Re: [ccp4bb] Twinning and R-Free

Hi Alun and Kay, PDB_REDO does some more extended twinning testing with among others Phaser, so it would be worthwhile to have a look at that. On the server it refuses to do twinned refinement if there is no clear indication of twinning even if the user assumed twinning before. The fact the

Re: [ccp4bb] variation in freerflag

Adding to this: the current test set generation in freerflag has one brilliant feature and that is reproducibility. If you misplace your test set, you can reproduce the same one if you run freerflag on the same complete set of reflections. This was an excellent design choice. It has proved very

Re: [ccp4bb] variation in freerflag

:29 To: Robbie Joosten Cc: CCP4BB@jiscmail.ac.uk Subject: Re: [ccp4bb] variation in freerflag Hi Robbie, I had long wondered how to flag the fields in game minesweeper with a deterministic algorithm. When I read about 'random sort and bin' I though this was quite a beautiful way. I wonder

Re: [ccp4bb] variation in freerflag

Hi Tim, I was discussing that with a student today, because we observe the same thing when we make test sets for k-fold cross validation. It is an implementation choice. You can random sort and then bin, or you can assign a random number to each reflection and translate that to a bin. The

Re: [ccp4bb] Unknown electron density blob, pdb convention for partially ordered ligands

Hi Tristan, There are PDB entries that have this, but this makes matters a bit more complicated in annotation. You have to define LINKs and leaving atoms. Consistency would be nice here, but that is lacking in these entries. Cheers, Robbie Sent from my Windows 10 phone Van: Tristan

Re: [ccp4bb] Unknown electron density blob

PEG likes to hang around where it is unwelcome: http://onlinelibrary.wiley.com/doi/10.1002/pro.2923/full Cheers, Robbie Sent from my Windows 10 phone Van: Bernhard Rupp Verzonden: dinsdag 24 januari 2017 23:20 Aan:

Re: [ccp4bb] Calculation of generalised R-factor?

uesday, December 20, 2016 15:46 > To: Robbie Joosten <robbie_joos...@hotmail.com>; CCP4BB > <ccp4bb@jiscmail.ac.uk> > Subject: Re: [ccp4bb] Calculation of generalised R-factor? > > Dear Robbie, > > > thanks for your reply. According to the REFMAC5 manual, the

Re: [ccp4bb] Calculation of generalised R-factor?

The value for the Hamilton test is written by Refmac as the weighted R-factor. There was a follow-up paper that showed that you shouldn’t use the normal R-factor for the Hamilton test. PDB_REDO does the Hamilton test automatically, but you can also feed two Refmac logfiles to the bselect

Re: [ccp4bb] jligand help

Hi Nicholas, CCP4 6.5 is end-of-life and no longer supported. Please upgrade to version 7.0. Apart from the obvious benefit of having up-to-date softeare, JLigand should also work. Cheers, Robbie Sent from my Windows 10 phone Van: Nicholas Larsen

Re: [ccp4bb] Message from the Uppsala EDS: "Morituri te salutant"

Hi Gerard, EDS has made the life of many structural biologist easier (and some crystallographers harder) by providing maps at a time when reading reflection files from the PDB was still a total nightmare and real-space scores when it still was a such a hassle to calculate them. I don’t know

Re: [ccp4bb] programmatically get mtz files from PDB_REDO

Hi Rob, You are right that the two characters are the middle two of the PDBid. The server that generates the list of entries is being fixed. Cheers, Robbie Verzonden vanaf mijn Windows 10-telefoon Van: R.D. Oeffner Verzonden: vrijdag 25 november 2016 18:52 Aan:

Re: [ccp4bb] FW: [ccp4bb] Fwd: [ccp4bb] just out of totally idle curiosity ...

