Re: [ccp4bb] opentrons pipetting robot

I have long thought about developing an open-source crystallization robot based on the now ubiquitous 3D printing linear motion systems. They are certainly plenty precise for doing crystallization plating. Probably having two heads, a 12-channel syringe system for screen dispensing and a second hea

[ccp4bb] SOLVED: configuring remote servers with qsub. SSH port option

Of course, almost immediately after posting I described that I simply need to add "localhost" to the server section to get qsub to work. However, I think it would be useful if developers would add a port option for anything that requires ssh/scp. Many people avoid keeping ssh on port 22. Curre

[ccp4bb] Configuring remote servers with qsub

I'm having issues getting ccp4i2 to submit jobs to remote servers. I would like to use qsub, but I have also tried ssh with no luck. CCP4 is fully updated. Regardless of the method I try I get the following error: Traceback (most recent call last): File "/share/apps/ccp4-7.0/share/ccp4i2/qt

Re: [ccp4bb] Off-topic: 3D printing tools for molecular models

l toy like a chinese puzzle, that you dissassemble and reassemble to see how the subunits fit together. Something like cytochrome oxdase (13 subunits), cytochrome bc1 (dimer of 11 subunits each),or Complex 1 (48? subunits). eab On 05/20/2017 09:37 AM, Paul Paukstelis wrote: Sorry for the somewha

[ccp4bb] Off-topic: 3D printing tools for molecular models

Sorry for the somewhat off-topic post. After getting interested in 3D printing I quickly found that making nice ball-and-stick objects was very difficult to do on the typical fused filament printers most people can afford. This is largely because of the amount of support structures needed for

[ccp4bb] Proper way to handle multiple conformations of ions/waters

We've been working on a high resolution (1.0 A) DNA structure that has several coordinated magnesium ions that have complete octahedral geometry via water or phosphate oxygens but are clearly in multiple conformations (which is related to the multiple conformations of the coordinating phosphate

Re: [ccp4bb] C2, I2, completeness, and lattice translocation defects

header so we can see the history list and the cell/space group info? Cheers -- Ian On 4 November 2016 at 14:39, Paul Paukstelis mailto:shocksofmig...@gmail.com>> wrote: Refmac and phenix.refine versions I used both seem to be problematic. Both are I2 i

Re: [ccp4bb] C2, I2, completeness, and lattice translocation defects

p; I haven't noticed anything like this. Can you tell which program is introducing this error, e.g. by looking at the mtzdump outputs? Cheers -- Ian On 4 November 2016 at 12:00, Paul Paukstelis <mailto:shocksofmig...@gmail.com>> wrote: Thanks to all that responded. I sorted thi

Re: [ccp4bb] C2, I2, completeness, and lattice translocation defects

beta angle is smaller) Everything should work in I2: if it doesn’t it’s a bug (similarly with space groups such as P 2 21 21 with a On 4 Nov 2016, at 12:00, Paul Paukstelis wrote: Thanks to all that responded. I sorted this out. It all appears to stem from the C2->I2 conversion. Forcing every

Re: [ccp4bb] C2, I2, completeness, and lattice translocation defects

Thanks to all that responded. I sorted this out. It all appears to stem from the C2->I2 conversion. Forcing everything in processing to stick with C2 fixes all the issues! Thanks again, --paul On 11/03/2016 12:39 PM, Paul Paukstelis wrote: CCP4BB, I posted some time back about a

[ccp4bb] C2, I2, completeness, and lattice translocation defects

CCP4BB, I posted some time back about a DNA oligonucleotide structure we were working on. I had difficulty phasing it despite strong signal from bromines, but finally managed to get reasonable enough maps from a few datasets to build, only to find that despite the density looking quite good,

Re: [ccp4bb] Interesting DNA contamination

Stepwise addition to 1% PEI (polyethylenimine) following cell lysis (before dialysis) should do the trick. --paul On 06/25/2015 05:23 PM, Pramod Kumar wrote Dear all Sorry for off topic and lengthy post, but I came across a very unique DNA contamination during one membrane protein purificati

Re: [ccp4bb] crystal habit/morphology and the relationship to unit cell contents

with the plate materials, would the crystals form a bipyramidal habit? Or do you see crystals in the current drop that have the same habit but are not in contact with the plate materials? Scott -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Beh

Re: [ccp4bb] crystal habit/morphology and the relationship to unit cell contents

; and which you call the "base." So, what exactly do you find confusing? On 06/01/15 12:20, Paul Paukstelis wrote: I'm interested in knowing how to figure out the relationship between the unit cell contents and the crystal habit in these crystals (small attachment, two roughly

