[ccp4bb] Postdoctoral position Greifswald/Germany

-greifswald.de). See also our homepage (http://www.chemie.uni-greifswald.de/~biochem/) for information on the group and research. Posting in behalf of Prof. Hinrichs, good luck Gottfried Palm

Re: [ccp4bb] Blob help

Dear Vin why don't you try glycerol with a carboxylate group, i.e. 2-hydroxymethyl- 3-hydroxy-propanoic acid, change the oxygens to carbons or vice versa according to the possible hydrogen bonds and then check if you can make sense out of the resulting molecule. greetings Gottfried ==

Re: [ccp4bb] [ccp4bb9 Need isolated crystals

Dear all, I am getting protein crystals in clusters. How can I achieve isolated crystals. Thanks Amit Sharma As Roger writes "One way to separate crystal cluster is to poke them with a tiny probe". We are often using acupuncture needles as easy to get and cheap microtools which have very lo

[ccp4bb] scripts for denzo with Saturn92

e the culprit is only some wrongly set parameter, not the images themself. Gottfried Dr. Gottfried Palm Ernst-Moritz-Arndt-Universität Inst. für Biochemie (MNF) Abt. Biochemie I Felix-Hausdorff-Straße 4 17489 Greifswald Tel. +49(03834)-864393 Fax. +49(03834)-864373 email [EMAIL PROT

Re: [ccp4bb] buried surface area

>What is the easiest way, these days, to calculate the buried surface area >between two subunits of a protein? >Thanks, and Happy Friday, Gloria The PISA server from EBI does a nice job: fast overview, but also details if necessary. http://www.ebi.ac.uk/msd-srv/prot_int/pistart.html greeting

Re: [ccp4bb] How to determine ligand binding from diffraction pattern?

I would like to expand on the question and answer below and compare your experiences: Looking for ligands in many different soaks / cocrystals of your protein of interest, you still should do molecular replacement and a bit of refinement. I agree with Steve, but how much refinement is necessary

Re: [ccp4bb] Protein color

local analytic company. greetings Gottfried Dr. Gottfried Palm Ernst-Moritz-Arndt-Universität Inst. für Biochemie (MNF) Abt. Biochemie I Felix-Hausdorff-Straße 4 17489 Greifswald Tel. +49(03834)-864393 Fax. +49(03834)-864373 email [EMAIL PROTECTED

[ccp4bb] postdoctoral position in Greifswald, Germany

([EMAIL PROTECTED] greifswald.de) before end of September. See also our homepage (http://www.chemie.uni-greifswald.de/~biochem/endex. htm) or http://www.rigaku.com/protein/sotm-002.html for an example of current equipment and research in the lab. Dr. Gottfried Palm Ernst-Moritz-Arndt-Universität

Re: [ccp4bb] off-topic:selective reduction

> We have a recombinant secreted glycoprotein produced in a mammalian culture system; the native protein has 12 cysteines which form 6 intramolecular disulfide bonds. We have introduced a new cysteine residue at a surface position, with the intention of targeting this residue for an in vitro s

[ccp4bb] postdoctoral position in Germany

Dear All, In the group of Winfried Hinrichs a postdoctoral position/staff scientist is available in Greifswald/Germany for initially 3 years. The position involves research and teaching. Knowledge in German is not mandatory but might be helpful. You may test your skills with the official posting

[ccp4bb] low UV reading on AKTA prime

Hi all, another reason to get low readings from the UV meter can be a drift in the baseline. The photometer is properly calibrated only when you turn it on, I think. Since we have our machine running in the coldroom without (usually) turning it off for month, we have observed wrong 260/280 r

[ccp4bb] postdoc position in Greifswald, Germany

homepage (http: //www.chemie.uni-greifswald.de/~biochem/). Posting in behalf of Prof. Hinrichs, good luck Gottfried Palm === WEB-Mailer der Uni-Greifswald ( http://www.uni-greifswald.de/ ) ===

Re: [ccp4bb] backbone B-factor

Dear Mohd, to plot the B-factors, I would read the pdb file in Excel (or similar). Take care that 5.45 is read as a number and not as a string, which happens at least in German versions because of the . instead of the German,. Specify the decimal separator. The sort by Atmon name to get all C