There is nothing wrong with discussing sex at work, either theorethical http://www.rcsb.org/pdb/search/structidSearch.do?structureId=1sex or experimental http://www.rcsb.org/pdb/explore/explore.do?structureId=3sex ?? Sent from my Windows 10 phone Van: Reza

[ccp4bb] Slightly off-topic: job opportunities at NKI, Amsterdam, NL

software development team of Robbie Joosten and Anastassis Perrakis, who run a research program in computational structural biology / structural bioinformatics (see for example PDB_REDO and CCD) and participate in multiple European projects: West-Life (a Horizon2020 Virtual Research Environment

Re: [ccp4bb] metal electron density detection

Hi Ansuman, Do you really want to do this in an automated way? Wouldn’t you rather figure it out for yourself? There is some automation in Phenix for ion building, but you still need to verify yourself. The CheckMyMetal server is quite good for that, but beware that to some extent you find

Re: [ccp4bb] Wilson B-factors recorded for all PDB's to 3.5Å

Hi Amit, Calculating the Wilson B at that resolution becomes a bit iffy. So I would be a bit careful with drawing any conclusions from it. We have the numbers calculated by sfcheck for the pdb_redo databank. Cheers, Robbie Sent from my Windows 10 phone Van: amit

Re: [ccp4bb] Structural biology software that does not run on Windows or gives important Windows-specific problems

I’ve made simple native Windows programs in fortran. There are proper compilers that run without the hassle of crosscompiling. Cheers, Robbie Sent from my Windows 10 phone Van: Patrick Loll Verzonden: vrijdag 14 oktober 2016 18:32 Aan:

Re: [ccp4bb] Structural biology software that does not run on Windows or gives important Windows-specific problems

Windows 10 now allows a full Ubuntu within Windows. It actually works quite easily. There is a good rsync for windows. I use it to make back-ups of the pdb_redo databank. Windows has it own system of incremental backups which works well in my hands. There are two scripting systems in Windows

Re: [ccp4bb] High B factor

Hi Sunanda, If you model is good, high average B-factors are just caused by the quality of your data. You can sometimes improve this a bit by careful reprocessing (e.g. by not using the last frames where radiation damage really kicked in). Sometimes you can have a better crystal and your data

Re: [ccp4bb] open old job list under a project in a newly installed ccp4

Hi Raj, You can just add the old project directory as a new project in your new installation. Cheers, Robbie From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Raja Dey Sent: Tuesday, October 11, 2016 21:53 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] open old job

Re: [ccp4bb] Ambiguous metal ion at active site.

Hi Dilip, There are a few things you might try. You have to make sure that all coordinating atoms (including waters) are in your model. If you refined with TLS for the protein, try resetting the B-factors for all atoms and refine without TLS. If this reduces the difference density, you

Re: [ccp4bb] on R-free label

Just run mtzdmp on your file and look at the data columns. The column label should be very obvious. Cheers, Robbie Sent with my Windows Phone Van: Smith Liumailto:smith_liu...@163.com Verzonden: ‎5-‎7-‎2015 10:01 Aan:

Re: [ccp4bb] paired refinement

But it is not the R-free of the shell here. In paired refinement you take the R-free of the reflections outside the shell. Cheers, Robbie Sent with my Windows Phone Van: Edward A. Berrymailto:ber...@upstate.edu Verzonden: ‎2-‎7-‎2015 18:43 Aan:

Re: [ccp4bb] paired refinement

. eab On 07/02/2015 12:52 PM, Keller, Jacob wrote: Wasn’t all of this put to bed through the implementation of CC measures? JPK *From:*CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of *Robbie Joosten *Sent:* Thursday, July 02, 2015 12:46 PM *To:* CCP4BB

Re: [ccp4bb] paired refinement

Hi Eric, Since you are asking your question on the CCP4 bulletin board, I will give a CCP4 answer. Take your model refined to 2.7A and through it into PDB_REDO with the full 2.3A dataset. It will automatically do paired refinement and pick a resolution cut-off in REFMAC. No mucking about with

