[ccp4bb] PhD position in Berlin at the MPICI available.

acceptor. You will work in our Biolabs in Berlin Dahlem within the vibrant campus of the Free University Berlin. The lab is equipped with state of the art instrumentation and is well connected within the MX community in Berlin. For further details you can contact Dr. Christian Roth directly. Please

Re: [ccp4bb] Reg. ITC machine

We had a PEAQ and a bit of bad luck. Broken Peltier, which means the instrument can only be replaced by a new one. Happened in a neighbouring University as well. Currently we have a Nano ITC from TA, It works fine. The software is more customizable. The syringe loading is not my favourite procedure

Re: [ccp4bb] H atoms in refined structure

Hi, just to clarify one point on the GUI. You can click or unclick the option "use hydrogens during refinement" on the first tab in i2 GUI in the options field. As indicated it used it only during refinement and does not put it into the output pdb. In the output tab you can choose what should happe

Re: [ccp4bb] Off topic - gene toxic for expression strains

Hi Andy, have you tried another promotor? Arabinose is much tighter, just to be sure that it is really not leaking. Cheers Christian On Mon, Apr 4, 2022 at 10:20 AM Andrew Lovering wrote: > Dear Board, > > > > Perhaps off-topic, but in the wider scope it’s relevant to many on here. > > > > We

Re: [ccp4bb] MrBUMP in CCP4I2

HI Derek, I don't know which options you need, but there is the interactive task of model preparation with mrbump and ccp4mg in the bioinformatic tasks, which might allow what you want to do. Cheers Christian On Thu, Oct 15, 2020 at 11:02 PM Derek Logan wrote: > Hi all, > > I'm looking for some

Re: [ccp4bb] Refmac use - water addition

Hi Luca, as Eleanor mentioned, in the i2 interface there is in the option menu an add water button. That will automatically run the coot find waters script similar to the old interface. Paul did use some very sensible values to look for blobs, which might be waters. These ones are used (basically

Re: [ccp4bb] real real-space-refinement

Would the stepped refinement protocol in Coot do what you want? It does a real space refinement for every residue automatically. Cheers Christian On Wed, Jul 29, 2020 at 5:20 PM Schreuder, Herman /DE < herman.schreu...@sanofi.com> wrote: > Dear BB, > > > > I would like to do a real real-space-re

Re: [ccp4bb] AW: Re: [ccp4bb] RES: [ccp4bb] Looking for suggestions with protein expression

I'm also old fashioned and use a cloning strain for plasmid preps. I've read that derivatives like Bl21 gold are suitable for both purposes. Though, never tried it by myself. Hughes, Jonathan schrieb am Fr., 10. Juli 2020, 08:38: > Of course! Using a B strain for cloning is just asking for troub

Re: [ccp4bb] AW: [ccp4bb] Accessing full list of programs in CCP4I2

ries >> just to find that it is the same old “wheel” just a bit more round. It is >> probably very personal, but I do not throw away old edition of >> Thermodynamics text book when new one is coming out. And I’m not a hoarder, >> do not have OCD or ADHD. >> >> >

Re: [ccp4bb] Accessing full list of programs in CCP4I2

in production and structure core facility - PTPSP > EPFL SV PTECH PTPSP > AI 2146 (Bâtiment AI) > Station 19 > CH-1015 Lausanne > Switzerland > Email: kelvin@epfl.ch > Phone: +41 21 69 30267 <+41%2021%2069%C2%A030267> > > If unreachable: +41 21 69 3449

Re: [ccp4bb] Accessing full list of programs in CCP4I2

lin mapout > > LABIN FP= and so on.. > > > On Tue, 7 Jul 2020 at 14:22, Christian Roth > wrote: > >> Hi Kelvin, >> well fft as single program is kind of not longer supported as is not >> ccp4i. In i2 internally, as well in communication with mg or coot,

Re: [ccp4bb] Accessing full list of programs in CCP4I2

mail: kelvin@epfl.ch > Phone: +41 21 69 30267 <+41%2021%2069%C2%A030267> > > If unreachable: +41 21 69 34494 <+41%2021%2069%C2%A030267> > > > > > > On 06.07.20, 13:34, "Christian Roth" wrote: > > > > Hi Kelvin, > > not quit