[ccp4bb] text color in coot buttons

believe it is not a problem from coot, rather from some other setting somewhere, but I don't know where. Can I get a hint, what to change /set? Thanks   Gottfried Gottfried Palm Universität Greifswald,Institut für Biochemie Felix-Hausdorff-Straße 4 D-17489 Greif

Re: [ccp4bb] text color in coot buttons

Theme - Look And Feel from default "openSUSE" to "Breeze Dark".  This results in white text on gray background. Thanks again   Gottfried On Thursday, 26-03-2020 at 17:53 Paul Emsley wrote: On 26/03/2020 16:46, Palm, Gottfried wrote:   I have problems re

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

For occasions like Laus, it would be useful to further on have access to the CCP4 v7.0 Program Documentation, even if the programs are not updated as Christian explained. I was for instance looking for translating coordinates as in pdbset, but couldn't find a replacement in the ccp4i2 gui. Gr

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

Eleanor   On Tue, 7 Jul 2020 at 17:16, Palm, Gottfried wrote: For occasions like Laus, it would be useful to further on have access to the CCP4 v7.0 Program Documentation, even if the programs are not updated as Christian explained. I was for instance looking for trans

Re: [ccp4bb] ligand bound to only one chain in the crystal

Dear all,    the tenor seems to be, if you see the ligand in any of the monomers, that's the mode the ligand binds. We have seen other cases, though, too. Usually the protein I am thinking of (TetR(D)) crystallizes with one molecules /a.u. In solution it is an obligate dimer. The dimer is forme

Re: [ccp4bb] how to swap chain IDs

Hi Christian, couldn't you simply change the position in a text editor after changing chain IDs in coot? Atom IDs should renumber after reading and writing in coot, but conversion to cif will probably ignore the atom IDs anyway.  Greetings   Gottfried On Monday, 07-12-2020 at 19:19 Pavel Afonin

[ccp4bb] version for old AMD processors

Dear all,   I am running into a "known issue" upon installing ccp4-7.1 on a pre2010 AMD machine. The download page says CCP4 7.1: Known issues ... Old AMD processors ... We are in the process of preparing an alternative release package for those processors. Is there a solution in the meanw

Re: [ccp4bb] version for old AMD processors

Thanks Tim and Oleg for suggestions. The legacy version works and should be sufficient for my purpose. Maybe there could be a link or hint in the chapter "Old AMD processors" to avoid unnecessary questions. Greetings   Gottfried On Thursday, 10-12-2020 at 12:46 Kovalevskiy, Oleg (STFC,RAL,SC

Re: [ccp4bb] AW: [EXTERNAL] [ccp4bb] refmac same residue different names

The situation might not be so rare, if you consider 50% Lys and 50% Acetyl-Lys or other post-translational modifications. Gottfried On Wednesday, 06-02-2019 at 18:05 Diana Tomchick wrote: If you have the odd case where one residue (of the same number in the polypeptide chain) is a Leu and the

[ccp4bb] Rigaku X-ray diffractometer open for bidding

t 11th and might not answer the emails before. Greetings   Gottfried Gottfried Palm Synthetic and Structural Biochemistry Institute for Biochemistry University of Greifswald Felix-Hausdorff-Str. 4 17489 Greifswald Germany ##

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

Dear Yang Meiting,    I have not solved protein - DNA complexes, but I have seen many protein densities with more or less ligand bound. When the ligand has a carboxylate group but doesn't bind tight enough, often an acetate or sulfate groups binds instead. Depending on how clear you see the phospha

Re: [ccp4bb] ligand binds to one molecule

Dear all,   I don't think, there is much to add to the statement of Bernhard or James that different protomers in the asymmetric unit (must) have some difference in there contacts and therefore often in their conformation. What it doesn't answer is a chicken or the egg question: do the differe

Re: [ccp4bb] Cysteine-S-Iodine interaction

Check the electron density (O, Cl, I ?) and the anomalous signal on your "iodine". Cysteine has an interesting chemistry and one is oxidation to the sulfenic acid, CSO, already mentioned. Probably, it is more common than we tend to expect and may be overlooked, because we don't look for it and be

[ccp4bb] Full professorship in biochemistry, Greifswald, Germany

, applications of female scientists are particularly welcome. The deadline for the application is June 24, 2022. Best regards, Gottfried Dr. Gottfried Palm Synthetische und Strukturelle Biochemie Institut für Biochemie Universität Greifswald Felix-Hausdorff-Straße 4, D-17489 Greifswald Tel.: 03834 420

