Re: [ccp4bb] Query on density fitting to phosphate

Have you tried sodium? From: CCP4 bulletin board On Behalf Of Arpita Goswami Sent: Sunday, December 17, 2023 11:47 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Query on density fitting to phosphate Dear All, Hope you all are doing well. The density in the image (in link below) is fitted

Re: [ccp4bb] Question about BIOVIA DiscoveryStudio 2021

Hi Fred, I don't know about Discovery studio but I know in Pymol you can select the peptide ligand yourself, e.g. via a sequence view. It just depends on what type of analysis you are doing. Joel -Original Message- From: CCP4 bulletin board On Behalf Of Fred Vellieux Sent: Monday,

Re: [ccp4bb] Protein models with Cofactors, metal clusters and heme

Thanks for the recommendations. From: Dias, Joao M. Sent: Thursday, 2 March 2023 10:17 AM To: Joel Tyndall ; CCP4BB@JISCMAIL.AC.UK Subject: RE: Protein models with Cofactors, metal clusters and heme Hi Joel, Have you tried Alphafill: AlphaFold Filled (alphafill.eu)<https://ap

[ccp4bb] Protein models with Cofactors, metal clusters and heme

models (that I am aware of). Is anyone aware of any webserver/package that will model these cofactors reliably (outside of modeller)? Many thanks J Joel Tyndall | BSc(Hons) PhD Professor in Medicinal Chemistry School of Pharmacy | He Rau Kawakawa University of Otago | Te Whare Wānanga o Otāgo PO

Re: [ccp4bb] Crystallised PEG / Lys/ Gln...ASN

Or ASN? From: CCP4 bulletin board On Behalf Of Joel Tyndall Sent: Friday, 4 November 2022 4:12 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Crystallised PEG / Lys/ Gln Hi all, Quick question. I am well aware of seeing PEG crystallised with my protein in a circular shape around lysine

[ccp4bb] Crystallised PEG / Lys/ Gln

Hi all, Quick question. I am well aware of seeing PEG crystallised with my protein in a circular shape around lysine residues. Can this also happen with GLN around the side chain nitrogen? Or even form an adduct? I see good evidence for at least the former option Happy Friday Joel Joel

Re: [ccp4bb] Issue with Phenix/Coot/PyMol after installing ccp4 v8

PC, mac or linux? -Original Message- From: CCP4 bulletin board On Behalf Of Dale C Sent: Wednesday, 27 July 2022 12:45 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Issue with Phenix/Coot/PyMol after installing ccp4 v8 Hi all, I recently updated my ccp4 package to Program suite

Re: [ccp4bb] Missing double bonds in the ligand

Thanks Nigel, I meant the mmcif coordinate file format as an alternative to the pdb file. I am now not convinced it contains the bond order etc Alternatively, saving as a .mol2 file should save atom types and bond order From: Nigel Moriarty Sent: Friday, 8 July 2022 12:31 pm To: Joel Tyndall

Re: [ccp4bb] Missing double bonds in the ligand

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, 8 July 2022 7:47 am To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Missing double bonds in the ligand Further reading

Re: [ccp4bb] circular peptide structure refinement

You will need to add the "link" line to the PDB file so the software recognises the covalent bond. See the pdb file for 6U6K Hope this helps J From: CCP4 bulletin board On Behalf Of Jiang Xu Sent: Thursday, 7 July 2022 10:15 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] circular peptide

[ccp4bb] Easy/Silly question

Hi folks, I frustratingly cant find “maltose” as a ligand in the pdb or ccp4 database. Does any one have the code for the ligand? Surely its been used before. Thanks in advance J Joel Tyndall | BSc(Hons) PhD Associate Professor in Medicinal Chemistry School of Pharmacy | He Rau Kawakawa

Re: [ccp4bb] [phenixbb] NORA workshop on AlphaFold2 and RoseTTAFold, 31 August and 1 September