Re: [ccp4bb] Accessing full list of programs in CCP4I2

Hi Kelvin, not quite sure if I understand you correctly, but if you press the Task Manager button you get on the right sight a list of topics (import data, Molecular Replacemnt etc.) each point can be open up like a file tree to see all programs or pipelines available. You can search with the sear

Re: [ccp4bb] problem in structure solution of multidomain protein

Hi, you mentioned that there is no electron density for your 5th domain. If there is nothing coming up even after refinement of the four domains, than maybe your 5th domain is not there, or so disordered that it doesn't show up. Christian On Wed, Feb 12, 2020 at 9:47 AM RAJNESH KUMARI YADAV wrot

Re: [ccp4bb] Unusual monomer-monomer interface in crystal

Hi Chris, it could be all Ni besides Zn. I've seen Ni carried over from the initial metal affinity chromatography I presume. Cheers Christian Chris Fage schrieb am Di., 21. Jan. 2020, 21:23: > Thanks to Guenter and Eleanor for their replies. I mentioned that there is > not adequate space for a

Re: [ccp4bb] TLS parameters

Purely from memory, I think TLS is refined in Phenix on the fly and the groups are updated in every run. It does split the B-Facs in isotropic and anisotropic part in the putput pdb file. I do not recall the tls groups to be recorded separately in a phenix pdb. But again distant memory. Christian

Re: [ccp4bb] Rfree too high

Hi Robert, your completeness is only about 90 % on average in shells of reasonably intensity. I presume Eleanor would love to see the FObs Fcalc plots from Refmac to get a better idea in which resolution region there are pronounced differences. Cheers Christian On Thu, Nov 7, 2019 at 2:52 PM Ro

Re: [ccp4bb] I am doing phenix refinement now. Is it a problem if the r-work and r-free values are equal?

No. As pointed out by Pavel, there are no reflections flagged as "free reflections" used to calculate Rfree. Therefore you don't get a real Rfree. No model bias issue etc. If you have a Rfree using ccp4 programs, than you should used that particular original mtz in phenix. It should detect the fla

Re: [ccp4bb] Refinement of Occupancy in Refmac

Hi Deniz, yes you can do that, though I don't know right now how B-factors are taken into account when refining occupancies. Anyway, in i2 you have to go to the advanced tab. There is a place to put keywords in (text area). There you put the right combination of keywords for your special cases. Re

Re: [ccp4bb] A ccp4I2 question

yes one can Cheers Christian On Tue, Apr 16, 2019 at 1:19 PM Eleanor Dodson < 176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote: > Can one export of project started under linux to a windows system? > > Eleanor > > -- > > To unsubscribe from the CCP4BB list, click t

Re: [ccp4bb] Coot issue with add residue

Well I think I recall one instance where it worked for me the way you describe. I think there was either a stray residue atom somewhere or a numbering not quite right. Could it be that this happens for you after autobuilding? Cheers On Wed, Apr 10, 2019 at 7:11 PM Hillen, Hauke wrote: > Dear al

Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] High Rfree - ice ring

There is an option in xds to exclude typical ice ring regions. It was usually in the XDS.INP but commented out by default. That should work as it should work with the ice ring button in mosflm. Cheers Christian On Tue, Apr 9, 2019 at 11:07 AM Harry Powell < 193323b1e616-dmarc-requ...@jiscmail

Re: [ccp4bb] Coot issue with add residue

One of the key bindings in Coot. Need to center on a residue surrounded by a residue on the left and the right. Press "Shift+T" and Coot will refine the three consecutive residues. There might be the refinement quality window popping up, though I'm not sure. There is another keybinding "h" or "s

Re: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] High Rfree - ice ring

I would also check carefully the other potential ice rings resolution ranges. I doubt there is just the one you can identify easily. On Thu, Apr 4, 2019 at 12:07 PM Eleanor Dodson < 176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote: > You cant exclude one resolution ring in REFMAC - there wo

Re: [ccp4bb] Current "best" software for computing volumes of active sites

Well, I don't know if that is the newest appropriate piece of software, but pdbsum does automatic calculation of clefts using MOLE I think. It does provide jmol and rasmol scripts and volume and surface calculations. Cheers Christian On Thu, Apr 4, 2019 at 8:24 AM Fred Vellieux wrote: > Hi CCP4

