Re: [ccp4bb] cif file uploading error

Ramu > Sent: Sunday, January 5, 2025 15:51 > To: CCP4BB@JISCMAIL.AC.UK > Subject: [ccp4bb] cif file uploading error > > Dear community, > > I encountered an issue while uploading data (attached) to generate the > validation rep

Re: [ccp4bb] cif file uploading error

CIF-pdbx and it is fully up to spec. The > file itself should not be the problem. > > Cheers, > Robbie > > > -Original Message- > > From: CCP4 bulletin board On Behalf Of Manjula > > Ramu > > Sent: Sunday, January 5, 2025 15:51 > > To: CCP4BB@JISC

Re: [ccp4bb] cif file uploading error

Given the session id, I could look at the logs. The issue with the backend software is that it requires the exptl category to be present as it needs to know the method to determine the type of analysis desired.   For instance, an NMR structure with multiple models will invoke clustering compar

Re: [ccp4bb] cif file uploading error

On 05/01/2025 16:02, Marcin Wojdyr wrote: I encountered an issue while uploading data (attached) to generate the validation report in Phenix. The error message states: "The PDB server reports a failure with your data. Please check that your input file follows the CIF specifications." That mes

Re: [ccp4bb] cif file uploading error

> Ramu > Sent: Sunday, January 5, 2025 15:51 > To: CCP4BB@JISCMAIL.AC.UK > Subject: [ccp4bb] cif file uploading error > > Dear community, > > I encountered an issue while uploading data (attached) to generate the > validation report in Phenix. The error message states: >

Re: [ccp4bb] cif file uploading error

Dear Manju, Thank you for alerting us about this issue. First, of course, the PhenixBB link for Phenix-related questions: https://phenix-online.org/archives/list/pheni...@phenix-online.org/ Indeed, Phenix has a tool "Get PDB validation report" as pointed out by Nicholas, which uses OneDep API: ht

Re: [ccp4bb] cif file uploading error

Dear Marcin, Thank you very much for this contribution to the discussion. As you know, the entire Global Phasing team is 200% behind every word you wrote, from the first to the last! With best wishes, Gerard. -- On Sun, Jan 05, 2025 at 05:26:42PM +0100, Marcin Wojdyr

Re: [ccp4bb] cif file uploading error

Thanks, Nicholas, Ezra and Marcin. I’ve used both the Phenix validation tool and the PDB validation server, following the standard protocol. I tried using CIF files generated after refinement as well as those generated after running the PDB extract. Unfortunately, I encountered issues in both case

Re: [ccp4bb] cif file uploading error

Nooo, don't do this! Use a refinement program and whatever the MX software suite that you are using is providing to get to deposition. You shouldn't need pdb-extract nowadays. On Sun, Jan 5, 2025 at 5:07 PM Nicholas Clark wrote: > > Manju, > > I agr

Re: [ccp4bb] cif file uploading error

Hi Ezra, The Phenix "Get PDB Validation Report" tool submits the data to the PDB validation server on your behalf: https://phenix-online.org/documentation/reference/get_pdb_validation_report.html. >From their page on the Phenix software: "Warning: This tool will send your model and data to RCSB se

Re: [ccp4bb] cif file uploading error

Are you talking about the wwPDB validation server - or validation report in Phenix. Nick mentioned server, Manjula said in Phenix. There are different email addresses for support from each service/software and you might try there. On 1/5/25 10:52 AM, Manjula Ramu wrote: Hi Nicholas, yes, I

Re: [ccp4bb] cif file uploading error

Manju, I agree with Marcin's answer. I have opened your CIF file in a text editor and am comparing it to a CIF I have on hand for deposition. The CIF file format in your file is not the same as what I have ready for deposition. You can try to use your PDB file and convert it to CIF for deposition

Re: [ccp4bb] cif file uploading error

> I encountered an issue while uploading data (attached) to generate the > validation report in Phenix. The error message states: > > "The PDB server reports a failure with your data. Please check that your > input file follows the CIF specifications." That message might be inaccurate. You seem