Hi, Any chance this will be recorded for those of us in a different dimension? J -Original Message- From: phenixbb-boun...@phenix-online.org On Behalf Of Randy John Read Sent: Friday, 27 August 2021 6:27 am To: CCP4BB@jiscmail.ac.uk; PHENIX user mailing list Subject: [phenixbb] NORA

Re: [ccp4bb] how to fix helices-sheets getting converted to coil,

HI, I simply opened this in Pymol, saw the non designated structed, typed dss (https://www.pymolwiki.org/index.php/Dss) and then saw the secondary structure... It "may" be that it is not designated in the pdb file (however I haven't looked). J From: CCP4 bulletin board On Behalf Of Firdous

Re: [ccp4bb] pymol 2.5 GUI font size too small

Hi Ursula, Can you provide some more information? What OS are you using, Mac, Windows or Linux? Are you referring to the text in the top window or labels in the graphical window? J From: CCP4 bulletin board On Behalf Of Ursula Schulze-Gahmen Sent: Wednesday, 21 July 2021 11:17 AM To:

Re: [ccp4bb] technical question

You could probably do this via a mutate option in coot . Or at least use the sulfoxide as a new residue (not mutate) From: CCP4 bulletin board On Behalf Of amit gaur Sent: Saturday, 30 November 2019 7:06 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] technical question Hi everbody, I want to

Re: [ccp4bb] collective term for hydrogen bonds and salt bridges

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

Re: [ccp4bb] Electron density

Did you happen to use glycerol as a cryoprotectant? From: CCP4 bulletin board On Behalf Of Daniel Garcia Sent: Monday, 14 May 2018 12:40 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Electron density Dear all, I am currently refining a structure and found a intriguing

Re: [ccp4bb] biological molecule?

Hi Charlie, I just visited the RCSB PDB website and looked up a random structure. You can still download the biological unit in pdb format from the download files pulldown J -Original Message- From: CCP4 bulletin board On Behalf Of Carter, Charlie Sent:

Re: [ccp4bb] Atom clashes in active site?

Could this be a covalent interaction? Difficult to judge without seeing anything From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Andrew Marshall Sent: Tuesday, 20 December 2016 2:48 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Atom clashes in active site? Hi all,

[ccp4bb] Last 2 updates - aimless and scala

version and it runs fine. Is this a bug? J _ Joel Tyndall, PhD Associate Professor in Medicinal Chemistry National School of Pharmacy University of Otago PO Box 56 Dunedin 9054 New Zealand Skype: jtyndall Ph: +64 3 479 7293

Re: [ccp4bb] pdb2pqr generation

Hi Tim, You have sparked my interest in Coot ESP. Do you know of a link to explain how to display/export it? I can generate it but nothing happens (other than the protein disappearing Cheers Joel -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of

[ccp4bb] Small molecule cif files

_ Joel Tyndall, PhD Associate Professor in Medicinal Chemistry National School of Pharmacy University of Otago PO Box 56 Dunedin 9054 New Zealand Skype: jtyndall Ph: +64 3 479 7293

Re: [ccp4bb] Hosed-Up X-Ray Structures: A Big Problem

Hi, I saw Jeffs post with interest and have held off until now. It is relatively easy to find structures with bad geometry for small molecules but it does not do any good simply pointing them out. What I believe is needed is a way to fix the problem. There are several possible ways. The pdb

Re: [ccp4bb] Hosed-Up X-Ray Structures: A Big Problem

Great news and I am in full support of the bug option. Where do we start? (Caveat: we all make mistakes, I am sure I have!) -Original Message- From: Ethan A Merritt [mailto:merr...@u.washington.edu] Sent: Friday, 13 June 2014 8:45 a.m. To: Joel Tyndall Cc: CCP4BB@jiscmail.ac.uk Subject

Re: [ccp4bb] Off topic: Homology modeling

Hi Theresa, I tackled a similar problem recently using modeller (Andrej Sali) which worked well. In the case of my transporter (or any model) your homology model will only be as good as the starting structure (resolution etc) and your sequence identity. I found that the homologues that I was