Re: [ccp4bb] visualising anis B factors

In ccp4mg it is the representation tab --> Thermal ellipsoids On Wed, Jan 23, 2019 at 4:51 PM Oliviero Carugo < oliviero.car...@univie.ac.at> wrote: > You might be interested in Chimera too (--> Tools --> Structure Analysis > --> Thermal ellipsoids) > > > > > On 23.01.2019 16:17, Eleanor Dodson

Re: [ccp4bb] conversion from pdb to cif format changes R factors ... why?

0J&hl=en> Twitter <https://twitter.com/DrAntonioAriza?lang=en> *Check out my latest paper!!!* Structural insights into the function of ZRANB3 in replication stress response <http://www.nature.com/articles/ncomms15847> ---

Re: [ccp4bb] conversion from pdb to cif format changes R factors ... why?

Hi Tony, is that for all structures or just some? I recall there was a problem when one has used TLS refinement. The deposition task runs a 0 cycle refmac job to recreate the statistics. If there is a difference, e.g no TLS included that might explain the difference. Cheers Christian A

Re: [ccp4bb] Literature on crystallization screen ingredients not showing up in crystal structure

Not quite what you were looking for, but there was just that paper from Alexander McPherson abut dye binding. They show that some of the dyes seem to bind really tight to the protein, but are invisible in the structure. Maybe there are also some interesting references in there. Sorry haven't got ar

Re: [ccp4bb] identifying bound ions

Hi Herman, out of the top of my head I think there is an option in Coot to check if the water is highly coordinated and might be an ion and I think there was also a function in Phenix to check for ions. Cheers Christian schrieb am Di., 31. Juli 2018, 14:39: > Dear BB, > > > > I know it has be

Re: [ccp4bb] Problems with HEC in CCP4

As far as my understanding goes, LINK records will not be replaced by LINKR records by default. If the Link is in the monomer library one has to delete th right atoms and the atoms to be linked have to be within a reasonable distance. Than refmac will automatically recognize that for the two residu

Re: [ccp4bb] Problems with HEC in CCP4

Technically, if I recall that correct from my memory, if the link is in the monomer library and the correct atoms are deleted, Refmac will use the link from the library and create a LINKR record. I am not sure right now if they are handled properly in the deposition process. Cheers Christian On T

Re: [ccp4bb] Compound with flexible conformation but nM Kd

Anectodal evidence I have heard from colleagues working with things, which are immobilized is that the measured Kd value on the surface can be wildly different from what is measured in solution. A superbinder on a surface might not be as good in solution. There seems still a lot of debate why that

Re: [ccp4bb] Cys Lys bond?

Don't know if I read about this before, but reading modelling, I would create a link dictionary with jligand and use that in refmac and coot. Cheers Christian Jonathan Davies schrieb am Di., 17. Apr. 2018, 19:03: > Dear CCP4BB, > > I've recently solved a structure to 1.15 Angstrom which has ex

Re: [ccp4bb] Good old SIMBAD

Contaminer surely have had taken longer. Poor unlucky soul who crystallised an impurity. On Wed, Apr 11, 2018 at 1:19 PM, Eleanor Dodson < 176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote: > > Lattice search completed in 0 days, 0 hours, 36 minutes, and 5 seconds > > Lucky you! SIMBAD worke

Re: [ccp4bb] How to get Imean/SIGImean from separated anomalous data?

It's quite a change compared to i1, but worth to learn it. On Wed, Mar 14, 2018 at 5:33 PM, Edward A. Berry wrote: > Thanks, that seems to work also, and with lots of nice graphical analysis. > With Task "Import merged data", or all in one go with "convert intensities > to amplitudes" selecting

Re: [ccp4bb] Finding Homologs with Specific Residues Conserved

Not sure if I understand the question right, but wouldn't phi-blast do trick. You supply on too your conserved pattern and blast again. Christian Am 20.12.2017 19:37 schrieb "Keller, Jacob" : > Dear Crystallographer-Bioinformaticians, > > > > Is anyone aware of a way to tweak BLAST or similar so