[ccp4bb] crystal habit/morphology and the relationship to unit cell contents

I'm interested in knowing how to figure out the relationship between the unit cell contents and the crystal habit in these crystals (small attachment, two roughly orthogonal views). Space group is P64 (enantiomeric) , and you can clearly see the six-fold. The question becomes how to determine

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

We found something similar for a DNA quadruplex not too long ago (4U92). This had surprisingly high resolution (1.5 Å) for having roughly half of the ASU being disordered. On 02/06/2015 06:51 AM, Andrew Leslie wrote: Just to give a concrete example of Randy's point, PDB entry 2ts1 for tyr

[ccp4bb] Disorder in crystal packing

Greetings, Currently working on a DNA quadruplex structure in which 4 of the 10 residues are partially disordered. 1.50 A resolution, and currently refined to R/Rfree of 12/14%. Apparent spacegroup is P4, two molecules in AU, both of which reside on the 4-fold to generate quadruplexes. Packin

Re: [ccp4bb] Continuing on the diffuse streak theme

ent of the structure. Eugene On 7 April 2014 19:03, Paul Paukstelis <mailto:shocksofmig...@gmail.com>> wrote: Seeing the diffuse streaking threads that have cropped up recently got me to thinking about many of the DNA data sets we have collected on. We always see diffuse stre

[ccp4bb] Continuing on the diffuse streak theme

Seeing the diffuse streaking threads that have cropped up recently got me to thinking about many of the DNA data sets we have collected on. We always see diffuse streaking along lattice lines. See images: http://vespa.chem.umd.edu/~paul/hex_streak01.png http://vespa.chem.umd.edu/~paul/hex_stre

[ccp4bb] unusually low B-factors

Greetings, We've been working on a number of related structures. Crystals are in P64 with fairly small unit cell (40,40,55) and only diffract to around 2.5-3.0, so we aren't working with a lot of reflections. For several of these data sets the maps look very reasonable but Refmac refinement g

Re: [ccp4bb] Cryo solution for crystals grown in magnesium formate

I find that odd because the first structure I ever worked on was a DNA oligonucleotide grown in 0.2 M magnesium formate and it did not require cryoprotection at all when flash cooled directly in the cryostream. I learned from Ned Seeman's group a long while back that Mg2+ itself worked reasonab

Re: [ccp4bb] Insertion of a Tag protein in of the molecules of a Dimer protein complex

Nicholas is right that it depends a lot on the dimer you are working with. I worked on a dimeric tRNA synthetase and was able to make heterodimers in a couple of ways. The most effective was to make a bicistronic version of the ORFs each with their own S-D. Each had a tag for tandem affinity pu

Re: [ccp4bb] Refinement of crystals containing a mixture in the asymmetric unit

; with two different residues? I would not be surprised if that would work with refmac. Best, Tim On 08/23/2013 05:39 PM, Paul Paukstelis wrote: Greetings, We have been working on a few DNA crystals in which the asymmetric unit contains a stoichiometric (or nearly so) mixture of two similar bu

[ccp4bb] Refinement of crystals containing a mixture in the asymmetric unit

Greetings, We have been working on a few DNA crystals in which the asymmetric unit contains a stoichiometric (or nearly so) mixture of two similar but distinct oligonucleotides. The resolution is medium to low (2.7-2.8) but for a few of these there are some hints from the density for two diff

Re: [ccp4bb] Missing DNA density in Protein DNA complex structure

How is the DNA packed in the crystal? Coaxially stacked pseudo-infinite helices? --paul On 05/05/2013 02:21 AM, ASHOK KUMAR Patel wrote: Hi all, I am working on a DNA binding protein (mol wt around 30 kDa), which binds to Duplex DNA in a non-specific sequence manner. The structure has been

Re: [ccp4bb] disulfide engineering

I don't know how much mileage you'd get out of it with your protein, but I was able to get very efficient disulfide linkage at the dimerization interface of my protein by dropping the salt to nearly nothing and running lots of buffer over it after immobilization on a cation exchange column (dur

Re: [ccp4bb] database-assisted data archive

file server that's periodically backed up) and let users browse through all the collected data of the lab with minimal effort later. I doesn't seem too hard to implement this, which is why I'm asking if anyone has done so already. Thanks. Andreas -- Paul Paukstelis, Ph.D Assistant

Re: [ccp4bb] Computer hardware and OS "survey"

