Re: [ccp4bb] outliers

Dear James, I hope I will not disturb this thread and you will further continue with the theoretical aspects. But, what is the motivation for such a general question? In my crystal structures, I usually have many bonds outside the 3-sigma interval. Especially in the case of ligands. And not only

Re: [ccp4bb] PAIREF, Anisotropy and STARANISO

Dear Gerard, A great remark! Thank you for starting this thread separately. I think that you are absolutely right in many of the points. However, it also raises several questions. Here are my favourite ones: 1) If STARANISO generally suggests "the same" resolution as PAIREF, there are fewer ref

Re: [ccp4bb] PAIREF - Warning - not enough free reflections in resolution bin

Dear Matt, There are great responses in this thread already. There are several points and questions from my side: 1) I did not get clearly what exactly was done. Where did you start your paired refinement? What were the statistics for your starting resolution? 2) Did it improve all the way to the

Re: [ccp4bb] Strange crystal packing in twined crystal -follow up

Dear Florian, I had a similar problem in the past. The uninterpretable electron density was mainly because of weird refinement of anisotropic ADPs. The resolution was about 1.2 AA. The refinement was somehow divergent. Is it also your case? You can check the ellipsoidal ADPs in Coot. Moreover, d

Re: [ccp4bb] Phasing a difficult RNA heteroduplex structure

Dear Charlie Nichols, when optimizing your SHELX runs, SHELIXIR may help you in some cases (https://kmlinux.fjfi.cvut.cz/~kolenpe1/shelixir). A couple of days ago, I created quick and dirty tutorial to SHELIXIR command line: https://www.youtube.com/watch?v=dqi5_yLhWOc and also the same quality t

[ccp4bb] Anomalous maps from twinned crystal

Dear colleagues, We have data from a twinned crystal (merohedral twinning with fraction of 0.71) for which we want to see the anomalous map. Could you please guide me how to calculate it using the i2? Running refinement with REFMAC5 with merohedral twinning does not allow simultaneous generation

Re: [ccp4bb] the complex structure of protein and DNA

Dear Yang Meiting, There are few things to know better about your structures first: 1) What is the resolution of the complex structure? 2) In what stage of structure refinement you are? Rwork/free would help. 3) Have you tried some automatic DNA building tools? I am not surprised that you can see o

Re: [ccp4bb] Different conformation of chains

Dear Shine.star1609, Your structural observation may be really different from the original one. There are several things to do now: 1. Check whether the same interpretation could be possible in the original structure. Are there maps or the original diffraction data? You could also reprocess

Re: [ccp4bb] criteria to set resolution limit

MAIL.AC.UK; Petr Kolenko Subject: Re: [ccp4bb] criteria to set resolution limit Hello Petr, I would like to understand more completely your assertion in the last email regarding completeness: "I would not care about low data completeness in case when PAIREF shows improvement of your model.&quo

Re: [ccp4bb] criteria to set resolution limit

Dear Farhan, Your dataset does not seem to be that critically anisotropic to me. But of course, try the STARANISO server and make your own decision. To me, the dataset seems to be collected with a suboptimal data strategy. Although I do not know your setup, I would make the crystal-to-detector d

[ccp4bb] PAIREF Webinar (23rd March 2021, 15:00 CET)

ENIX users. 3. Short tutorial (files will be provided). 4. Discussion. Feel free to contact us with your data. Best regards, Petr Kolenko, Martin Maly, Kay Diederichs and Jan Dohnalek To unsubscribe from the CCP4BB l

Re: [ccp4bb] Anomalous signal to noise details

Dear David, Although this is not exactly a topic of your question, an alternative approach is to use the resolution screening and compare the results. I have implemented this approach to my program SHELIXIR (because it uses SHELX C/D/E), which can be found here: http://kmlinux.fjfi.cvut.cz/~kole

Re: [ccp4bb] Twin law definition in REFMAC5

u for your response, Petr From: Eleanor Dodson Sent: Tuesday, July 7, 2020 7:08:44 AM To: Petr Kolenko Cc: CCP4BB@jiscmail.ac.uk Subject: Re: [ccp4bb] Twin law definition in REFMAC5 Is that twin law possible? Presumably the cell lengths for b and c are clos

[ccp4bb] Twin law definition in REFMAC5

Dear colleagues, I have a crystal with space group P21212 and merohedral twinning according to "-h, l, k" twin law. If I click "twin" in the interface, REFMAC5 recognizes a different twin law and does not refine the structure properly. Is there a way to tell REFMAC5 the proper twin law? I tried

[ccp4bb] Paired refinement proves data quality goes beyond the spatial limits of the detector

Dear colleagues, We, the developers of a program for paired refinement, have found a remarkable feature that should be shared with the community. The fact that data beyond the arbitrary cutoff may cause an improvement of electron density and make your models better is generally accepted. We foun

Re: [ccp4bb] Raw diffraction images for SARS-CoV-2 related structures

For those of you who are in touch with these data, would deposition of unmerged intensities in P1 in the whole detector range instead of complete dataset be good enough to „correctly“ re-evaluete the structure? Or is there a doubt that even this approach would not lead to optimal structure? My

