[ccp4bb] Determining number of surface atoms with AREAIMOL

Dear all, This is more of a scientific question than a technical one - I hope this is the right place to ask. I'm new to the CCP4 bundle. So far I've only used the AREAIMOL tool, which determines the accessible surface area of a system. My system is an irregular periodic slab and so I have

Re: [ccp4bb] CCP4: scalepack2mtz problem

I suspect this is an external problem - there is no failure message in the P212121 case.. Obviously the input data is different for the 2 sets, do you know why? The integration should be identical. And you have NCS translation at 0,0,0.5 which makes it hard to be sure if the SG is P21212 or

[ccp4bb] Open positions in chromatin biology and gene silencing at the University of Geneva, Switzerland

Two positions at PhD student or postdoctoral level are available for highly motivated, creative individuals at the Department of Molecular Biology of the University of Geneva in Switzerland. The laboratory of Thomas Schalch (http://www.molbio.unige.ch/eng/research_groups/schalch/lab) is

[ccp4bb] pdb2pqr generation

Dear All, I wish to generate electrostatics surface cartoon for a protein, which is a tetramer. I am using pdb to pqr server (http://nbcr-222.ucsd.edu/pdb2pqr_1.8/) to generate .pqr files as part of this process. I find that server is able to genetrate .pqr file contents, only when input pdb

Re: [ccp4bb] unknown densities

Yamei, This is not unusual, particularly for many proteins that bind nucleotide derivatives, especially GDP/GTP binding proteins, as Nat said. If it is GDP that is tightly bound at high occupancy, it should be quite easy to identify because of the pyrophosphates and the guanine ring. To

Re: [ccp4bb] pdb2pqr generation

Dear abhishek, one work-around is to split the PDB-file into four different PDB-files, one per chain, and concatenate the results back together. Alternatively you can try Coot to calculate the ESP. Bst, Tim On 12/09/2014 02:23 PM, abhishek jamwal wrote: Dear All, I wish to generate

Re: [ccp4bb] CCP4: scalepack2mtz problem

Hi, Eleanor: Thank you for your suggestions. In HKL, I integrated the data set with P222, and scaled it with P222 and P212121. From pointless, it says the data better fit with P212121. So I would like to process the data with P212121 as well. And you have NCS translation at 0,0,0.5 which

[ccp4bb] Ramachandran maps

Hi guys, Sorry for the repost in COOT/CCP4/PHENIX. It is possible on of the users in one of these communities might know the answer I was wondering if there is a small script I can use to generate the outline of the allowed regions of Ramachandran map on to which I can superimpose my

Re: [ccp4bb] CCP4: scalepack2mtz problem

Processing (integration and scaling) only depends on the point group, not the space group, so it is the same in P222 and P212121. Structure solution is different so you may need to try different space groups Phil On 9 Dec 2014, at 14:36, Uma Ratu rosiso2...@gmail.com wrote: Hi, Eleanor:

Re: [ccp4bb] CCP4: scalepack2mtz problem

No - no - failure has nothing to do with the SG - only the point group matters.. You dont need to reintegrate - integration only requires knowledge of thecrystal class. That must be why you get some different results. If you like to send me the 2 sca files I can check more carefully. Eleanor

[ccp4bb] השב: [ccp4bb] pdb2pqr generation

Hi, I don't recall having this problem with pdb2pqr through the apps link. Did you try it? If all fails I suggest that contact the apbs/pd2pqr support. They're very helpful. Boaz הודעה מקורית מאת abhishek jamwal jamwalabhis...@gmail.com תאריך: 09/12/2014 8:29 (GMT-05:00)

Re: [ccp4bb] Ramachandran maps

The UCSF Chimera program does this very well. I don’t know about script based, but the GUI is very good and plots are publication quality. David Da-Neng Wang Lab Structural Biology Program New York University School of Medicine Publications via Google

Re: [ccp4bb] Challenging Mol.Rep. Problem

Generally fab geometry presents problems for mr due to variable interdomain angle. Assuming your sg is correct and this is not a twin, i would try searching at 4 or even 5 a resolution. I would not reject the chance that you have high solvent content, so you might have fewer molecules in au than

Re: [ccp4bb] Challenging Mol.Rep. Problem

Thank you cell phone typing for the inadvertent prophanity. Sorry! On Dec 9, 2014 1:00 PM, Artem Evdokimov artem.evdoki...@gmail.com wrote: Generally fab geometry presents problems for mr due to variable interdomain angle. Assuming your sg is correct and this is not a twin, i would try

Re: [ccp4bb] Challenging Mol.Rep. Problem

Try othercell to look for other indexing - C2 is a possible alternate SG to H32. And have you run pointless to check on symmetry operators? You certainly have 4 independent 3 fold rotations which would generate 12 mols per ASU. But first think about higher symmetry SGs - that will make the whole

Re: [ccp4bb] unknown densities

Hi Yamei, Depending on your dataset and collection, if you have collected any anomalous data, you can check for peaks that indicate phosphorus atoms in anomalous maps. It might even be worth feeding into ANoDe ( http://shelx.uni-ac.gwdg.de/SHELX/anode.php) if you have sufficiently high

Re: [ccp4bb] Challenging Mol.Rep. Problem

Hi, We’ve had good luck with Phaser in placing many copies of proteins or domains, if the model is reasonably good. Because of the variable elbow angle, you probably want to place the domains separately. However, as soon as you find one convincing assembly you can switch to searching for the

Re: [ccp4bb] pdb2pqr generation

Hi Tim, You have sparked my interest in Coot ESP. Do you know of a link to explain how to display/export it? I can generate it but nothing happens (other than the protein disappearing Cheers Joel -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of