Re: [ccp4bb] AW: appropriate torsion angles

the way I believe it should go, I just need the parameters. Regularizing in Coot doesn't help Thanks both. Joel Joel Tyndall, PhD Associate Professor in Medicinal Chemistry National School of Pharmacy University of Otago PO Box 56 Dunedin 9054 New Zealand http

[ccp4bb] appropriate torsion angles

molecules. This has meant that the auto generated cif files gave the wrong geometry for the nitrogen in the first place. Many thanks Joel _ Joel Tyndall, PhD Associate Professor in Medicinal Chemistry National School of Pharmacy University of Otago PO Box 56

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

Dear Xiaoming, I would try using the graphical interface within phenix refine to add in the bond length/angle constraints for your link. This seemed to work fine with our system without actually needing a link record. J -Original Message- From: CCP4 bulletin board

Re: [ccp4bb] question on charge charge interactions

Tom, I would think the case can be made for sharing a proton (one ionised and one not) in either case but more so for acidic residues. See HIV protease Asp-Asp as a well-established example Hope this helps J -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK]

Re: [ccp4bb] Large Conformational Change Upon Binding Ligand...

Trying not to state the obvious but...HIV protease -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Keller, Jacob Sent: Friday, 28 February 2014 8:43 a.m. To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Large Conformational Change Upon Binding

Re: [ccp4bb] New ligand

Carsten, Phenix does do this a little differently and yes it ignores existing ligands (which I like). CCP4 comes with is own library of existing ligand cif files from the pdb which coot also uses. The best way is to try and find a unique code to call your new ligand. That way you can have some

Re: [ccp4bb] Water or ion

I agree with Robbie. It is difficult for an ion to interact with both oxygen (ionised) and amide N-H at the same time. You can also have bifurcated h-bonds Hope this helps J From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Uma Ratu Sent: Sunday, 24 November 2013 1:15 p.m.

[ccp4bb] refmac-linux-I'm out of touch question

. I have downloaded the binaries for refmac 5.8 which gives me refmacgfortran and libcheckgfortran. And now I am stuck. Would someone be so kind as to instruct me on where to put these, if they need compiling etc? Many thanks Joel _ Joel Tyndall, PhD Senior

Re: [ccp4bb] atomic coloring for the color blind

Why not use yellow carbons (colour by atom menu) and hit the builder button in pymol which shows bond order (carbonyls). You could also type colour gray, name o, this colours the carbonyls gray (or any other colour that works) name o* colours all oxygens Hope this helps From: CCP4 bulletin

[ccp4bb] Overide refmac restraints

something? Any help muchly appreciated. (I am using the most upto date version of the CCP4 package on a PC) Joel _ Joel Tyndall, PhD Senior Lecturer in Medicinal Chemistry National School of Pharmacy University of Otago PO Box 56 Dunedin 9054 New Zealand Skype

Re: [ccp4bb] Modelling Software for beta turn design

Dear Wenzong, Could you provide a bit more details please? Do you simply require some visualisation tool e.g. pymol to superimpose your turn mimic on your protein/peptide structure or are you looking for more indepth modelling to say identify new scaffolds to build amino acid sidechains onto

Re: [ccp4bb] Modelling Software for beta turn design

[mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Wenzong Li Sent: Monday, 22 April 2013 4:17 p.m. To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Modelling Software for beta turn design I want to build the loop based on a computer screen against my peptide. Thanks Wenzong - Original Message - From: Joel

Re: [ccp4bb] 2013年4月9日 16:39:16 自动保存莞

Hi Quanju, Pymol is good as it will show you polar contacts (h-bonds and electrostatic interactions/salt bridges). However pi-stacking and pi-cation interactions comes with experience to some extent i.e. being able to recognise them. Coot will help as it shows polar contacts as well as “close