Re: [ccp4bb] Rfree below Rwork

Hi Wolfram, You didn’t tell us where your model came from but 10 cycles of TLS and 10 cycles of restrained refinement is not enough for a refinement to converge if you just picked your test set. Try resetting your B-factor and doing 30-40 cycles refinement in REFMAC. Cheers, Robbie

Re: [ccp4bb] Generating Restraints for a Synthetic Peptide

Dear Sean, For a synthetic peptide, you should only make restraints for the non-standard amino acids that are not already in the dictionary. You can do this graphically in jLigand which is part of CCP4. If you give the atoms names consistent with regular amino acids and define the

Re: [ccp4bb] Residual density feature

Hi Colin, You can define an UNL (unknown ligand) in the blob. This is the standard name for such a compound. It becomes a bit messy in refinement in terms of restraints, but it does exactly what you want it to do: say you noticed the blob but couldn't figure out what it was. Cheers, Robbie

Re: [ccp4bb] Refmac fatal error with newly added ligand

Hi Sze Yi, There is already a compound named LIG in the Refmac dictionary. So either you have to choose a new name or you overrule the dictionary by supplying a restraint file in your Refmac run. Cheers, Robbie -Original Message- From: CCP4 bulletin board

Re: [ccp4bb] calculation of map correlation coefficient

You can try EDSTATS in CCP4 to get the numbers you want. This works very well for us. Cheers, Robbie Sent with my Windows Phone Van: Andreas Heinemailto:hei...@mailer.uni-marburg.de Verzonden: ‎3-‎6-‎2015 15:43 Aan:

Re: [ccp4bb] How many is too many free reflections?

Hi Graeme, We have had similar discussion with PDB_REDO that is frequently forced to assign a new R-free set when the input data doesn’t have one (this still happens with new PDB entries!). The ‘500/1000/1500/2000 reflections’ is enough school seems to look only at the variance of R-free

Re: [ccp4bb] PyMOL v. Coot map 'level'

Hi Emilia, Did you construct the map at the same sampling rate as COOT uses? This makes a big difference. You can also just use CCP4mg. You can make very nice pictures with that and you can do all the map things there. CCP4mg supports mtz files directly, so no mucking about with map files.

Re: [ccp4bb] HIS related crystallography issue

You can typically assign the histidine orientation based on analysis of the hydrogen bond network. In ambiguous cases you might have to look a few residues deep. WHAT_CHECK does this for you by a global optimization of the hydrogen bond network. Cheers, Robbie Sent with my Windows Phone

Re: [ccp4bb] [RANT] Reject Papers describing non-open source software

I strongly disagree with rejecting paper for any other reasons than scientific ones. A paper describing software should properly describe the algorithms to ensure the reproducibility. The source should be available for inspection to ensure the program does what was claimed, for all I care this can

Re: [ccp4bb] 3BDN, 16.5% Ramachandran Outliers!!!!!

The PDB_REDO entry for 3bdn was pretty old, so I replaced it using a newer version of PDB_REDO that can use nucleic acid restraints from LibG: http://www.cmbi.ru.nl/pdb_redo/bd/3bdn/index.html. Obviously, the new structure model is far from brilliant (PDB_REDO doesn't rebuild at this

Re: [ccp4bb] AW: [ccp4bb] on NCS restraint

programs would require NCS related subunits to be similar, but not identical to each other. As Robbie Joosten pointed at, this can help a lot, especially when you do not have high resolution data. So for data with better than 2.0 Å resolution, including NCS restraints would probably not make a big

Re: [ccp4bb] on NCS restraint

The modern implementations of local NCS restraints are quite forgiving when it comes to structural differences, so normally they work very well with very little risk. In a practical CCP4 sense: Just switch on local NCS restraints in Refmac. They will do the trick. Using those is also the

Re: [ccp4bb] Refmac- riding hydrogen

Hi Sasha, Yes, it does and I highly recommend using this option all the time. It really makes the VdW restraints much more effective. Cheers, Robbie -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Sasha Pausch Sent: Wednesday, April 15, 2015