Re: [ccp4bb] cif file uploading error

Hi Nicholas, yes, I renamed the file I tried too. I still get the error. Thanks, Manju On Sun, Jan 5, 2025 at 10:49 AM Nicholas Clark wrote: > Hi Maju, > > This might be a simple solution, but have you tried removing the ".pdb" > from the ".pdb.cif" file n

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, > >

Re: [ccp4bb] CIF file Cannot Open by Coot

Dear All, I sincerely appreciate everyone’s contributions and suggestions—the issue has now been resolved! Following Oliver's instructions, I used the Grad Web Server to obtain the coordinates and restraint files for input, then adjusted the conformation using real-space refinement in Coot. Th

Re: [ccp4bb] CIF file Cannot Open by Coot

Hi Martin, I hope you are getting on well with one of the restraints for your molecule. But if choose to tweak the restraints to agree with a CSD small molecule structure for BODIPY, then I thought I should let you know that the structure you have downloaded YOWVOW has a high R-factor 10.29% >

Re: [ccp4bb] CIF file Cannot Open by Coot

, Martin From: CCP4 bulletin board on behalf of Jon Cooper <488a26d62010-dmarc-requ...@jiscmail.ac.uk> Date: Monday, August 19, 2024 at 14:24 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] CIF file Cannot Open by Coot ⚠ Caution: External sender I made your cif into a pdb (attached)

Re: [ccp4bb] CIF file Cannot Open by Coot

Dear Martin, My approach to your problem is to download an MOL2 of the small-molecule compound from WebCSD rather than the small-molecule CIF file. MOL2 files have the advantage that both the coordinates and the CCDC-curated bond orders are included in the file. MOL2 files can be read by AceDRG

Re: [ccp4bb] CIF file Cannot Open by Coot

Monday, August 19, 2024 at 6:43 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] CIF file Cannot Open by Coot Dear All, Thank you all for your help. I’ve tried several approaches to input this file, including changing the format to mmCIF, importing it as coordinates, and checking the restr

[ccp4bb] Your restraint file from acedrg Re: [ccp4bb] CIF file Cannot Open by Coot

Dear all, The attached is a restraint file generated by aceDRG, using your 713483.txt as the input file. The latest version of aceDRG, currently not released yet and under the final testing, can generate restraint or dictionary files of ligands using input files in form of small molecule cif

Re: [ccp4bb] CIF file Cannot Open by Coot

> Martin >> >> From: CCP4 bulletin board on behalf of Jon Cooper >> <488a26d62010-dmarc-requ...@jiscmail.ac.uk> >> Date: Monday, August 19, 2024 at 14:24 >> To: CCP4BB@JISCMAIL.AC.UK >> Subject: Re: [ccp4bb] CIF file Cannot Open by Coot >> &

Re: [ccp4bb] CIF file Cannot Open by Coot

On 19/08/2024 14:42, Hu, Wenhao wrote: Dear Jon, Thank you so much for all your effort! I really appreciate it. I’ve just tried to load the files, but unfortunately, it still won’t open and continues to show the error message I’ve attached here. Martin, These are not restraints. They a

Re: [ccp4bb] CIF file Cannot Open by Coot

ay, August 19, 2024 at 14:24 > To: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] CIF file Cannot Open by Coot > > ⚠ Caution: External sender > > I made your cif into a pdb (attached) which looks OK. Maybe worth trying with > that. > > Best wishes, Jon Cooper. > jon.b

Re: [ccp4bb] CIF file Cannot Open by Coot

of Jon Cooper <488a26d62010-dmarc-requ...@jiscmail.ac.uk> Date: Monday, August 19, 2024 at 14:24 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] CIF file Cannot Open by Coot ⚠ Caution: External sender I made your cif into a pdb (attached) which looks OK. Maybe worth trying with that.