Re: [ccp4bb] Macromolecular Crystallography workshop in South America 2020

I apologize for the 1st April joke, but I could not resist. And it would not be actual in three months. I guess that if the workshop were announced this way, nobody would even care. Dear colleagues, We are pleased to announce the 8th South American Macromolecular Crystallography School: Macromo

Re: [ccp4bb] protein expression in human cells

Dear colleagues, I wonder if there were a bit less controversial possibility. No matter if that was less efficient. Would there be an option of using human cell lines that do not origin from killed children? As far as I know, the HEK cells do. Sometimes, the science can be pretty cruel. I am sor

Re: [ccp4bb] Unable to receive mails

Dear Manjula, #metoo :-D I think it is just a rare occasion that nobody has posted anything (except you, of course). ;-) Best regards. Petr From: CCP4 bulletin board On Behalf Of Manjula Ramu Sent: Tuesday, April 30, 2019 12:46 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Unable to receive ma

Re: [ccp4bb] select from a pdb file a sphere of atoms

This is easy to do in Pymol again. If you have atoms in selection "nameX", the command is "select nameX, br. nameX". Very simple. Best regards, Petr From: CCP4 bulletin board on behalf of Gianluca Santoni Sent: Wednesday, April 3, 2019 5:13:59 PM To: CC

Re: [ccp4bb] select from a pdb file a sphere of atoms

Dear Stephen, PyMOL can do it. You have to choose your atom and then use following command: select your-name, (sele) expand 10; where (sele) is your selection - atom or a group of atoms and 10 is the radius in AA. Best regards, Petr From: CCP4 bulletin bo

[ccp4bb] Bright future of CIF

Dear colleagues, As all of you know, CIF will soon be the only acceptable file format in macromolecular crystallography. CIF file has many advantages when compared to traditionally used stone-aged formats like PHS, MTZ, or archaic PDB. One of the advantages is the includability and mergability o

[ccp4bb] Backup of whole synchrotrons

Dear colleagues, We all are very happy about the storage of raw crystallographic datasets. But, is it really enough? No! Can we do better? Yes, of course! The problem is that the crystal after the measurement is usually burned. It does not make sense to store them any more. But, in order to maxim

[ccp4bb] Inquiry - active and non-active state in alternatives

Dear colleagues, We are working on a paper, where we want to discuss our crystal structure. We have determined structure of non-active state first (much easier). Than we tried to convert the protein into active state by soaking (direct crystallization not possible). We have observed more than

Re: [ccp4bb] Composit omit map vs. ligand

for your help! Petr Dne 08.02.2017 v 9:05 Petr Kolenko napsal(a): 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

[ccp4bb] Composit omit map vs. ligand

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 th

Re: [ccp4bb] raw data deposition

J Phys Chem Lett. 2010 Oct 7;1(19):2898-2902 > [2] Acta Crystallogr D Biol Crystallogr. 2009 Mar;65(Pt 3):294-6. > [3] Manuscript in progress > > > Katherine Sippel, PhD > Postdoctoral Associate > Baylor College of Medicine > -- Petr Kolenko kole...@imc.cas.cz http://kolda.webz.cz

Re: [ccp4bb] Is there a protein that it could interact with different proteins by the same part?

ent proteins by the same part (maybe the same part but in > different conformations?)? Thank you in advance!! > > yamei > -- Petr Kolenko kole...@imc.cas.cz http://kolda.webz.cz

Re: [ccp4bb] Waters in ADIT

inal Message- > From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Petr > Kolenko > Sent: 22 June 2011 12:18 > To: CCP4BB@JISCMAIL.AC.UK > Subject: [ccp4bb] Waters in ADIT > > Dear colleagues, > > I want to deposit one structure, but ADIT reports tens

[ccp4bb] Waters in ADIT

ot in this case, but the previous one) I do not have to solve this problem, but I do not want to have so strange Validation Report from ADIT. Many thanks for any idea. Petr PS: Not important, but refined with REFMAC5 at medium resolution. -- Petr Kolenko kole...@imc.cas.cz http://kolda.webz.cz

Re: [ccp4bb] Problems in refinement

t add the TLS contribution to the output > coordinates when you use Refmac except in the last run before to deposit the > file into to PDB. Phenix removes it automatically. > Kind regards, > David > > On 05/27/2011 10:57 AM, Petr Kolenko wrote: >> >> Dear colleagues, >

Re: [ccp4bb] Problems in refinement

od picture of what's > going on ..probably a feature which would disappear with newer versions > anyway. > > What's the version of Refmac you use, Petr? > > Jan Dohnalek > > > On Thu, May 26, 2011 at 12:11 PM, Petr Kolenko wrote: >> >> Dear col

Re: [ccp4bb] Problems in refinement

istry & Molecular Biology > Johns Hopkins Malaria Research Institute > 615 North Wolfe Street, W8708 > Baltimore, MD 21205 > Phone: +1-410-614-4742 > Lab:      +1-410-614-4894 > Fax:      +1-410-955-3655 > http://web.mac.com/bosch_lab/ > > On May 26, 2011, at 6:11, Petr