Re: [ccp4bb] how to recover my data

Hi Smith, If this is really the problem Ian describes, you can try the Linux programs unix2dos and dos2unix the change the line endings. A potential source of the problem might be copying the file with certain (S)FTP clients: in 'text-mode' they change the line endings to your OS default to be

Re: [ccp4bb] adjusting bad Ramachandran angles

is that the conformational torsion angles are eminently suited for validation purposes, but only when they are unrestrained. in other words, once you restrain phi and psi, you can't use ramachandran plots any longer (well, you can, but they are useless as validation tools) On 02/25/2015 12:21 PM, Robbie Joosten

[ccp4bb] New: PDB_REDO version 6 (now also for OSX)

for their software on the server. Developers in the PDB_REDO project: Amsterdam: Robbie Joosten, Bart van Beusekom, Krista Joosten, Anastassis Perrakis Nijmegen: Wouter Touw, Gert Vriend Cambridge: Fei Long and Garib Murshudov Special thanks to: Doug Kuntz, Luca Jovine, and Richard Bunker for requesting

Re: [ccp4bb] Absence of contact between layers in a crystal

Not in real crystal structures ;) Cheers, Robbie Sent with my Windows Phone Van: Kerff Fredmailto:fke...@ulg.ac.be Verzonden: ‎6-‎2-‎2015 12:02 Aan: CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK Onderwerp: [ccp4bb] Absence of contact between layers in a

Re: [ccp4bb] Absence of contact between layers in a crystal

a bad job of making up a structure. Randy On 6 Feb 2015, at 11:09, Robbie Joosten robbie_joos...@hotmail.com wrote: Not in real crystal structures ;) Cheers, Robbie Sent with my Windows Phone Van: Kerff Fred Verzonden: ‎6-‎2-‎2015 12:02 Aan: CCP4BB@JISCMAIL.AC.UK Onderwerp: [ccp4bb

Re: [ccp4bb] Bin R and Rfree values

Hi Faisal, A lower R-free than R in the highest bin is not a big problem. The test set in you highest resolution bin may be quite small which makes the values not so reliable. Phenix uses different bins from what Refmac uses so you cannot compare the values. If you performed your final

Re: [ccp4bb] Bin R and Rfree values

Hi Bernhard, The rmsZ only says something about the deviations from 'ideal' values given their esd. It is by no means a strong validation criterion. Values over 1.000 only say that your distribution is wider than expected (if you have no serious individual outliers). So by changing target esds

Re: [ccp4bb] proton scattering by X-rays

Hi Peter, I don't have access to the paper from here, but the abstract implies that the H+ is attached to a cysteine sulphur. In that case it have the shared electrons to scatter X-rays. The text a proton (H+) attached to the sulphur of a cysteine ligand is not very pretty. I would call it a

Re: [ccp4bb] fitting peptide with non-standard and standard amino acids

Dear Emmanuel, Is the modified residues are really new, you can make restraint files with jligand or acedrug (both in CCP4). Make sure the backbone atoms have the same names as in standard amino acids. Now open de cif-file(s) in a text editor and set the residue type to 'peptide' (you can use

Re: [ccp4bb] Visualizing Stereo view

Hi Jeorge, The easiest was of making a stereo image is with CCP4mg. You just need to tick a box when you make an image. Looking at stereo images takes practice, but it is a useful skill. It also helps with those spot-the-differences puzzles :) Cheers, Robbie -Oorspronkelijk bericht-

Re: [ccp4bb] additional density on cysteine residue

Hi Sreetama, The water S-gamma distance made me think that it might be a cysteine beta-mercaptoethanol adduct. Try building CME instead of CSO. Cheers, Robbie -Oorspronkelijk bericht- Van: sreetama das somon_...@yahoo.co.in Verzonden: ‎17-‎1-‎2015 19:27 Aan: CCP4BB@JISCMAIL.AC.UK