Re: [ccp4bb] CIF file Cannot Open by Coot

Dear All, Thank you all for your help. I’ve tried several approaches to input this file, including changing the format to mmCIF, importing it as coordinates, and checking the restraints in the file. However, I am still unable to install the experimental ligand structure into the protein. It see

Re: [ccp4bb] CIF file Cannot Open by Coot

On 8/15/24 16:08, Hu, Wenhao wrote: Hi Paul, I’ve attached screenshots that show the error message from Coot, along with the contents of the line that the message refers to. Since this CIF file contains experimental data and restrains that would be difficult to rebuild in other software, I’

Re: [ccp4bb] CIF file Cannot Open by Coot

: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] CIF file Cannot Open by Coot Hi Paul, Thank you for your reply. I’ve attached screenshots that show the error message from Coot, along with the contents of the line that the message refers to. Since this CIF file contains experimental data and

Re: [ccp4bb] CIF file Cannot Open by Coot

solutions to successfully import this file into Coot. Any help you can provide would be greatly appreciated. Best regards, Martin From: Paul Emsley Sent: Thursday, August 15, 2024 3:09 PM To: Hu, Wenhao ; CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] CIF file Cannot

Re: [ccp4bb] CIF file Cannot Open by Coot

On 8/15/24 15:01, Tang, Jiazhi wrote: -- It happens sometimes when you can not open the downloaded cif files properly. One solution is to draw the compound yourself in Chemdraw, copy the smiles and generate the cif in Elbow within the phenix suit or other ligand software within ccp4. Just

Re: [ccp4bb] CIF file Cannot Open by Coot

could cause some issues. Regards, Jiazhi 发件人: CCP4 bulletin board 代表 Martin Hu 发送时间: Thursday, August 15, 2024 2:44:46 PM 收件人: CCP4BB@JISCMAIL.AC.UK 主题: [ccp4bb] CIF file Cannot Open by Coot Dear [Recipient's Name], I have downloaded a CIF file of a liga

Re: [ccp4bb] CIF file Cannot Open by Coot

On 8/15/24 14:44, Martin Hu wrote: Dear [Recipient's Name], Dear [Correspondent's Name], I have downloaded a CIF file of a ligand of interest directly from WebCSD, which was originally obtained from experimental crystallography research, and attempted to import it into Coot. However, Coot

[ccp4bb] CIF file Cannot Open by Coot

Dear [Recipient's Name], I have downloaded a CIF file of a ligand of interest directly from WebCSD, which was originally obtained from experimental crystallography research, and attempted to import it into Coot. However, Coot indicates that it cannot read the file for some reason. I've also tri

Re: [ccp4bb] cif file for ALF3O

Dear Jinyu, Are you sure you have AlF3? I mean, when you prepare your mixture to get AlF3 actually you produce AlF3 and AlF4 (Goldstein, 1964). Indeed depending on the initial concentration of F ion you used you may have a 50% of AlF3 and 50% of AlF4, and any of them could be bound to your prot

Re: [ccp4bb] cif file for ALF3O

Did not design compound strings for some time, the atom O should be without brackets… O[Al](F)(F)F works Cheers Jeroen -- Dr. math. et dis. nat. Jeroen R. Mesters https://orcid.org/-0001-8532-6699 University of Lübeck Institute of Biochemistry https://www.biochem.uni-luebeck.de phone: +49-

Re: [ccp4bb] cif file for ALF3O

oops, sorry, have to correct the smiles string... (O)[Al](F)(F)F Cheers Jeroen -- Dr. math. et dis. nat. Jeroen R. Mesters https://orcid.org/-0001-8532-6699  University of Lübeck Institute of Biochemistry https://www.biochem.uni-luebeck.de phone: +49-451-3101-3105 Ratzeburger Allee 160 23

Re: [ccp4bb] CIF file problem

Hi > Does anybody know why I got this error message: > Checking for embedded fcf data in CIF ... > No extractable fcf data in found in CIF > as I uploaded the CIF file to https://checkcif.iucr.org/ > for structure validation? The CIF file was directly from phenix.ref

