[ccp4bb] Registration Open. Macromolecular Crystallography School, Madrid (May 12–16, 2025)

/MCCS2025/ <https://www.xtal.iqf.csic.es/MCCS2025/index.html> We look forward to seeing you in Madrid! Best regards, Armando Organizers: Armando Albert, Juan A. Hermoso, María J. Sánchez-Barrena, and Lourdes Infantes Departamento de Cristalografía y Biología Estructural Instituto de Química

Re: [ccp4bb] Running coot from CCP4i2

> and stdout.txt. Please can you send them to us here? > Cheers, > Martin > > > On 19/11/2024 08:25, Armando Albert wrote: >> Dear all, >> >> I am trying to run coot from CCP4i2 and I’ve got the following message: >> >> Error Report for Job 6: Ma

Re: [ccp4bb] Running coot from CCP4i2

t; > If it does we'll have to try some other tests. If it does not work, is > XQuartz installed? > > Best wishes, > Stuart > > On Tue, 19 Nov 2024 at 08:25, Armando Albert wrote: >> >> Dear all, >> >> I am trying to run coot from CCP4i2 and I’

[ccp4bb] Running coot from CCP4i2

Dear all, I am trying to run coot from CCP4i2 and I’ve got the following message: Error Report for Job 6: Manual model building - COOT -ERROR- Ccoot_rebuild:56 Error in wrapper coot_rebuild 0.0:: External process exited with exit code != 0 Process: coot

[ccp4bb] Good electron density but poor affinity

Dear all, Is there any study that analyzes the relationship between the quality of the electron density of a ligand and its affinity? Armando To unsubscribe from the CCP4BB list, click the following link: https://www.jiscma

[ccp4bb] On the production of a two domain protein

Dear all, We are trying to characterize a protein consisting of two domains. We have successfully produced, purified and crystallized both domains independently. However, we are unable to overexposes a soluble form of the full-length protein. Can anyone provide a strategy to merge back the ind

Re: [ccp4bb] Structural alignment and classification

>>> Dear Armando, >>> >>> besides THESEUS, you could use SUPERPOSE (in CCP4) or USalign >>> (https://zhanggroup.org/US-align/). >>> In my tests, THESEUS sometimes crashed in different ways. USalign is very >>> robust; SUPERPOSE is fast. >>

[ccp4bb] Structural alignment and classification

Dear all, I want to align several structures we obtained from a fragment screening campaign and cluster them according to RMSD. Is MNYFIT still running? What else can I run? Thank you Armando To unsubscribe from the CCP4B

[ccp4bb] Macromolecular Crystallography School in Madrid from the 8th to the 12th of May 2023

?a=https%3a%2f%2fwww.xtal.iqfr.csic.es%2fMCCS2023%2findex.html&c=E,1,_6Q8g0pWDL046-LZ44gvaksBnMuEWPEnWs6dSM5ITyKFmfGLAZ-wAw4EL1OnPKfrAoDf9Hb1ndh68dyB4NhRkcMi2E59E10oYdB7mBQqlSCr&typo=1>) Hoping to see you In Madrid Juan and Armando Armando Albert and Juan A. Hermoso Departamento

[ccp4bb] Macromolecular Crystallography School in Madrid from the 8th to the 12th of May 2023

?a=https%3a%2f%2fwww.xtal.iqfr.csic.es%2fMCCS2023%2findex.html&c=E,1,_6Q8g0pWDL046-LZ44gvaksBnMuEWPEnWs6dSM5ITyKFmfGLAZ-wAw4EL1OnPKfrAoDf9Hb1ndh68dyB4NhRkcMi2E59E10oYdB7mBQqlSCr&typo=1>) Hoping to see you In Madrid Juan and Armando Armando Albert and Juan A. Hermoso Departamento

Re: [ccp4bb] Installing new version of CCP4

Now it is working. Thank you Armando > El 2 may 2020, a las 16:15, Armando Albert escribió: > > Is this normal? Waiting for ages….. > > > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?