[ccp4bb] Problems in refinement

here again. It is always one or two atoms from the same residues - sometimes Calpha, sometimes Cbeta, sometimes C, sometimes NH1, but still on the same five residues. Does anyone have any idea how to solve this problem? Many thanks for any response. Petr -- Petr Kolenko petr.kole...@bioch

Re: [ccp4bb] Space group vs. gap between Rwork and Rfree?

pointing out a lower real symmetry (I23) than suggested by > POINTLESS or PHENIX.XTRIAGE (I432)? I have tried different selection > of free reflections in I432 dataset already, but with almost the same > results. > > Many thanks for any response. > Petr > > -- > Petr Kolenko &

Re: [ccp4bb] Space group vs. gap between Rwork and Rfree?

values (at the level of CORRECT) vere very similar > both for P222 and for P6 integration. > > HTH, > > Fred. > > Petr Kolenko wrote: >> >> Dear colleagues, >> >> I appreciate any help, or any suggestion with my difficult data. Many >> thanks at l

[ccp4bb] Space group vs. gap between Rwork and Rfree?

results. Many thanks for any response. Petr -- Petr Kolenko petr.kole...@biochemtech.uni-halle.de http://kolda.webz.cz

Re: [ccp4bb] Problem with finding of spots

. Actually, I have tried more than half of your suggestions before, but I still learned a lot from you. I think that this community is so far the best what internet offers. ;) Many thanks again. Petr -- Petr Kolenko petr.kole...@biochemtech.uni-halle.de http://kolda.webz.cz 2010/11/23 Petr Kolenk

[ccp4bb] Problem with finding of spots

Does anyone have any suggestion, please? Btw, we have several structures in the PDB from this experimental setup. This is the first problem I have met. Many thanks for any response. Petr -- Petr Kolenko petr.kole...@biochemtech.uni-halle.de http://kolda.webz.cz

[ccp4bb] Low-resolution structure refinement with Refmac

for low-resolution structure, or should I spent a long time to fix them all? Many thanks. Petr Petr Kolenko kole...@imc.cas.cz --- Institute of Biochemistry/Biotechnology Martin-Luther-Universität Halle-Wittenberg Kurt-Mothes-Str. 3 06120 Halle (Saale

Re: [ccp4bb] OFF: Intein-chitin purification method

Yes, I know. I am already working on some other modifications, or analogues. The questions was only to know some experience from different labs. Thanks. Petr 2010/7/5 Vellieux Frederic > Petr Kolenko wrote: > >> Dear all, >> >> I am working on crystallization of a prote

[ccp4bb] OFF: Intein-chitin purification method

, e.g. Has anyone of you observed something similar for intein-chitin chromatography? Is there any serious "structural" damage to the target protein during the purification? -- Petr Kolenko kole...@imc.cas.cz http://kolda.webz.cz

Re: [ccp4bb] xds undefined data_range error

create a "new directory" in your "directory with XDS.INP" with symbolic link to the images to have the path like "../my-data/crystal1_001.img" because long path may not work in XDS. It may not solve your problem, but I would try this at first. Best wishes. ;) Petr P

Re: [ccp4bb] sugar ligand refinement in coot

records. I would prefer the most similar ones. ;) Best wishes, Petr Petr Kolenko [EMAIL PROTECTED] protein.awardspace.com lei feng wrote: Hello Carlos thanks for your kindly reply. I think the cif file ( GLC_mon_lib.cif ) is only for one glucose molecule, it can not regulate the bond

Re: [ccp4bb] Missing space group in ?.mtz file

Petr Kolenko [EMAIL PROTECTED] Martyn Winn wrote: Dobre den, If all else fails, use a text editor! I use emacs for this ... Most of the file will look like garbage, but the header at the end of the file can be edited. Be very very careful not to change the number of characters just do

Re: [ccp4bb] Missing space group in ?.mtz file

oes it show the path? Either Solve or CCP4? On Tue, Jul 8, 2008 at 10:15 AM, Petr Kolenko <[EMAIL PROTECTED]> wrote: Unfortunately, it also failed: Failed to find spacegroup in SYMINFO! MTZTONA4: Fatal error in ccp4spg_register_by_symops Does anybody know how to fix it? Petr

Re: [ccp4bb] Missing space group in ?.mtz file

Unfortunately, it also failed: Failed to find spacegroup in SYMINFO! MTZTONA4: Fatal error in ccp4spg_register_by_symops Does anybody know how to fix it? Petr

[ccp4bb] Missing space group in ?.mtz file

, please? Thanks for all of them. Best Regards, Petr Petr Kolenko [EMAIL PROTECTED]

Re: [ccp4bb] Coot for Fedora Core 8?

Hi Fred, we use this version and we did not have any problem. http://www.ysbl.york.ac.uk/~emsley/software/binaries/nightlies/pre-release/coot-0.4-pre-2-revision-618-binary-Linux-i386-redhat-8.0.tar.gz We usually use redhat-8.0 binary versions. Best wishes! Petr Kolenko Vellieux wrote: hi