Re: [ccp4bb] CIF file problem

Thank you for the information. On Thu, Apr 20, 2023 at 5:14 PM Tim Gruene wrote: > Dear Ning, > their is some confusion. When a small molecule crystal structure is > determined, the coordinates and data are usually submitted to the CCDC > or the COD (crystallographic open database). The structu

Re: [ccp4bb] CIF file problem

Dear Ning, their is some confusion. When a small molecule crystal structure is determined, the coordinates and data are usually submitted to the CCDC or the COD (crystallographic open database). The structure receives a checkcif report which, as Phil has pointed out, is specific to small molecule

Re: [ccp4bb] CIF file problem

Hi Phil, Thank you for the clarification, I didn't realize the CheckCIF is for small molecules. We tried to submit the manuscript to a chemical magazine and found "CheckCIF reports must be submitted to the Cambridge Crystallographic Data Centre (CCDC) *prior to manuscript submission". In fact I ha

Re: [ccp4bb] CIF file problem

Hello Ning CheckCIF checks small molecule crystallographic cif files - the dictionaries and expectations on the contents are not the same as for mmcif, although the underlying syntax is the same. I'm unaware of anything that does the equivalent of CheckCIF for macromolecular cif files. Phi

[ccp4bb] CIF file problem

Hi all, Does anybody know why I got this error message: *Checking for embedded fcf data in CIF ...* *No extractable fcf data in found in CIF* as I uploaded the CIF file to https://checkcif.iucr.org/ for structure validation? The CIF file was directly from phenix.refine during structure refinem

Re: [ccp4bb] .cif file generator for compound stereochemical restraints

Thanks Paul for addressing my inquiry late hours. Kudos to your huge contributions to the vast crystallography community. All my best wishes, Jacob On Sun, Mar 22, 2020 at 11:15 PM Paul Emsley wrote: > On 23/03/2020 03:05, Jacob Wong wrote: > > I love the ccp4 suite. I'm interested in knowing if

Re: [ccp4bb] .cif file generator for compound stereochemical restraints

On 23/03/2020 03:05, Jacob Wong wrote: I love the ccp4 suite. I'm interested in knowing if there is any other solution out there that may be more economical in licensing, especially if I only go as far as coot as a "commercial user". Are you suggesting that coot may not be a freeware anymore in

Re: [ccp4bb] .cif file generator for compound stereochemical restraints

Thanks Paul - I love the ccp4 suite. I'm interested in knowing if there is any other solution out there that may be more economical in licensing, especially if I only go as far as coot as a "commercial user". Are you suggesting that coot may not be a freeware anymore in the near future? Yours, Ja

Re: [ccp4bb] .cif file generator for compound stereochemical restraints

Just would love to know what else is out there in addition to ELBOW in Phenix? Acedrg is the modern dictionary generator distributed by CCP4. My utility is to generate the .pdb and .cif files from a SMILES string that would allow me to do compound fitting and real-space refinement in coot, I

[ccp4bb] .cif file generator for compound stereochemical restraints

Dear all, Just would love to know what else is out there in addition to ELBOW in Phenix? My utility is to generate the .pdb and .cif files from a SMILES string that would allow me to do compound fitting and real-space refinement in coot, and then reciprocal refinement elsewhere (assuming I won't

Re: [ccp4bb] cif-file macro?

Edwin Pozharski writes: > I expect this not to exist, but is there a way to define a variable in > a cif-file (e.g. a global esd target for, say, angles)? No, I don’t think either CIF or CIF2 have such variables/macros, I’m afraid. -- Ian Clifton ⚗ ℡: +44 1865 275677 Chemistry R

[ccp4bb] cif-file macro?

