography Newsletter, Volume 8, Number 1

I am pleased to announce the publication of the latest issue of the Computational Crystallography Newsletter: http://www.phenix-online.org/newsletter/ A listing of the articles and short communications is given below. Please note that the newsletter accepts articles of a general nature of

[ccp4bb] Computational Crystallography Newsletter (CCN) submissions

Folks Calling for articles and short communications of interest to structural biologists. The initial deadline for submission in the January 2017 issue is 15 December 2016. However, if you have a brilliant idea during your holiday break please don't hesitate to forward it. The Computational

Re: [ccp4bb] phenix.refine error

Yamei You should ask questions about Phenix on the PhenixBB http://www.phenix-online.org/mailman/listinfo/phenixbb. You problem arises because you also need to supply the data_link.cif (most likely file name). Contact me directly if you need more help. Cheers Nigel --- Nigel W. Moriarty

Re: [ccp4bb] Generating Restraints for a Synthetic Peptide

You can also do it using ReadySet! which makes all the calls to eLBOW. phenix.ready_set 2yjd.pdb phenix.geometry_minimization 2yjd.updated.pdb 2yjd.link.edits 2yjd.ligands.cif Cheers Nigel --- Nigel W. Moriarty Building 64R0246B, Physical Biosciences Division Lawrence Berkeley National

Re: [ccp4bb] New ligand 3-letter code

fast, though! locust 123% elbow.get_new_ligand_code AC Unique ligand code : AC3 locust 129% elbow.get_new_ligand_code A?3 Unique ligand code : A?3 eab On 06/06/2015 12:13 PM, Nigel Moriarty wrote: I wrote something a while ago the finds an unused code. % elbow.get_new_ligand_code

Re: [ccp4bb] New ligand 3-letter code

I wrote something a while ago the finds an unused code. % elbow.get_new_ligand_code Unique ligand code : 7V8 % elbow.get_new_ligand_code A Unique ligand code : A6E Cheers Nigel --- Nigel W. Moriarty Building 64R0246B, Physical Biosciences Division Lawrence Berkeley National Laboratory

Re: [ccp4bb] Deletion of hydrogens

Reduce also has an option to remove hydrogens at the command line. [phenix.]reduce -Trim model.pdb Cheers Nigel --- Nigel W. Moriarty Building 64R0246B, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email :

[ccp4bb] Submissions for Comput. Cryst. Newsletter

Folks Calling for articles and short communications of interest to structural biologists. The deadline for submission in the July 2015 issue is 15 June 2015. The Computational Crystallography Newsletter (CCN) is an electronic newsletter for structural biologists, and is published online every 6

[ccp4bb] Computational Crystallography Newsletter - Volume 6, Number 1

I am pleased to announce the publication of the latest issue of the Computational Crystallography Newsletter: http://www.phenix-online.org/newsletter/ A listing of the articles and short communications is given below. Please note that the newsletter accepts articles of a general nature of

[ccp4bb] Submissions for Comput. Cryst. Newsletter

Folks Calling for articles and short communications of interest to structural biologists. The deadline for submission in the January 2015 issue is 17 December 2014 (with some leeway if you are still working on the text, especially as it can be polished over the break). The Computational

Re: [ccp4bb] double bonds in oleoyl-CoA

Wei I ran your SMILES string in the latest version of eLBOW and generated the attached file which has a more reasonable bond length for C9-C10. I notice you are using version 1.8.2 which is from Feb 2013. I suggest you upgrade your Phenix installation to 1.9 (or a nightly build) to obtain all the

[ccp4bb] Computational Crystallography Newsletter - Volume 5, Number 2

I am pleased to announce the publication of the latest issue of the Computational Crystallography Newsletter: http://www.phenix-online.org/newsletter/ A listing of the articles and short communications is given below. Please note that the newsletter accepts articles of a general nature