[ccp4bb] Test

This is a test Sent from my Windows Phone

Re: [ccp4bb] Small molecule cif files

Hi Joel, If you fixed an existing restraint file you can send it to the CCP4 support staff preferably with a description of what was changed and why. A PDBid for a structure model with that particular compound (for testing) is also very welcome. New compounds will end up in the dictionary

Re: [ccp4bb] water at the same exactly position

Hi Luzuok, Any validation program that detects clashes should hind these. Cheers, Robbie Sent from my Windows Phone Van: luzuok Verzonden: 30-10-2014 10:58 Aan: CCP4BB@JISCMAIL.AC.UK Onderwerp: Re: [ccp4bb] water at the same exactly position Dear Nat, But if

Re: [ccp4bb] Merge PDB chains

Dear Lu, You could do this in Coot as well if you are uncomfortable doing this in a text editor. First change the residue numbers so they do not overlap, then change the chainID. Rather than putting all your sulfates in a separate chain, it is better to add them to the correct protein chain.

Re: [ccp4bb] molprobity clashscore, symmetry-related molecules?

Hi Tim, AFAIK MolProbity is not symmetry aware. If you want to detect cross-symmetry clashes you can use WHAT_CHECK. Cheers, Robbie -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Tim Sent: Thursday, October 23, 2014 12:43 To:

Re: [ccp4bb] Refinement of Iron-sulphur clusters

Dear Stephen, The dictionary is very specific about atom names. If you have them swapped (as many PDB entries do). The angle and chiral volume restraints will wreck your cluster. You also need to make sure to provide LINK records to attach the cluster to the surrounding cysteines. HTH, Robbie

Re: [ccp4bb] 3 letter code

Hi Faisal, You can also look in LigandExpo http://ligand-expo.rcsb.org/index.html If you don't find a result immediately, you can also search by formula, even without hydrogens. Cheers, Robbie -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of

Re: [ccp4bb] How to generate cif file?

HI Gaelle, If both the nucleotide already exists in the PDB (you can check on LigandExpo), you can just create a LINK description with Jligand in CCP4. See this tutorial: http://www.ysbl.york.ac.uk/mxstat/JLigand/tutorial_link.html If you have the cif file with the LINK description, you can just

Re: [ccp4bb] software or server to validate ligand density

Dear Ansuman, The PDB_REDO server has extensive ligand validation, but it won't tell you explicitly whether the ligand is there or not. You have to figure that out from the validation scores. High real-space R values or low real-space correlation coefficients are a hint that your ligand isn't

Re: [ccp4bb] KRAS maps

Hi Nick, Not sure what happened here, it seems like a bug in this EDS entry. You can try PDB_REDO for maps. In recent versions of COOT (version 0.8*) the button for getting maps and a model is just under that for EDS. There is a plugin for older versions of COOT. They look okay, but the model

Re: [ccp4bb] correlated alternate confs - validation?

Hi Bernhard, The validation of alternates is indeed quite poor and any improvements would probably depend on proper annotation by the depositor, particularly in complex correlated cases. For your model I would probably make the two waters alternates of each other. That way, it is easier to

Re: [ccp4bb] validation report

Hi Faisal, It is here: http://wwpdb-validation.wwpdb.org/validservice/ Cheers, Robbie -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Faisal Tarique Sent: Saturday, July 19, 2014 14:26 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] validation

Re: [ccp4bb] Invisible atoms in ligands

Hi Tim, The problem with missing atoms in ligands is that you cannot use the coordinates for any follow-up calculation that requires ligand topology (e.g. restraint generation). That forces you to rely on the annotation of the compound, for instance at the PDB. That can be quite messy and

Re: [ccp4bb] Invisible atoms in ligands

Joosten; CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Invisible atoms in ligands -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi Robbie, maybe it is good not to use coordinates for calculations if you cannot measure the coordinates? Cheers, Tim On 06/13/2014 12:35 PM, Robbie Joosten

Re: [ccp4bb] H-Bond Energy Vs. Length/Geometry/Charge?