[ccp4bb] Installing new version of CCP4

Is this normal? Waiting for ages….. To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1

Re: [ccp4bb] Structural Alignment

ce alignment). > > Hope this helps, > > Guillaume > > >> On 8 Apr 2020, at 19:04, Armando Albert > <mailto:xalb...@iqfr.csic.es>> wrote: >> >> Dear all, >> I want to align two

[ccp4bb] Structural Alignment

Dear all, I want to align two structures and then, I want to align several sequences to that structural alignment. How can I do this? Armando To unsubscribe from the CCP4BB list, click the following link: https://www.jisc

[ccp4bb] Protein concentration for the initial crystallisation trials

Dear all, I was wondering how to guess the optimal protein concentration for the initial crystallisation trials. Is there any trick or assay other than the classic PCT from Hampton? Armando To unsubscribe from the CCP4BB

Re: [ccp4bb] how to generate a complete biomolecule out of the BIOMOLECULE record

irst one, of course, the identity). > > Best, > Tim > > On Wednesday 18 January 2017 11:13:21 AM Armando Albert wrote: >> Dear all, >> Does any one know how to generate a complete biomolecule out of the >> BIOMOLECULE record from a pdb file that contains one of th

[ccp4bb] how to generate a complete biomolecule out of the BIOMOLECULE record

Dear all, Does any one know how to generate a complete biomolecule out of the BIOMOLECULE record from a pdb file that contains one of the four molecules forming a tetramer This is an Crio-EM model. Armando REMARK 350 BIOMOLECULE: 1 REMAR

[ccp4bb] Bulk solvent

Dear all, Is there any reason for using Babinet scaling for bulk solvent correction instead of mask based scaling? Armando

[ccp4bb] Negative electron density in the Fo-Fc map at the binding site

Dear all, I am screening a small library of ligands against my protein crystals. Following a soaking with different ligands, I collect datasets to 1.9A resolution and refine them against an empty model without any problem. What is the meaning of a rather large negative electron density in th

[ccp4bb] Naccess

Dear all, Does anyone know how to properly cite Naccess for calculation of solvent accessible area (http://www.bioinf.manchester.ac.uk/naccess/)? Armando

Re: [ccp4bb] C2/I2 space groups

If you do not specify that you prefer C2, pointless change to I2. This is sometimes odd, for instance when running molrep or shelx (hkl2map) afterwards Armando I am out of the lab > El 21/05/2014, a las 18:54, Roberto Battistutta > escribió: > > Dear All, > a question about C2 and I2 space g

[ccp4bb] problem with refmac and xloggraph

Dear all, does anyone experience a problem viewing refmac results with Log Graph? The window appears and disappears in less than one second and this is the output on the terminal window: Error in startup script: syntax error in expression "10 11 12 + 12": extra tokens at end of expression

Re: [ccp4bb] Low 280 absorbance imidazole?

Hi Phoebe, Could you please explain me how do you stain the piece of paper? Thank you Armando El 21/08/2013, a las 17:03, Phoebe A. Rice escribió: > Hi Bernhard, > If your cheap imidazole works fine aside from the absorption problem, > there's always my favorite stone-age detection method:

Re: [ccp4bb] about coot

Dear Paul, >> 2, And is there any option to prevent coot auto-loading ~/.coot file? > > No. Why would you want to do that? You may want to open a different session in the same directory and not spoil the one you are using for refinement Armando I am out of the lab El 23/11/2012, a las 12:32

Re: [ccp4bb] Lithium versus Sodium

Dear Matt, We were working with Hal2p a lithium inhibited Ins-mono-PPase like protein 10 years ago. We had good biochemistry showing that lithium replaced mg at the active site. We grow crystals in presence of Li and we worked with 1.6 A diffraction data. Unfortunatelly we did not see any el

[ccp4bb] Off topic question. NACCESS

Does anyone has got some information about how to get a mac version (intel), of the old unix program naccess?. It was meant to calculate the solvent accessibility per residue from a pdb file. Armando

Re: [ccp4bb] Will 3mFo-2DFc maps have less model bias than 2mFo-DFc maps?

Does anyone have got a script to compute 3fo2fc map with CCP4? Armando El 29/07/2010, a las 23:38, Ian Tickle escribió: On Thu, Jul 29, 2010 at 8:25 PM, Pavel Afonine wrote: Speaking of 3fo2fc or 5fo3fc, ... etc maps (see classic works on this published 30+ years ago), I guess the main rat

[ccp4bb] Expression of a protein of 43KDa

I am trying to overexpress a His-tagged protein of 29KDa in E.coli (BL21-codon plus) and I end up with a highly expressed product that of 43KDa that binds to the Ni-column. I also have nice crystals. Does anyone have any experience on this. Armando

[ccp4bb] Bad r factor at low resolution

What does it mean having the R factors a high resolution lower than at low resolution?. Could be related to the fact my model is incomplete? Armando