Re: [ccp4bb] homology modeling of dimeric proteins

I have successfully used modeller (standalone software; Sali lab) to generate multimeric complexes up to 24-mers Hope tis helps From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Sudipta Bhattacharyya Sent: Friday, 22 March 2013 5:00 a.m. To: CCP4BB@JISCMAIL.AC.UK Subject:

Re: [ccp4bb] unidentified density

Do you have matching 2Fo-Fc density? It is not obvious from the pictures. From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Sudhir Kumar Sent: Thursday, 18 October 2012 12:07 a.m. To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] unidentified density Dear all, I have been working

Re: [ccp4bb] OFF TOPIC

Hi Rex, In Coot, under the file menu, “Get Fragment” and the type LBT (upper case). This (LBT) is the three letter code for alpha-lactose. Unfortunately it is not that easy to find the codes. However on my windows machine the list is here: C:\CCP4\6.3\lib\data\monomers\list Hope this helps

Re: [ccp4bb] Problem with making PDB from Coot

You should type Dss into pymol and this will assign more appropriate secondary structure From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of meisam nosrati Sent: Tuesday, 24 July 2012 9:47 a.m. To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Problem with making PDB from Coot

Re: [ccp4bb] Chiral volume outliers SO4

Hi all, Thanks very much to all who responded so quickly. The fix is a one liner in the SO4.cif file (last line) SO4 chir_01 S O1 O2 O3both which I believe is now in the 6.3.0 release. Interestingly the chirality parameters were not in the SO4.cif file in 6.1.3

Re: [ccp4bb] Chiral volume outliers SO4

. I'll look at swapping the oxygens in the SO4's. Cheers Joel -Original Message- From: Dale Tronrud [mailto:det...@uoxray.uoregon.edu] Sent: Friday, 13 July 2012 10:22 a.m. To: Joel Tyndall Cc: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Chiral volume outliers SO4 While this change has

[ccp4bb] Chiral volume outliers SO4

- PDB_REDO) which talks about this issue and mentions the development of Chiron which could fix this issue. Is there a way to fix this problem using existing tools (or editing). We have ~20 sulfates in our protein (10-mer system) Thanks heaps Joel _ Joel Tyndall

[ccp4bb] PS: Chiral volume outliers SO4

Sorry I should have added, that the issue occurs following refinement in refmac. (error in log file and SO4's are distorted) _ Joel Tyndall, PhD Senior Lecturer in Medicinal Chemistry National School of Pharmacy University of Otago PO Box 56 Dunedin 9054 New

Re: [ccp4bb] Capping peptide

Hi Chris, Depending on your caps the monomers should be available to import directly into Coot and refine in refmac. You can find a full list of available monomers if you drill down in the ccp4 libraries directory. I'm guessing you may have and acetylated amino terminus which would be ACE.

[ccp4bb] Coot get monomer issue

and there is cross talk with ccp4 6.2.0. The coot-real.exe window comments Refmac monomer code Ile BL INFO: We founds C:\\CCP4 packages...\libcheck.exe This does not happen with windows XP with ccp4 6.1.13. Any thoughts? Thanks Joel _ Joel Tyndall, PhD Senior Lecturer

Re: [ccp4bb] Off-topic: Supplying PDB file to reviewers

Marc, As someone with limited experience in publishing structures but with other experience reviewing the same I feel strongly about this. I am hoping to submit any future papers with the pdb structure already released or submit the coordinates as supplementary material. As a reviewer I find

Re: [ccp4bb] refining phosphorylated residues

As a follow up question the bulletin board, why is SEP a peptide (L-peptide) and TPO not (non-polymer)? Joel _ Joel Tyndall, PhD Senior Lecturer in Medicinal Chemistry National School of Pharmacy University of Otago PO Box 56 Dunedin 9054 New Zealand Skype

Re: [ccp4bb] Water

Hope this helps. _ Joel Tyndall, PhD Senior Lecturer in Medicinal Chemistry National School of Pharmacy University of Otago PO Box 56 Dunedin 9054 New Zealand Skype: jtyndall http://www.researcherid.com/rid/C-2803-2008 Pukeka Matua Te Kura Taiwhanga Putaiao Te