Hi Jacob, Modeling programs need to take hydrogen bonding into account in their force fields so they typically have good measures for hydrogen bonds. I personally use YASARA to get the numbers you want. This is also what PDB_REDO uses to give you the hydrogen bond energy and the the number of

Re: [ccp4bb] ideal rms bond and rms angle

Hi Faisal, There are no clearly defined targets for rmsd because it is the rms of values with different standard deviations. You should use rmsZ instead (reported by Refmac) because the deviations are on the same scale. For rmsZ, any value below 1.0 is fine if it gives you the best fit with the

Re: [ccp4bb] TER in PDB file

Dear Felix, I recently had the same problem. I didn't think TER records were a big deal. I never had a program that did weird thing because of missing TER records. But well, orders are orders, so we need TER records for deposition. It would be nice if all refinement programs would write those.

Re: [ccp4bb] 100.000?

Hi Tim, PDBe always posts the number of new releases on Facebook (gotta like that). The recent average is about 175 new entries per week. Cheers, Robbie Sent from my Windows Phone Van: Tim Gruene Verzonden: 10-5-2014 22:00 Aan: CCP4BB@JISCMAIL.AC.UK Onderwerp:

Re: [ccp4bb] How to get a CIF configure for a designed ligand

Hi Robert, This is very easy with the CCP4 program JLigand. Just start a new ligand with the sulfur atom, add the phenyl groups, the extra bond and the hydrogens. Then regularise and save the restraint file. HTH, Robbie -Original Message- From: CCP4 bulletin board

Re: [ccp4bb] coot problems to decrease R FREE

Hi Pavel, I agree that you bias R-free after the real-space refinement well, ok, isn't it enough to realize that this is bad and should be avoided ? (I guess we all know we should never bias Rfree!) My point was that we normally do not calculate R-free after real-

Re: [ccp4bb] coot problems to decrease R FREE

.asp From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Robbie Joosten [robbie_joos...@hotmail.com] Sent: Monday, April 21, 2014 4:40 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] coot problems to decrease R FREE Dear Peter, I'm

Re: [ccp4bb] coot problems to decrease R FREE

to the test set. However, this bias is lost after (converged!) reciprocal-space refinement. I think that for the final R-free these are equivalent. Cheers, Robbie -Original Message- From: Pavel Afonine [mailto:pafon...@gmail.com] Sent: Thursday, April 24, 2014 17:27 To: Robbie Joosten

Re: [ccp4bb] coot problems to decrease R FREE

Dear Peter, I'm a novice of coot and ccp4. Now I'm doing refinement using both refmac5 and coot.Here are some problems I'm facing. Really hope you can give me some suggestions. 1、THE RESOLUTION OF THE DATA IS 2.5 angstrom. After first refinement of refmac5 I got R factor which is 0.26 and R

Re: [ccp4bb] Display MTZ header in tooltips in Windows Explorer

Hi Rob, Thank you for that cool tool. Such a thing would be nice to have in the CCP4 distribution (hint!). Cheers, Robbie -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Robert Oeffner Sent: Sunday, April 13, 2014 17:11 To:

Re: [ccp4bb] EDS server - R-value

Hi, Did you look at the same structure in the PDB_REDO databank (www.cmbi.ru.nl/pdb_redo)? If the problem can be solved, the structure and maps should be there. If it cannot, you might get a slightly more informative error message from the WHY_NOT server. Cheers, Robbie Sent from my Windows

Re: [ccp4bb] twin refinement

Dear Wolfram, First of all you should make sure you have substantial twinning. Is the twin fraction close to zero, then don't use a twin target. Is twinning detected by several test, then there is a good chance your data are twinned. As for validation, if you do not completely trust your

Re: [ccp4bb] Validity of Ion Sites in PDB

Dear Jacob, There are a lot of potential problems with ion validation, that make obtaining a reliable answer difficult. If you want to datamine ion validation results, you can use the ready-made WHAT_CHECK files in the PDBREPORT databank for original PDB files or in the PDB_REDO databank for

