Re: [ccp4bb] Validation of structure prediction

The Molprobity server can be run online and only requires the coordinates in PDB format: http://molprobity.biochem.duke.edu/. Best, Nick Clark On Mon, Dec 20, 2021 at 11:10 AM Reza Khayat wrote: > ​Hi, > > > Can anyone suggest how to validate a predicted structure? Something > similar to wwPDB

Re: [ccp4bb] Validation of structure prediction

Reza, Thus far, it seems we’ve all assumed this was an AlphaFold or RobettaFold model. If this is not indeed the case, it may be worthwhile to “validate” your mode by running your sequence through one of these two and using the validation from them. The AlphaFold DB can be found here, with a numb

Re: [ccp4bb] Coot on Mac OSX Monterey

Dr. Pearl, I have used the pre-built installer here: http://scottlab.ucsc.edu/xtal/wiki/index.php/Stand-Alone_Coot This worked on my Mac running Monterey OS with an intel i7. Best regards, Nick Clark On Fri, Feb 11, 2022 at 4:53 PM Laurence Pearl wrote: > Does anyone know where I can downlo

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

Hi Dale, I recently updated Phenix and CCP4 on iOS had a similar issues with Phenix/Coot. I fixed the issues with the restraint dictionary by directing Phenix to the new location for Coot (in the CCP4 program libraries) in the Phenix settings. This resolved the lack of restraints for every amino

Re: [ccp4bb] Missing restrains for standard amino acid

I had the same issue in the past. To resolve this issue, point Phenix (in settings -> Graphics, if I recall correctly) to the Coot location in CCP4. As you suspected, Coot does not know where the Restraint Library is when opened from Phenix. Best, Nick Clark On Sun, Aug 7, 2022 at 2:00 AM Cryo E

Re: [ccp4bb] circular peptide structure refinement

Phenix in the past, and I’m assuming still, does not recognize “link records”. You’ll likely need to generate the peptide in AceDRG, making sure to link the carboxy- and amino-termini, and include the cif during refinement. This was the only way I was able to get Phenix to properly refine an inhib

Re: [ccp4bb] Coot issue

Mirek, Yes, this is a known issue (I read about it previously either here or on the Coot webpage, I can't recall which). The only "workaround" is to check the "keep delete active" box before you begin deleting. It took me a bit to realize this, so I'll share: The window is still open and can be a

[ccp4bb] Fwd: [ccp4bb] Issues with Coot and PyMOL on MacOS Ventura 13.2

-- Forwarded message - From: Nicholas Clark Date: Mon, Feb 6, 2023 at 6:44 AM Subject: Re: [ccp4bb] Issues with Coot and PyMOL on MacOS Ventura 13.2 To: Julia Griese Julia, I have the same issue with PyMOL. After it opens the blank session, if you return to the file explorer

Re: [ccp4bb] Way to resolve Ramachandra outliers in a structure

Hi Medhanjali, In Coot, there are two additional options for "automated" correction of Ramachandran outliers. You can find them under "Calculate". For the entire structure in the "Calculate->all molecule" tab, select Refine/Improve Ramachandran Plot. For a specific region, you can use the "Calcul

Re: [ccp4bb] Coot crashes when delete side chain

Jinhua, As Michael stated, ticking "keep delete active" will prevent the window from closing. Additionally, if you accidentally forget to do this, Coot does not actually crash. The window gets "hidden" or "minimized". If you right click on the XQuartz icon, you will see the window at the top of th

[ccp4bb] Issue with CSO in Coot & Refmac

I have a cysteine residue that is oxidized and needs to be modeled as CSO. In the past, when "replace residue" was used to substitute for CSO, the CSO would "behave" during real-space refinement and essentially take the place of the Cys. However, when Cys is replaced by CSO now the CSO is behaving

Re: [ccp4bb] Issue with CSO in Coot & Refmac

gt; > Sent from Proton Mail mobile > > > > Original Message ---- > On 27 May 2023, 00:43, Nicholas Clark < ndcla...@buffalo.edu> wrote: > > > I have a cysteine residue that is oxidized and needs to be modeled as CSO. > In the past, when "replace r

Re: [ccp4bb] Issue with CSO in Coot & Refmac

Hey Paul, I'm not sure how to check that? Would you be able to provide a resource to check this? Best, Nick Clark On Fri, May 26, 2023 at 9:21 PM Paul Emsley wrote: > > On 27/05/2023 00:43, Nicholas Clark wrote: > > I have a cysteine residue that is oxidized and needs to

Re: [ccp4bb] Issue with CSO in Coot & Refmac

e* HN2 H2" I've attached the file I have for your reference, as I may not be looking in the correct place. Also, if I'm looking in the wrong file location, please let me know. Best, Nick Clark On Fri, May 26, 2023 at 10:04 PM Nicholas Clark wrote: > Hey Paul, > > I'