[ccp4bb] Zero occupancy and bad geometry

in this case occurs between CG (1.00 occ) and CD (0.00 occ). Any thoughts on why this is occurring? Cheers Joel _ Joel Tyndall, PhD Senior Lecturer in Medicinal Chemistry National School of Pharmacy University of Otago PO Box 56 Dunedin 9054 New Zealand Skype

Re: [ccp4bb] surface residue mutation

., Yeates, T.O., Kent, S.B., Journal: (2010) Chem.Commun.(Camb.) 46: 8174-8176 _ Joel Tyndall, PhD Senior Lecturer in Medicinal Chemistry National School of Pharmacy University of Otago PO Box 56 Dunedin 9054 New Zealand   Skype: jtyndall http://www.researcherid.com

Re: [ccp4bb] Generating parameters/cif files for macrocyclic ligands

are complicating the issue _ Joel Tyndall, PhD Senior Lecturer in Medicinal Chemistry National School of Pharmacy University of Otago PO Box 56 Dunedin 9054 New Zealand Skype: jtyndall http://www.researcherid.com/rid/C-2803-2008 Pukeka Matua Te Kura Taiwhanga Putaiao Te

[ccp4bb] Generating parameters/cif files for macrocyclic ligands

Coot I can refine the whole ligand but not certain components. Any suggestions greatly appreciated . ( I may stick to coot refinement with fixed atoms at this stage) Regards Joel _ Joel Tyndall, PhD Senior Lecturer in Medicinal Chemistry National School

Re: [ccp4bb] How to make covalent bond in COOT

Oops, Meant to hit reply all... Hi there, You can generate a link via jligand which gives you a covalent linkage with your enzyme / ligand.as well as a cif file Try the tutorial ftp://ftp.ccp4.ac.uk/JLigand/tutorial_link.html J _ Joel Tyndall, PhD Senior

Re: [ccp4bb] sugar and coot

You can also try Jligand to generate your cif file J From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Jan van Agthoven Sent: Tuesday, 22 November 2011 1:17 p.m. To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] sugar and coot Hi everyone! Does anyone know if there is a way of

Re: [ccp4bb] crystallization of synthetic peptides

Some HIV protease structures have been done using synthetic HIV protease (99 amino acid monomers). Look at J. Martin et al from UQ in Queensland. I believe this was done with Steve Kent. The protein contains some non-natural amino acids too. Hope this helps -Original Message- From:

Re: [ccp4bb] Installation of ccp4 on 64bit fedora core 13

Hi folks, Anyone know if this site is temporarily down or is it more permanent? http://bioscreencastwiki.com/Crystallography_Howtos/Installing_ccp4-6.0.99e_on_64_bit_Ubuntu Cheers Joel _ Joel Tyndall, PhD Senior Lecturer in Medicinal Chemistry National

Re: [ccp4bb] error after install

: 2011-09-26 09:11:48.946003302 +1300 Modify: 2011-08-16 02:26:38.0 +1200 Change: 2011-09-22 16:24:09.857165116 +1200 It maybe that python was not installed correctly, will update after the core group gets back to me. Cheers Joel _ Joel Tyndall, PhD

[ccp4bb] error after install

_ Joel Tyndall, PhD Senior Lecturer in Medicinal Chemistry National School of Pharmacy University of Otago PO Box 56 Dunedin 9054 New Zealand Skype: jtyndall http://www.researcherid.com/rid/C-2803-2008 Pukeka Matua Te Kura Taiwhanga Putaiao Te Whare Wananga o Otago Pouaka Poutapeta 56 Otepoti

Re: [ccp4bb] Saving distances drawn in Coot 0.6.1

Hi Romain, I am not aware of how to do this in Coot but you can easily do this in PyMOL using the save session option (with maps etc). Cheers Joel _ Joel Tyndall, PhD Senior Lecturer in Medicinal Chemistry National School of Pharmacy University of Otago PO Box