Re: [ccp4bb] PyMOL now packaged as a snap on Linux

[Arunabh Athreya]

Thanks for sharing this.

Get Outlook for Android


From: CCP4 bulletin board  on behalf of David Schuller 

Sent: Thursday, May 16, 2019 11:41:19 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] PyMOL now packaged as a snap on Linux

It seems to work on Fedora 30 and on Scientific Linux 7 (which means it should 
also work on RHEL7 and Centos 7)

Thank you.



On 5/16/19 10:47 AM, Darren Hart wrote:
Some more info:

https://snapcraft.io/pymol-oss

It seems to work exactly as expected.

Darren


On 16/05/2019 16:05, Folmer Fredslund wrote:
Hi Darren,

That's brilliant!

I'll give it a spin and see how it works.

Best regards
Folmer


tor. 16. maj 2019 13.02 skrev Darren Hart 
mailto:darren.h...@ibs.fr>>:
Since yesterday, PyMOL (open source version v2.3) has been packaged as a
distro-independent "snap" that can be installed easily on linux
platforms - no more cloning from gitlab and compiling after installing
the dependencies.

On Ubuntu, install from software centre or:

sudo snap install pymol-oss

Many distros have the snap architecture already installed. If not, you
just need to install snapd in the regular way first (e.g. on Debian:
sudo apt install snapd).

Hope this is useful for some folks.

Best regards,

Darren



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Re: [ccp4bb] weight term and geometry

[Robbie Joosten]

Hi Luca,
 
You should not settle for poor results here. With the most recent CCP4 and 
PDB-REDO versions refining with an N-terminal CXM works fine. I guess there is 
something wrong with the restraint generation. Make sure your residues are 
sequentially numbered and in your PDB file the CXM appears right in front for 
your HIS without a TER record in between. You should not need LINK records, but 
they won't harm (you can use PDB/PDB-REDO entry 1ev5 as an example of the 
format).

HTH,
Robbie 

> -Original Message-
> From: CCP4 bulletin board  On Behalf Of Luca
> Mazzei
> Sent: Friday, May 17, 2019 16:41
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] weight term and geometry
> 
> Dear all,
> 
> I have a question about how PBDREDO and REFMAC treat the geometry
> weight (gw). In particular, I have a structure with a N-terminal CXM bound to
> a HIS as a second residue. After complete refinement, I run PDBREDO to
> choose the most appropriate gw. Let’s say best results are found using gw =
> 0.1. I run REFMAC using that value, but the carbonyl carbon of CXM detaches
> from the amidic N of HIS (distance 1.84 A). If i run the same job using a gw 
> of
> 0.2, 0.3 and so on, that distance decreases and the C-N bond is restored. By
> the way, increasing the gw Rfree increases as well as the difference between
> Rfactor and Rfree.
> Any idea on how to solve the problem? Should I keep higher Rfree and
> worse stats with still having a peptide bond there?
> 
> Thank you,
> 
> Luca
> 
> Luca Mazzei - PhD
> Department of Pharmacy and Biotechnology University of Bologna Viale
> Giuseppe Fanin, 40 - 40127 Bologna - Italy
> 
> 
> 
> 
> ###
> #
> 
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[ccp4bb] weight term and geometry

[Luca Mazzei]

Dear all,

I have a question about how PBDREDO and REFMAC treat the geometry weight (gw). 
In particular, I have a structure with a N-terminal CXM bound to a HIS as a 
second residue. After complete refinement, I run PDBREDO to choose the most 
appropriate gw. Let’s say best results are found using gw = 0.1. I run REFMAC 
using that value, but the carbonyl carbon of CXM detaches from the amidic N of 
HIS (distance 1.84 A). If i run the same job using a gw of 0.2, 0.3 and so on, 
that distance decreases and the C-N bond is restored. By the way, increasing 
the gw Rfree increases as well as the difference between Rfactor and Rfree. 
Any idea on how to solve the problem? Should I keep higher Rfree and worse 
stats with still having a peptide bond there?

Thank you,

Luca

Luca Mazzei - PhD
Department of Pharmacy and Biotechnology
University of Bologna
Viale Giuseppe Fanin, 40 - 40127
Bologna - Italy






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Re: [ccp4bb] crystals mounted in microRT capillaries

[David Schuller]

How far are you sending them? If they go by aircraft, they may 
experience unexpected pressure differentials and temperature extremes.


On 5/17/19 2:20 AM, Michael Colaneri wrote:

Dear all,

how can one mail crystals mounted in loops using the microRT 
capillaries of Mitegen?


Thank you.

Mike Colaneri



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===
All Things Serve the Beam
===
   David J. Schuller
   modern man in a post-modern world
   MacCHESS, Cornell University
   schul...@cornell.edu




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[ccp4bb] AW: [EXTERNAL] [ccp4bb] crystals mounted in microRT capillaries

[Herman . Schreuder]

For glass X-ray capillaries, we used a Styrofoam box with some cooling blocks 
at room temperature to prevent any fast temperature changes, which may lead to 
condensation problems. Of course, you should add some materials to protect the 
capillaries and keep them in place.

Best,
Herman

Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Michael 
Colaneri
Gesendet: Freitag, 17. Mai 2019 08:20
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [EXTERNAL] [ccp4bb] crystals mounted in microRT capillaries


EXTERNAL : Real sender is owner-ccp...@jiscmail.ac.uk

Dear all,

how can one mail crystals mounted in loops using the microRT capillaries of 
Mitegen?

Thank you.

Mike Colaneri



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