Re: [ccp4bb] Issue with CSO in Coot & Refmac

Paul, Yes, it appears that the upper level group is "NON-POLYMER". However, there is an alias at the bottom that does state polymer. Best, Nick Clark On Fri, May 26, 2023 at 10:37 PM Paul Emsley wrote: > > On 27/05/2023 03:23, Nicholas Clark wrote: > > Hey Paul, >

Re: [ccp4bb] Issue with CSO in Coot & Refmac

Hi Paul, Thank you for providing that information. Editing the restraints for CSO corrected the issue! Your assistance is greatly appreciated. I figured I was missing something :) Best, Nick Clark On Fri, May 26, 2023 at 10:55 PM Paul Emsley wrote: > > On 27/05/2023 03:46, Nicholas

Re: [ccp4bb] Issue with CSO in Coot & Refmac

paper Paul mentioned. > > Refmac would work, if "refmacat" (explained in the paper) is used. The > command is already available in the latest CCP4 update, but not from > the interfaces at the moment. > > Best regards, > Keitaro > > On Sat, 27 May 2023 at 04:02, Ni

Re: [ccp4bb] Issue with CSO in Coot & Refmac

for execution of refmacat. Best, Nick Clark On Mon, May 29, 2023 at 1:48 PM Nicholas Clark wrote: > Hi Keitaro, > > Thanks for the response. Is there documentation somewhere on how to run > refmacat (like an example for Crystallographic data refinement, I found the > one for CryoEM data

Re: [ccp4bb] how to increase b factor for water in protein- ligand crystal structure

Mandar, It would also be helpful if you could share the statistics in the highest resolution shell. But to me (which is admittedly a bit subjective), as noted by Eleanor, the R-merge seems a bit high and the your I/sigma and CC1/2 seem a bit low. Which doesn’t really matter if you can build a reas

Re: [ccp4bb] how to increase b factor for water in protein- ligand crystal structure

This is why I said this is somewhat subjective. I would agree I/sigI of 0.6+ and cc1/2 of 0.5+ in high res shell is fine but these values are overall, as the resolution range is 23-2.6 angstroms. On Thu, Nov 2, 2023 at 12:16 PM Eleanor Dodson < 176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote

Re: [ccp4bb] how to increase b factor for water in protein- ligand crystal structure

gt; >> *Wilson B-factor (Å)* >> >> 28.9 >> >> *Number of non-hydrogen atoms* >> >> 4302 >> >> *Macromolecules* >> >> 4086 >> >> *Ligands* >> >> 94 >> >> *Solvent* >> >> 124 >> >>

Re: [ccp4bb] HH-Suite, HHBLits, HHSearch query

Hello Harry, I have successfully used the HH-Suite in the recent past. I might be able to assist you. You can contact me off-list, since this isn’t directly related to CCP4. Best, Nick Clark On Mon, Nov 13, 2023 at 7:15 AM Harry Powell < 193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote: >

Re: [ccp4bb] Fragile Crystals

Hi Morgan, Have you tried MMS? https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4157405/ If you can reproducibly grow crystals MMS might give you hits in different conditions during screening. I’ve used this successfully multiple times for crystals that wouldn’t optimize with standard methods. We we

Re: [ccp4bb] Error in "Prepare and validate files for deposition" task"

Hi Maria, I'm not sure if anyone has replied to this chain. However, I had a similar issue when I was trying to prepare files for deposition in the past. You can use the PDB file and upload it to https://pdb-extract.wwpdb.org/ to generate the CIF file for deposition. Best, Nick Clark On Tue, Ja

Re: [ccp4bb] Error in "Prepare and validate files for deposition" task"

Maria, Apologies for the second email. I forgot that "Prepare files for deposition" also merges the CCP4 formatted files into an MTZ. If I recall correctly, I used "CONVERT2MTZ" in the command line to complete the merging of the CCP4 files to generate the necessary MTZ for deposition. Instructions

Re: [ccp4bb] [off topic] Recovering pET expression plasmid from BL21 strain

Hi Javier, For a few years (during an industry job) we regularly cloned directly into BL21 (we made our own high competency cells) and confirmed via expression before plasmid sequencing. Only after sequencing did we transform into a cloning strain for miniprep and “long term storage”. We didn’t s

Re: [ccp4bb] mmCIF files from PDB format for AlphaFill

Hi Harry, Have you tried MAXIT from the PDB? It can be installed locally: https://sw-tools.rcsb.org/apps/MAXIT/index.html Best, Nick Clark Nicholas D. Clark (He/Him) PhD Candidate Malkowski Lab University at Buffalo Department of Structural Biology Jacob's School of Medicine & Biomedical Scien