I expect this not to exist, but is there a way to define a variable in a cif-file (e.g. a global esd target for, say, angles)? I am certainly capable of putting together a bash script to emulate this, so please don't bother with suggesting a workaround unless you really enjoy that kind of thing :)

Re: [ccp4bb] cif-file with restraints for HC4

Hello Marius, not being familiar with the chromophore, but could this be done by the prodrg-server? http://davapc1.bioch.dundee.ac.uk/prodrg/ Tim On Fri, Jun 24, 2011 at 12:06:54AM +0200, marius.schm...@ph.tum.de wrote: > is there someone out there who worked out a > cif-file WITH restraints f

[ccp4bb] cif-file with restraints for HC4

is there someone out there who worked out a cif-file WITH restraints for the central p-hydroxy-cinnamoyl chromophore (HC4) in photoactive yellow protein? I'd appreciate a copy. Thanks very much Marius Dr.habil. Marius Schmidt Asst. Professor University of Wisconsin-Milwaukee Department of Phys

Re: [ccp4bb] cif file for NAD

Dear RajeshCould you please try the attached dictionary. Please let me know if it still has a problem. What are the issues around O1N-PN-O2n and O3N-PN-O5?regardsGarib nad_exp.cif Description: Binary data On 8 Oct 2009, at 15:11, RK Singh wrote:Dear All,I would like to request to send me a working

Re: [ccp4bb] cif file for NAD

I guess phenix.elbow or/and phenix.ready_set can do it Pavel. On 10/8/09 7:11 AM, RK Singh wrote: Dear All, I would like to request to send me a working and correct cif file for NAD. I obtained the same from Prodrg and ebi. But seems to have an issues around O1N-PN-O2N O3-PN-O5. Thanks With

[ccp4bb] cif file for NAD

Dear All, I would like to request to send me a working and correct cif file for NAD. I obtained the same from Prodrg and ebi. But seems to have an issues around O1N-PN-O2N O3-PN-O5. Thanks With best regards Rajesh Rajesh Kumar Singh, PhD Biochemical Engg. Group Chemical Engg. Division Dr. Homi

Re: [ccp4bb] .cif file

Hello Vineet, This seems old one and doesn't have all restraints. you may use refmac dictionary for spermine. I am sure this will work in coot also. you may find it at /ccp4-6.0.2/lib/data/monomers/s/SPM.cif thanks Manish Vineet Gaur <[EMAIL PROTECTED]> wrote: Hi all I am using COOT for

Re: [ccp4bb] .cif file

Your cif-file contains coordinates, but as far as I could see it does not contain bond lengths, and angles and their deviations. That is what coot complains about. Unless your cif-file describes a modified spermine you could use the spermine already described in the refmac5 library: In coot, g

[ccp4bb] .cif file

Hi all I am using COOT for model building and refinement. i have to introducea ligand in my model i have downloaded .cif file from RCSB. However while importing the cif file i m getting the warning message of having No restraints in the CIF file is there any problem in the format of the following

Re: [ccp4bb] Cif file in coot

Hello Yang, You need dictionary for the residue 'abc' which will have all the geometric restraints defined. You can read the residue co-ordinates in Monomer Library Sketcher in CCP4i and writeout the dictionary file using LIBCHECK. You will be able to refine abc once you import monomer CIF di

Re: [ccp4bb] Cif file in coot

Dear Yang Li, What to do depends on whether what you call ABC is the same thing as is in the Refmac dictionary. Refmac thinks ABC is for 'MODIFIED ACARBOSE HEXASACCHARIDE'. If that is what you have - and the atom names match, then simply Get Monomer -> ABC. That will run libcheck and

Re: [ccp4bb] Cif file in coot

Dear Yang Li, you probably can download your library file (CIF) from the Hic-up website: http://xray.bmc.uu.se/hicup/ Infact an heterocompound named "abc" is already existing there... that's a "modified acarbose hexasaccharide". Is that the one you were looking for? In this case, here it is: http:/

[ccp4bb] Cif file in coot

Hi All, If I have a pdb with some residues named "abc" in it, coot can read it and display it well, but I cannot do real space refine to such residues. The tips asks me to import a CIF file, I wonder what is the format of this CIF file? How can I create it and let coot recognise these residu