[ccp4bb] Problem with ref format (from Rigaku)

has also changed and the new .img files (from the Saturn92 detector) are not read anymore (whereas they used to be processable in xds before). Greetings   Gottfried Dr. Gottfried Palm Ernst-Moritz-Arndt-Universität Inst. für Biochemie (MNF) Abt. Biochemie I Felix-Hausdorff-Straße 4 17489 Greifswald

[ccp4bb] Problem with *.ref format (from Rigaku)

the images has also changed and the new .img files (from the Saturn92 detector) are not read anymore (whereas they used to be processable in xds before). Greetings   Gottfried Dr. Gottfried Palm Ernst-Moritz-Arndt-Universität Inst. für Biochemie (MNF) Abt. Biochemie I Felix-Hausdorff-Straße 4

[ccp4bb] solution for the ref format problem

milar problem: The format of the images has also changed and the new .img files (from the Saturn92 detector) are not read anymore (whereas they used to be processable in xds before). Greetings   Gottfried Dr. Gottfried Palm Ernst-Moritz-Arndt-UniversitÀt Inst. für Biochemie (MNF) Abt. Bioche

[ccp4bb] anomalous data usage

Dear all,   I have a few questions handling (non) anomalous data: By default aimless seems to produce Iplus and Iminus columns. Can I force it to (also) create an Imean column? What does refmac do, when it gets Iplus and Iminus (and their sigmas) as input. Does it take only one of them or does it

[ccp4bb] effect of torsion angle definition in cif file

Dear all,   I have a problem in fine tuning the cif file for my new ligand. I try to force a specific torsion angle, but coot doesn't "obey". The ligand has more than 50 atoms , so I tried with simple ethane diol, EDO. I copied the EDO.cif from the library and changed the C1-C2 torsion angle def

[ccp4bb] solvent mask for partial ligands

Dear all,   I have a modelling problem, which probably has something to do with the solvent mask. There is a positive density blob at the surface of my protein, which I can more or less satisfy with a Hepe (EPE). Hepes is in the buffer, the sulfonic acid H-bonds to a lysine side chain and a mai

[ccp4bb] solvent mask for partial ligands, addendum

Dear all,   I have a modelling problem, which probably has something to do with the solvent mask. There is a positive density blob at the surface of my protein, which I can more or less satisfy with a Hepe (EPE). Hepes is in the buffer, the sulfonic acid H-bonds to a lysine side chain and a

[ccp4bb] Handling of alternate main chain conformations in refmac

Dear all, specifically refmac developers,     I have an unexpected observation, when refining alternate main chain conformations for residues 22 and following in refmac. Residue 21 has one conformation, residues 22-25 have two conformations. There are four chains. I have coordinates with PRO 21, A

[ccp4bb] mtz/cif file for depostion

Dear all,   I have problems preparing my experimental data (XRD) for deposition. I have two mtz files, which work well for refmac5, with an FREER column in one file and Iplus, SIGIplus, Iminus, SIGIminus columns in the second file. I merged them into one mtz file with cad (in ccp4i). The validati

Re: [ccp4bb] mtz/cif file for depostion

on Cooper. jon.b.coo...@protonmail.com Sent with Proton Mail [1] secure email. On Friday, 9 February 2024 at 17:54, Palm, Gottfried wrote: Dear all,   I have problems preparing my experimental data (XRD) for deposition. I have two mtz files, which work well for refmac5, with an FREER colu

[ccp4bb] depositing a posttranslational modification

ve to reupload the renamed coordinates again in the deposition process, thereby loosing all extra information I typed in already. Can I prevent this loss? (ok, that's a minor problem) Best rergards   Gottfried Dr. Gottfried Palm Universität Greifswald Inst. für Biochemie (MNF) Synthetische und St

[ccp4bb] ITC suppliers

. I can find the NanoITC from Waters, but there might be others out there. If you happen to be near to Greifswald (Berlin or Hamburg or so), we might be interested to visit you, as well. Greetings   Gottfried Dr. Gottfried Palm Universität Greifswald Inst. für Biochemie (MNF) Synthetische und