Re: [ccp4bb] mmCIF files from PDB format for AlphaFill

Harry, After a little digging, it seems this was previously reported as an issue to AlphaFold… see: https://github.com/google-deepmind/alphafold/issues/252 There are a few options others recommended or got to work in the comments. Notably, MAXIT was used: “Huiwenke: MineProt (https://github.com

[ccp4bb] Fwd: [ccp4bb] mmCIF files from PDB format for AlphaFill

.”" Best, Nick -- Forwarded message - From: Nicholas Clark Date: Fri, Feb 23, 2024 at 8:03 AM Subject: Re: [ccp4bb] mmCIF files from PDB format for AlphaFill To: Harry Powell Cc: Harry Powell Hi Harry, MAXIT binaries are located here: https://sw-tools.rcsb.org/apps/MA

Re: [ccp4bb] [ccp4bb] mmCIF files from PDB format for AlphaFill

Hi Harry, I did stumble upon this python mmCIF handler for modelCIF: https://github.com/ihmwg/python-modelcif/blob/main/examples/README.md Maybe this will have something of use to your efforts? Best, Nick Clark Nicholas D. Clark (He/Him) PhD Candidate Malkowski Lab University at Buffalo Depa

Re: [ccp4bb] Superimposition save as PDB for ccp4 refmac question

Hi Marco, "Superpose" in *Coot* will also take any associated ligands along during the superposition. You can do this under "Calculate-> SSM Superpose". Be sure to check "move copy of moving structure". The one that moves will show as "copy of xxx", with xxx being the name of the one that was move

Re: [ccp4bb] add ligand with AceDRG

Hi Stefanie, Why can you only use "taken" three letter codes? In the "output monomer" box, you should be able to enter whatever you'd like for the "Three letter code for output monomer". In the attached image, this is shown as "DRG" but can be changed to any 3 letter code of your choice. Obviously

[ccp4bb] Fwd: [ccp4bb] Crystal optimization

Apologies, my response was directly to the OP and not to the BB. I have forwarded the response to maintain the chain. -- Forwarded message - From: Nicholas Clark Date: Fri, May 31, 2024 at 7:23 AM Subject: Re: [ccp4bb] Crystal optimization To: 白雪慧 I had a protein that no

[ccp4bb] Off-topic: UCSF Chimera Download

I’m trying to navigate to the download page for UCSF Chimera but it does not seem to be working. Does anyone know of an alternative location? Thanks, Nick Clark To unsubscribe from the CCP4BB list, click the following link

Re: [ccp4bb] Off-topic: UCSF Chimera Download

kov...@mpinat.mpg.de> wrote: > Hi Nick, > > their web site goes offline from time to time. If you are on linux, I can > share recent binaries. > > Best, > > Oleksiy > > > On 18. Jun 2024, at 17:53, Nicholas Clark < > b2b1c7e93c2d-dmarc-requ...@jiscmail.ac

Re: [ccp4bb] Off topic ; how to remove fluorescein from superdex increase

Hi Flavio, I’d recommend reaching out to Cytiva directly ( scientificsupport...@cytiva.com). We had an issue with oxidized metal on our S200 and they were able to provide useful suggestions (plus side is, you know what they suggest won’t ruin the resin). Best, Nick Clark Nicholas D. Clark, PhD

Re: [ccp4bb] SUMO and SUMO protease

Hi Gloria, I have extensively used SUMO and echoing Artem's sentiment. SUMO has worked well in my hands for most instances. The additional benefit is that, assuming you use His-SUMO-target, following His-tag affinity purification, you can cleave the SUMO tag, followed by reverse IMAC (i.e., collec

Re: [ccp4bb] cif file uploading error

nown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=Mv5C9HdN0WpuNuFGeGRMUArYw1bpjLZPN0KRynjw0H0%3D&reserved=0> > > > On Sun, Jan 5, 2025 at 10:49 AM Nicholas Clark > wrote: > >> Hi Maju, >> >> This might b

Re: [ccp4bb] cif file uploading error

b50a20250%7C0%7C0%7C638716891677944265%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=YxdHps%2BE29OZml22fxA0xQ%2BuWFfbtXnF9mghJAh2IBI%3D&reserved=0> > > > On Sun, Jan 5, 2025 at 10:49 AM Nicholas Clark > wrote: > >> Hi Maju, >> >> This might b

Re: [ccp4bb] cif file uploading error

Hi Maju, This might be a simple solution, but have you tried removing the ".pdb" from the ".pdb.cif" file name (i.e. renaming the file)? Maybe it's confusing the file reading package on the validation server? Best, Nick On Sun, Jan 5, 2025 at 10:02 AM Manjula Ramu wrote: > Dear community, > >