Re: [ccp4bb] New ligand

Hi Louise, You can go through the mon_lib_list.cif file of the CCP4 dictionary to get a name that is free (e.g. A97). It would be nice is a certain name would be reserved for this by the PDB. LIG was a good candidate, but it's gone just like other nice options (XXX, ZZZ, 000). Cheers, Robbie

Re: [ccp4bb] keep ligand conformation

Dear Koji, In addition to all the things Tim said, you may also have a conflict between the ligand conformation you modelled and the conformation described in your restraint file. The Refmac logfile will mark any really severe outliers, but smaller problems can still exist. Try regularising

Re: [ccp4bb] Sister CCPs

eleanor.dod...@york.ac.uk wrote: I agree with Frank - it keeps crystallographers modest to know how challenging wet lab stuff still is.. Eleanor On 12 February 2014 19:23, Robbie Joosten robbie_joos...@hotmail.com wrote: It's not an e-mail bulletin board, but Researchgate seems to be quite

Re: [ccp4bb] Sister CCPs

It's not an e-mail bulletin board, but Researchgate seems to be quite popular for wet lab questions. IMO the QA section of the social network is a bit messy. That said, the quality seems to improve gradually. Cheers, Robbie Sent from my Windows Phone Van: Paul

Re: [ccp4bb] no link_id

Just to add to Matthew's good advice, UNK is the standard residue name for unidentified amino acids. Using it for your compound may cause conflicts in other programs such as COOT. Cheers, Robbie Sent from my Windows Phone Van: Matthew Franklin Verzonden:

Re: [ccp4bb] depositing PDB files from refmac

Dear Laurent, 1) Refmac mentions gaps explicitly in the LINK records, the PDB does it in a REMARK record (by comparing the atom records to the sequence of your crystallised construct). If you just remove the gap-LINKs before deposition (without adding TER records) it should work. 2) First of

Re: [ccp4bb] resubmission of pdb

of small molecule chemistry. Cheers - M *https://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg33403.html From: Robbie Joosten robbie_joos...@hotmail.com To: CCP4BB@JISCMAIL.AC.UK Sent: Saturday, 1 February 2014, 12:48 Subject: Re: [ccp4bb] resubmission of pdb Hi

Re: [ccp4bb] resubmission of pdb

Hi Folmer, Perhaps because of the one year limit of keeping PDB entries in the 'HPUB' status. So when a PDB entry is retracted before release, is the PDBid recycled after a while? Cheers, Robbie -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf

Re: [ccp4bb] pdbredo

Dear Faisal, The PDB_REDO server returns a .pdb file with residual B-factors after TLS, to submit a model to the PDB it has to have total B-factors. To get those you can run the CCP4 program TLSANL. The program can read the TLS information straight from the .pdb file, but if you have an older

Re: [ccp4bb] TRUNCATE CTRUNCATE issues.

Hi Ian, This probably doesn't affect the MTZ file that comes out of it but it will affect the statistics of the twinning tests. I'd be interested to see if this solves the cases where ctruncate goes into an infinite loop during the twinning tests. Cheers, Robbie Date: Sat, 30 Nov 2013

[ccp4bb] Announcement: PDB_REDO web server

Dear all, We are happy to announce the PDB_REDO web server at http://xtal.nki.nl/pdb_redo The PDB_REDO server refines any structural model you are working on, by optimising REFMAC refinement and by partial model rebuilding. The process is fully automated [1] so you only need to provide

Re: [ccp4bb] Water or ion

Dear Uma, These look like waters to me. Generally, for ion detection you can use WASP or WHAT_CHECK and for validation of built ions you can use the CheckMyMetal server. Cheers, Robbie Sent from my Windows Phone Van: Uma Ratu Verzonden: 24-11-2013 1:15 Aan:

Re: [ccp4bb] monovalent cation binding sites

Hi Ed, WHAT_CHECK checks water that may be ions and also checks the identity of ions already built. The check my metal server is also very good for final validation of ions. Cheers, Robbie Sent from my Windows Phone Van: Edward A. Berry Verzonden: 9-11-2013

Re: [ccp4bb] Is it possible for a ligand cif file from the CCP4 library to contain errors ?