Re: [ccp4bb] Problem with making covalent bonds in phenix by LINK or edits file

Xiaoming Can you send me the three residues in question (or the whole model) and the files you have so I can point you in the right direction. Cheers Nigel On Thu, Apr 3, 2014 at 1:17 PM, Xiaoming Ren xiaomingre...@gmail.comwrote: Dear all: I am encountering a problem. I built a monomer

[ccp4bb] Computational Crystallography Newsletter - Volume 5, Number 1

Dear Colleagues, I am pleased to announce the publication of the latest issue of the Computational Crystallography Newsletter: http://www.phenix-online.org/newsletter/ A listing of the articles and short communications is given below. Please note that the newsletter accepts articles of a

[ccp4bb] Submissions for next CCN newsletter

Folks Calling for articles and short communications of interest to structural biologists. The deadline for submission in the January 2014 issue is 15 December 2013 but if you can send me an email we can make exceptions so you can use the holiday break to work on your drafts. The Computational

[ccp4bb] July 2013 Computational Crystallography Newsletter

Folks The latest edition of the Computational Crystallography Newsletter is available at http://phenix-online.org/newsletter The table of contents is listed below. Articles *cctbx* tools for transparent parallel job execution in Python. III. Remote access *phenix.ensemble_refinement*: a test

[ccp4bb] Submissions for next CCN newsletter

Folks Calling for articles and short communications of interest to structural biologists. The deadline for submission in the June 2013 issue is 31 May, 2013 but if you can send me drafts before the 15th of May we can get started on generating proofs. The Computational Crystallography Newsletter

[ccp4bb] January 2013 Computational Crystallography Newsletter

Folks The latest edition of the Computational Crystallography Newsletter is available at http://phenix-online.org/newsletter The table of contents is listed below. Articles cctbx tools for transparent parallel job execution in Python. I. Foundations cctbx tools for transparent parallel job

[ccp4bb] July 2012 Computational Crystallography Newsletter

Folks The latest issue of the Computational Crystallography Newsletter is available on-line at http://www.phenix-online.org/newsletter for download. The articles are of general interest to protein crystallographers and are listed below. Enjoy Nigel Moriarty Articles --- cctbx tools

[ccp4bb] Computation Crystallography Newsletter

Folks The latest issue of the Computational Crystallography Newsletter is available on-line at http://www.phenix-online.org/newsletter for download. The articles are of general interest to protein crystallographers and are listed below. Enjoy Nigel Moriarty Articles CCTBX tools

[ccp4bb] Call for submissions to Computational Crystallography Newsletter

Calling for articles and short communications of interest tostructural biologists. The deadline for publication in the January2012 issue is 1st Dec, 2011. The Computational Crystallography Newsletter (CCN) is an electronicnewsletter for structural biologists, and is published online every

[ccp4bb] Third issue of Computation Crystallography Newsletter - Volume 2, Number 2

Dear Colleagues, I am pleased to announce the publication of the third issue of the Computational Crystallography Newsletter: http://www.phenix-online.org/newsletter/ A listing of the articles and short communications is given below. Please note that the newsletter accepts articles of a

Re: [ccp4bb] Extracting information from set of pdbs.

Or eLBOW with a Python script. I can provide a start if you desire. On Thu, Dec 2, 2010 at 9:29 AM, Bryan Lepore bryanlep...@gmail.com wrote: On Thu, Dec 2, 2010 at 12:17 PM, Justyna Wojdyla jw...@york.ac.uk wrote: get values for chosen torsion angles of ligand ... moleman with a script.

Re: [ccp4bb] restraints for cis-bonds, ACD cif file

Nathaniel The atom names in the file I sent have the correct atom names as defined by the PDB for ACD. Naturally, the atom names in your PDB file and the restraints CIF file should match and given that you need the correct names to deposit your structure into the PDB, then I would recommend doing

Re: [ccp4bb] restraints for cis-bonds, ACD cif file

Nathaniel I made a small mod to eLBOW (which will be available in the next nightly build) that allows you to get an all cis ACD from a SMILES string. I have attached the result. Note that the name of the file has for the four cis (zusammen) configurations. As Paul suggested, the torsion