Re: [ccp4bb] Creating a covalent bond

The easy way is Coot Extensions Link two atoms which should create a Link record in the pdb. I think the better way is use jligand which creates a full dictionary describing the particular link with proper restraints. Load your ligand, load the Asp monomer link the two atoms in question create t

Re: [ccp4bb] Sugar-Pi-stacking

Dear Bernhard, the explanation can be found in here with additional references in. J Am Chem Soc. 2015 Dec 9;137(48):15152-60. doi: 10.1021/jacs.5b08424. Epub 2015 Nov 30. Carbohydrate-Aromatic Interactions in Proteins. Hope tha

Re: [ccp4bb] doubt regarding setting resolution cutoff

Your plots look strangely different to the old Scala output you posted before, but never mind. Paul is right that a negative intensity is not desired and your crystal has some issues with ice. That one icering around 2.26 must be massive taken into account how haywire your curve goes there.

Re: [ccp4bb] About weighting factor settings in new ccp4i2

The simple matrix weighting option (x-ray/restraints weight) is under main refinement option and set automatically. Change that to manually and you can put the value in if you want to avoid too many keywords. There is even an option in advanced parameters to run several quick refinements to get

Re: [ccp4bb] ATP analog

Hi, one word of caution with Metal fluoride complexes. Though they can provide valuable inside in the reaction mechanism, even better than some ATP-analogues, one has to be careful what metal to use to get the right complex. See review below, which summarises the problems which can occur, es

Re: [ccp4bb] radiation damage-induced phasing (RIP) tutorial

There was a tutorial for MX including UV RIP available from the HZB in Berlin (BESSY MX group). Have a look at there website. I'm sure it is still available, or maybe they can send you the files on request. Cheers Christian Am 28.04.2017 um 17:12 schrieb Murpholino Peligro: Hi lads... Do y

Re: [ccp4bb] off topic: Alternatives to GE HiTrap columns

Hi Markus, BioRad has columns as well (prepacked and empty), which follow the establiched connector standard. So usable without the need of adapters. Cheers Christian Am 15.02.2017 um 16:57 schrieb Markus Seeliger: Dear all, we are happy users of all that GE offers around their FPLC system

[ccp4bb] Off topic: Fellowship Day Department of Chemistry University of York/YSBL

Dear all, on behalf of the Department of Chemistry, to which the York Structural Biology Lab (YSBL) belongs, I post this notice about the Fellowship Open Day. If you are interested to work in York in YSBL as a Fellow please register, come to York and find out how the Department supports you in

Re: [ccp4bb] help with Buccaneer

Depending on the actual thing you want to do. The options vary a lot. If you have a MR model I strongly recommend gui2 and the MR mode. In that case you supply the model and Buccaneer runs Refmac in advance to generate the necessary phase information it needs. If you have run CRANK2 in gui2 use th

Re: [ccp4bb] How to align maps in CCP4

In Coot it is under Extensions--> Maps --> Transform map by lsq model fit Please correct me if it is not what you mean Eleanor Cheers Christian On Sat, Jan 21, 2017 at 8:22 PM, Eleanor Dodson wrote: > This is quite possible but I am at home and have forgotten the menu item.. > is it under th

Re: [ccp4bb] Refmac5 update water option

Hi, the adding water option is basically a COOT script to find waters, which get subsequently refined. There is no automatic evaluation and deletion of waters based on certain criteria. That you have to do manually. You can always try to automatically add new waters, which is done by this opt

Re: [ccp4bb] does Refmac5 do density modification in the refinement of a structure?

Dear Alex, Refmac doesn't do density modification. If you want take advantage of better starting phases you have to do DM prior Refmac or model building with Buccaneer for example. I recommend PARROT for that. I would use i2 Parrot and this as input in the Buccaneer pipeline with precomputed p

Re: [ccp4bb] good images

hi What you get out of mg is png. Depending for what you need it you might want to have between 300 to 600 dpi. if you then do postprocessing in corel you should go for tiff to avoid too much loss in quality due to the compression. Christian Am 02.11.2016 um 18:09 schrieb chemocev marker:

Re: [ccp4bb] Help with MR result

Hi, it seems you haven't found a solution. If there is no model you might want to try experimental phasing. With that resolution and the right sg a S-SAD might be possible. So you might not even need a HA derivative. Cheers Christian Am 26.10.2016 um 14:53 schrieb SUBSCRIBE CCP4BB Liuqing

Re: [ccp4bb] Software to know the common folds in a protein

Hi, You could try the DALI server or pdbefold. Both give you pretty much the same information. Christian Am 13.10.2016 um 13:03 schrieb Vikram Dalal: Hi everyone, We are solving a protein structure and we want to know the folds which are present in it. Suggest me the best software or serv

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

Hi, If you have a crystal you could do a x-ray fluorescence scan to see what might be in your crystal and collect anomalous data at higher wavelength close to the manganese edge to see if it is manganese. These enzymes can also deal with Zinc which is a bit heavier and might be still bound fro

Re: [ccp4bb] Refmac refinement R factors going up..... TLS issue? update

is behaving weirdly, is to check with the PARVATI server (http://skuld.bmsc.washington.edu/parvati/). If your TLS group boundaries set off flags, you have some more work to do on the refinement. Shane Caldwell McGill University On Thu, Jun 18, 2015 at 4:30 PM, Christian Roth mailto:christian.r.

[ccp4bb] Refmac refinement R factors going up..... TLS issue?

Hi all, I refine a structure with TLS and restrained refinement in Refmac. After the run finished, I fixed a few outliers manually in Coot, saved that file and used that with the original TLS file from TLSMD for the next round of refinement. As soon as the restrained refinement starts the R-f

Re: [ccp4bb] Online server for generation of topology cartoons

Dear Mohammad, there is for example pdbsum (www.ebi.ac.uk/pdbsum), where you can upload a pdb and you get various outputs including a topology diagram. Cheers Christian Am 20.05.2015 um 10:50 schrieb Mohammad Khan: Dear all, Is there any good online server for the generation of topology ca

Re: [ccp4bb] Refinement at 4A resolution

Hi Appu, you start already with a fixed spacegroup (scaled merged data) according to your pointless log. So you can't get another possible solution from pointless. Cheers Am 22.04.2015 um 22:28 schrieb Appu kumar: Dear CCP4 Member, I seek your advice on the refinement issues at the low res

Re: [ccp4bb] How to Run ensembler:CCP4

Hi, ensembler dont't like/recognize your alignment file. Probably just the ending. Try to convert it to .pir or .aln. I guess both file formats should work. Christian Am 14.11.2014 14:13, schrieb yogesh khandokar: Dear ALL, I am trying to use ensembler program to generate MR ensembler, av

Re: [ccp4bb] Guard columns from FPLC

Hi Anita, never heared about Guard columns for Superdex columns. These guard columns are usually for HPLC columns (RP) or Silica High pressure gelfiltration columns like from Tosoh Bioscience and part of the acutal column itself, though replaceable. Christian Am 16.09.2014 09:29, schrieb An

Re: [ccp4bb] Shelx Search for Heavy Atom Cluster

Hi Alex, I am not sure about the possibility to search for a cluster in ShelX. However if not you can search for your cluster with the appropriate cluster model using Molrep and your DANO signal. The details can be found in the mentioned paper. Depending on the resolution it might work. Lo

Re: [ccp4bb] Exporting Omit Maps for use in Pymol using CCP4i FFT

Hi Wei, have you supplied a valid pdb file? That is the mentioned missing parameter. Cheers Christian Am 20.08.2014 20:54, schrieb Wei Shi: Hi all, I am trying to display F0-Fc omit map in PyMol. I got the mtz file from Phenix, and now use CCP4i FFT to generate the map for PyMol. I followed

Re: [ccp4bb] the f' and f'' of heavy cluster

Hi, one could indeed get much better phases with the correct positions of the HA cluster. If there is sufficient anomalous signal one could use the cluster as search model for Molecular replacement using the anomalous data as described in Dahms et al. to get the exact position of the cluste

Re: [ccp4bb] Off Topic- Cystine Detection

Am Mittwoch 06 Februar 2013 17:10:35 schrieb Yuri Pompeu: > Dear All, > I am trying to probe the existence of a disulfide bond on the surface of my > protein. I have attempted Ellman´s and my results were not as clear as I > would have hoped for. I am not a sulfur/cysteine chemist and would > ap