Can the fixes in the CCP4 dictionary be rolled out through the update system of CCP4? That way we can avoid (at least to some extent) that people keep working with erroneous restraint files. Some of these errors can really mess up your structure. Cheers, Robbie -Original Message- From:

Re: [ccp4bb] R and R free from CIF file deposited in PDB

Hi Mahesh, They will be close but not the same. RMSDs should be very close normally, but different treatment of hetero compounds (ligands and such), outliers and LINKs added during annotation may cause small deviations. The deviations in R-factors can be much larger for all sorts of reasons. The

Re: [ccp4bb] Code to handle the syntax of (mm)CIF data correctly.

Hi Peter, Thanks for posting the startools, I think many developers can benefit from these. [snip] One final point on this: line-by-line processing needs to allow for the fact that there is no requirement at the format specification level for reflection data to be one reflection per

Re: [ccp4bb] Code to handle the syntax of (mm)CIF data correctly.

Hi Phil, When I wrote cif2cif to deal with reflection files from the PDB I opted for good-enough parsing to provide input for cif2mtz. This was a while ago, reflection files were still a mess at the time and my programming skills never tested in practice. I just added support for anything that

Re: [ccp4bb] Resolution, R factors and data quality

Hi Frank and Ian, We struggled with the small changes in free R-factors when we implementing the paired refinement for resolution cut-offs in PDB_REDO. It's not just the lack of a proper test of significance for (weighted) R-factor changes, it's also a more philosophical problem. When should you

Re: [ccp4bb] Resolution, R factors and data quality

Hi Bernhard, snip But the real objective is – where do data stop making an improvement to the model. The categorical statement that all data is good is simply not true in practice. It is probably specific to each data set refinement, and as long as we do not always run paired refinement

Re: [ccp4bb] TLS group assignment near poorly ordered loop

. Cheers, Robnie Sent from my Windows Phone Van: Andrew Leslie Verzonden: 22-8-2013 10:01 Aan: Robbie Joosten CC: CCP4BB@JISCMAIL.AC.UK Onderwerp: Re: [ccp4bb] TLS group assignment near poorly ordered loop Hi Robbie, I was interested in a couple

Re: [ccp4bb] TLS group assignment near poorly ordered loop

Hi Shane, Option one and two may both work. The extra group is not a problem unless it doesn't actually improve the fit with the data much. If you really have very little data, you should consider first using one overall residual B-factor and try to get the most out of the TLS. You can try

Re: [ccp4bb] RSCC

Dear Monica, The CCP4 program EDSTATS will give you the number you need, without any hassle. Give it a try. Cheers, Robbie Sent from my Windows Phone Van: MONICA MITTAL Verzonden: 13-8-2013 7:57 Aan: CCP4BB@JISCMAIL.AC.UK Onderwerp: [ccp4bb] RSCC Dear all I

Re: [ccp4bb] mmCIF as working format?

Apart from editors we also need tools to validate mmCIF files for integrity, similar to what W3C has for (x)html and css. I've mostly dealt with mmCIF reflection files so my experience with what can go wrong is limited. So far, I encountered these 'issues' that may be flagged. 1) Data items

Re: [ccp4bb] TLS refinement and ANISOU records

Hi Omid, Sometimes the choice of TLS groups and to a lesser extent the initial B-factor matter a lot. You should try a few other TLS group selections and see if these give nicer results. Things to try: TLSMD, including or excluding ligands and carbohydrates, other common-sense or gut-feeling

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

Hi Joel, You can just replace your current 'refmac5' and 'libcheck' files. Perhaps after making a backup. They are in the 'bin' directory of your CCP4 installation. The easiest way to find them is using 'which refmac5'. HtH, Robbie Verzonden met mijn Windows Phone

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