Donnie Berkholz wrote: On 14:02 Mon 04 May , Paul Paukstelis wrote: Openoffice with Zotero/Firefox works very nicely for refs. I've found the OpenOffice plugin for Zotero to be very flaky on my Linux system. In my experience, it's crash-prone, slow, and likely to corrupt my do

Re: [ccp4bb] Computer hardware and OS "survey"

-paul -- Paul Paukstelis, Ph.D. Research Associate Institute for Cellular and Molecular Biology The University of Texas at Austin P: 512-471-4778, F: 512-232-3420 p...@icmb.utexas.edu

Re: [ccp4bb] Secondary structure restraints

ices are reasonably straightforward (I can see how to do them from eg DSSP), but sheets are more complicated. Any suggestions? I'm sure that someone must have done this Phil -- Paul Paukstelis, Ph.D. Research Associate Institute for Cellular and Molecular Biology The University of Texas at Austin P:

Re: [ccp4bb] crystallisation and mosaicity

I have also observed this. In my cases I have also been able to get away with using less cryoprotectant when freezing in the cryostream. --paul Daniel Pomeranz Krummel wrote: Dear Sajid, I have observed a consistent reduction in mosaicity (from approx. 0.95 to 0.45) for one case by freezing t

Re: [ccp4bb] Removal of glycosylation sites in Picha expression construct

Radisky, Evette S., Ph.D. wrote: The residues at these positions by sequence alignment are D, P, G, and S. Don't Perturb Glycosylation Sites. Sorry, I couldn't resist. -- Paul Paukstelis, Ph.D. Research Associate Institute for Cellular and Molecular Biology The University of Texas

[ccp4bb] Glu+Arg solutions for solubility

posting for a colleague: In Golovanov et al. 2004 they indicate it is possible to make a 1M solution of free amino acids (not amino acid salts) Glu+Arg in the context of generating solutions for keeping proteins soluble. Has anyone been able to do this?

Re: [ccp4bb] Vista

Oren, PhD Manager, Structural Biology Resource Center Rockefeller University 1230 York Avenue New York, NY 10065-6399 phone: 212- 327-7429 fax: 212-327-7389 -- Paul Paukstelis, Ph.D. Research Associate Institute for Cellular and Molecular Biology The University of Texas at Austin P: 512-471

Re: [ccp4bb] secondary structure restraints

For a (very) low resolution RNA/protein complex in which we had high(er) resolution structures for both components, I used the optimal hydrogen bonds from these structures (WHATIF output) as restraints. I made a couple perl scripts to take this output and generated either CNS or REFMAC restrain

Re: [ccp4bb] xtalview and mifit

This is my response to Marius from earlier today. I should have sent it to the list as well. This was done in Fedora 8, but it I'm guessing similar commands in the other distros that now use libxcb will also work. BTW, I tried upgrading to libxcb-1.1 and using the sloppy_lock variable that fix

Re: [ccp4bb] detecting RNA from possible protein-RNA complex crystals

easily fished out. They can be dyed > so definitely > not salt crystals. > > Thanks > > Rongjin Guan -- Paul Paukstelis, Ph.D. Research Associate Institute for Cellular and Molecular Biology The University of Texas at Austin P: 512-471-4778, F: 512-232-3420 [EMAIL PROTECTED]

[ccp4bb] Number of refinement parameters

A couple of basic questions concerning the number of refinement parameters: How do you come up with the number of parameters based on the number of atoms? I was under the impression it was simply the number of atoms times 4 (x,y,z,B), but I've seen some reported numbers that have left me confu

[ccp4bb] NCS-averaged composite omit map?

I'm working on a 4.5-A structure with 4-fold NCS. I've generated a SA composite omit map and all the protomers look pretty good, but with weaker density in mostly different parts for each. Am I correct that CNS doesn't do any NCS averaging automatically, and is there any reason why I shouldn't

[ccp4bb] Refinement of low resolution structures

as validation for the correctness of a model at this resolution and phased by MR? Omit maps of key features? Yes, I am trying to get higher resolution data. Thanks in advance. --paul -- Paul Paukstelis, Ph.D. Research Associate Institute for Cellular and Molecular Biology The University of

[ccp4bb] Refmac5 site?

I'm in need of the source code for Refmac5 (latest version) to recompile with an increased number of atoms. It seems the refmac site is down. Does anyone know another location of the latest source, or the status of the refmac site? --paul -- Paul Paukstelis, Ph.D. Research Associate Inst