Re: [ccp4bb] strict structure based alignment

schrieb Christian Roth: > Dear all, > > I want align a couple or protein structures by secondary structure matching > to one target and want get a kind of aminoacid alignment file e.g. what > residue fit the other, without adjustments due to sequence based > alignments. >

[ccp4bb] strict structure based alignment

Dear all, I want align a couple or protein structures by secondary structure matching to one target and want get a kind of aminoacid alignment file e.g. what residue fit the other, without adjustments due to sequence based alignments. I tried Strap, but as far as I understood it, it takes also

Re: [ccp4bb] cryo for high salt crystal

Hi, I have used pure malonate (above 3M) for a similar condition. Sometimes the cryoprotectant alone, without reservoir works quite well Cheers Christian Am Dienstag 10 Juli 2012 18:28:30 schrieb m zhang: > regaentDear All, > I am sure this question was discussed before. But I am wondering

Re: [ccp4bb] Dihederal Angle Calculation

Hi, if I remember correctly Molprobity computes all that angles and put them in a table for comparison to the ideal values. Best Regards Christian Am Dienstag 19 Juni 2012 20:11:18 schrieben Sie: > Hi, > Does anyone know of a program that computes _all_ dihedral (phi/psi/chi) > angles from crys

Re: [ccp4bb] zero mosaicity

Hi Ed, the mosaicity is always zero after xds, because the processing is different as Graeme mentioned. If the cell refinement is unstable and mosaicity becomes zero, I estimate the mosaicity from a few pictures and write my own value in the mosaicity estimation window of the gui. Than one fix

Re: [ccp4bb] Desalting columns

If you want test a lot of different conditions a Thermofluorecence assay might work for your protein and you may find a condition which stabilise your protein. However there is no warranty that it crystallise better afterwards. Christian Am Montag 27 Februar 2012 17:01:33 schrieb Sangeetha Vedu

Re: [ccp4bb] Bond Length Outliers (correction)

Hi, If I remember correctly this angle is for the planarity of the peptide bond. Maybe you have a real deviation which might occur not so seldom than expected. You have a quite high resolution. If the density is really convincing then you may accept this outlier. Not every outlier is a mistake.

Re: [ccp4bb] protein degradation

attached gel picture regarding protein > > Sivasankar Putta > -- Christian Roth Institut für Bioanalytische Chemie Biotechnologisch-Biomedizinisches Zentrum Fakultät für Chemie und Mineralogie Universität Leipzig Deutscher Platz 5 04103 Leipzig Telefon: +49 (0)341 97 31316 Fax: +49 (0)341 97 31319

Re: [ccp4bb] On pKa of Aspartic acid

Hi, you may also look into the papers of John A. Gerlt, who did a lot on protonabtraction reactions and the theory behind this. Esspecially the pKa disturbance and the match to the pkA of the substrate of the reaction. Best Wishes Christian Am Dienstag 07 Februar 2012 12:48:26 schrieb Deepa

Re: [ccp4bb] off-topic:schematic representations for secondary structure

Aline does also read a dssp file and print the schematic representation above. Probably this is also possible with STRAP. I am not sure which program exactly the pdb use for their diagrams. Regards Christian Am Samstag 04 Februar 2012 12:11:09 schrieb Vellieux Frederic: > I believe Procheck ge

Re: [ccp4bb] off-topic: "special" format for multiple sequence (protein) alignment

Hi Wenhe, if you have already your alignment file you could also load it in Charlie Bonds "ALINE". The program allows to color by similarity in grayscale as well as in colour mode. Regards Christian Am Freitag 03 Februar 2012 06:32:08 schrieb WENHE ZHONG: > Dear members, > > Apologize for

[ccp4bb] pointless eats FP column

Hi, I want determine the spacegroup with pointless and it should directly write out the mtz in the best sg. When I give a mtz with Structure Factor amplitude pointless recognize the file (9 columns) change the space group and the new file in the new space group has just 7 columns and FP and S

Re: [ccp4bb] Question about drawing disulfide bonds in Pymol

Hi, I think it should also work with the cartoon side chain helper option which adjust the cartoon slightly to prevent such situations. Christian Am Mittwoch 26 Oktober 2011 16:15:55 schrieb Ke, Jiyuan: > Dear All, > > I have a question regarding making disulfide bonds in Pymol. The overall >

Re: [ccp4bb] help me to determine ligand's b fator?

Hi, as Tim pointed out Rsym, I/sigma, Redundancy could not be obtained from a pdb, but you find it in the ouptut of SCALA, XSCALE, or similar scaling programs. I use Moleman2 from the Uppsala Software Factory to get the B values out of my pdb. F.e. "Bf St Type" provide B-Factors for every compon

Re: [ccp4bb] XSCALE!!! ERROR

Am Mittwoch 07 September 2011 21:39:07 schrieb Muhammed bashir Khan: > Dear All; > > I am trying to to xsale several data sets together, but it gives an error > of > > !!! ERROR !!! INSUFFICIENT NUMBER OF COMMON STRONG REFLECTIONS. >PROGRAM IS UNABLE TO PRODUCE A SCALED DATA SET.

Re: [ccp4bb] Help with deleting reflections from an mtz file

Am Mittwoch 17 August 2011 17:55:59 schrieb Eleanor Dodson: > There are 2 rogue reflections in a data set I have here. How can I > eliminate them? > I thought sftools did this but i cant seem to get the syntax right. > Short of dumping the whole file, using an editor, then reconstructing it > I am

[ccp4bb] conversion of ccdc cif to pdb

Dear all, I want convert a small molecule cif into pdb. Unfortunately coordvonv failed with the following error message: CCP4I TERMINATION STATUS 0 "At line 537 of file /usr/local/xtal/ccp4-6.1.3/src/coordconv.f Fortran runtime error: Bad value during floating point read I am able to read the

Re: [ccp4bb] JLigand: Handedness related issue

Hi Vineet, I did not used JLIGAND so far, so I cannot explain what happend, but maybe the quickest solution would be a manual intervention in the cif-files. Type at at the chirality remark "positiv or negativ" or whatever nomenclature is used and save it again. I do it sometimes for my ligands

[ccp4bb] strange fortran error in refmac

Dear CCP4ler, I have a strange fortran error attached below when I started a restrained refinement with Refmac. I tried also for the beginning a simple rigid body refinmet for comparison and except that it complains about the Hessian B Array, which ist too big, it runs to completion. Has anyone

Re: [ccp4bb] off-topic: 2 peaks on Cation

Hi, you did not mention anything about your protein, but if it shows a metal dependency, than different amounts of the metal ion might changen the overall charge and influence the interactions with the ion exchanger. There might be also a modification of an aminoacid f.e. decarboxylation of an a

[ccp4bb] Molrep with two models

Dear all, I tried MolRep with a two domain protein. I have cut the two domain as one domain rotates which prevent a search with the complete model. After I finished the first run. I put this solution as fixed input model in the second molrep run with the second domain. The resulting solution p

Re: [ccp4bb] exploding hydrogens during real space refinement in coot

That happens also for me with all hydrogens, regardless if they belongs to a ligand or protein. Best solution for me is stripping all hydrogens out of the pdb. Manipulating the file in coot and readding them and start of the renfinement. Christian Am Donnerstag 10 Februar 2011 17:04:18 schrieb

Re: [ccp4bb] mono S vs. mini S vs. S-HyperD

Hi Jonas, a Mini S has a even lower bead radius of 5 µm, if I remember correctly. Its available as prepacked column from GE. I have a 1 ml column which is quite expensive. i guess you won't spent such an amount of money. It is also more for analytical purposes and not preparative scale. Never h

Re: [ccp4bb] SP Sep HP tight binding of proteins

Hi Meg, I think with your pi you may also test a Q-Sepharose at neutral to slightly alkaline pH. Maybe your protein is more comfortable with this condition compared to a pH of 4.5. As mentioned befor your protein is most likely precipitated on the column. Best regards Christian Am Dienstag

Re: [ccp4bb] AKTA Prime dead/delay volume...and a transmembrane protein...

Hi Jim, If I remember correctly the delay volume from the pumps to the top of the column is roughly 8 ml for Äkta Purifier, Explorer and also Prime. The actual volume from the bottom of the column to the fractionator, or more important from the UV cell to the fractionator depends on the tubing

Re: [ccp4bb] limit for number of files for CAD...

Hi Francis, the limit ist for CAD. You can put as much datasets as you want in one mtz, but you have to run cad than stepwise. Be careful with the column labels. Duplicate labels lead to problems. Christian Am Mittwoch 03 November 2010 18:11:34 schrieb Francis E Reyes: > CCP4'ers, > > Are 9 d

Re: [ccp4bb] Refmac TLS plus experimental phase refinement failed

Hi , i just tried the extra information because I had a serious "overfitting" of my model. Roughly 10 % difference for 1.9 Ang. resolution and experimantal phasing. I thought maybe the extra information and the adjustment of the weighting parameters helps me to figure this out. A refinement usi

Re: [ccp4bb] Refmac TLS plus experimental phase refinement failed

. I'm sorry about that and thanks again for your help Christian Am Montag 11 Oktober 2010 19:50:10 schrieb Ethan Merritt: > On Monday, October 11, 2010 11:01:10 am Christian Roth wrote: > > Dear all, > > > > I want refine my model using TLS plus phase information fr

[ccp4bb] Refmac TLS plus experimental phase refinement failed

Dear all, I want refine my model using TLS plus phase information from experimental phases. I used the TLSMD server to generate the initial tls parameters and started Refmac After an initial round of TLS refinement Refmac stops and and claims a problem but nevertheless writes at the end "Task c

Re: [ccp4bb] LIGPLOT or similar

Hi Mark, MOE from ChempComp does something similar, but I think it is not for free. Regards Christian Am Mittwoch 25 August 2010 19:51:08 schrieben Sie: > Dear All, > > Having just installed LIGPLOT under Windows, I find it rather convoluted to > run. It has to be run via de command line wi

Re: [ccp4bb] bacillus protein expression

Hi, you did not mention if you just look for soluble expression. However you could try an other fusion construct like MBP or GST-Tag to check if the RNA do some strange things (secondary structures). There are more strains available. For some unknown reason some strains work some not. Sometimes

Re: [ccp4bb] crystals of 1D

Hi, i'm not sure if you try just seeding in your original condition. If yes, you could try matrix seeding. Another option would be addtitves or the silver bullets from McPherson. Sometimes sitting drop vs. hanging drop make a difference. Mutations at the surface are quite often an excellent alt

[ccp4bb] Reg Protein purification

Dear Sivaraman, it might be difficult if the DNA binding is an intrinsic property of your protein and important for the function. But you can try of course to degrade the DNA using DNAseI and hope that the resulting small pieces and nucleotides will not bind to your protein, I use sometimes st

[ccp4bb] combine more than 9 datasets

allow up to 20 derivatives, if I understood the manual correct. Best regards Christian -- Christian Roth Institut für Bioanalytische Chemie Biotechnologisch-Biomedizinisches Zentrum Fakultät für Chemie und Mineralogie Universität Leipzig Deutscher Platz 5 04103 Leipzig Telefon: +49 (0)341 97

Re: [ccp4bb] Manganese buffers for protein crystallization

. Christian -- Christian Roth Institut für Bioanalytische Chemie Biotechnologisch-Biomedizinisches Zentrum Fakultät für Chemie und Mineralogie Universität Leipzig Deutscher Platz 5 04103 Leipzig Telefon: +49 (0)341 97 31316 Fax: +49 (0)341 97 31319

Re: [ccp4bb] Making really good chemically competent cells

*108 is possible with this method. In rare cases I got 109, but I tend to use the lower value to be on the safe site. The cells are used successfully for a lot of mutagenesis experiments and standard cloning. HTH Christian -- Christian Roth Institut für Bioanalytische Chemie Biotechnologisch

[ccp4bb] GST fusion-Expresson problem - NOT GST

. -- Christian Roth Institut für Bioanalytische Chemie Biotechnologisch-Biomedizinisches Zentrum Fakultät für Chemie und Mineralogie Universität Leipzig Deutscher Platz 5 04103 Leipzig Telefon: +49 (0)341 97 31316 Fax: +49 (0)341 97 31319

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