[ccp4bb] ORCID

Dear all, It's been a while since last time I deposited structures to PDB. Do I really need an ORCID (Open Researcher and Contributor IDentifier) now to submit files? Is it mandatory? Thank you! Jie To unsubscribe from

Re: [ccp4bb] Dynamic light scattering instrument

Thank you. Jie From: Roger Rowlett <rrowl...@colgate.edu> Sent: Tuesday, May 2, 2017 1:36:48 PM To: Jie Liu; CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Dynamic light scattering instrument We've had a Malvern Zetasizer for many

[ccp4bb] Dynamic light scattering instrument

Dear all, We are interested in using dynamic light scattering to evaluate crystallizability of proteins. What instrument would you recommend? Many thanks and with best regards. Jie

[ccp4bb] Docking structure to EM map

Dear you all I am a novice in docking a structure to an EM map. The map was downloaded from the EM database with all the header infomation. I used some software to dock my structure. However the structure looks a little bit bigger than the map region where it is doceked in. My question is: is

[ccp4bb] Protein model size is much bigger than EM map

Dear you all May I ask a question? I tried to dock my protein structure onto an cryo-EM density map. I loaded both the map file and my model coordinates into Chimera. But it looks apparently that they are not in the same size scale. My model is much bigger than the size of the EM map region

Re: [ccp4bb] ctruncate error

Hi I also encountered the same problem after recent updates (not the most recent one, but a couple of updates back). Choosing to run old-truncate will get it around. Best wishes Jie - Original Message - From: Stephen Carr stephen.c...@rc-harwell.ac.uk To: CCP4BB@JISCMAIL.AC.UK

[ccp4bb] Postdoc positions

...@njms.rutgers.edu. Jie Liu

Re: [ccp4bb] odd phaser failure

Dear Eleanor I've been getting this error for a while. Switching back to ccp4-6.3 would solve the problem. I guess it's a bug of version 6.4. Best Jie - Original Message - From: Eleanor Dodson To: CCP4BB@JISCMAIL.AC.UK Sent: Tuesday, May 20, 2014 5:26 AM Subject: [ccp4bb]

Re: [ccp4bb] odd phaser failure

Dear Airlie and Randy Thank you! I have seen this error for quite some time and get it around by using ccp4-6.3 for Phaser. Will try to be the first to report next time :-) All the best Jie - Original Message - From: Airlie McCoy ajm...@cam.ac.uk To: jie liu jl1

[ccp4bb] MrBUMP not running after update

Dear All I just installed CCP4-6.4 and all the subsequent updates. Now MrBump failed with the following error message: The program run with command: /usr/local/ccp4-6.4.0/bin/ccp4-python -u /usr/local/ccp4-6.4.0/bin/mrbump HKLIN /home/jie/Structures/local/se-p26c8newn6/ccp4_6.3/high_x4c.mtz

[ccp4bb] Please recommend linux workstation

Dear All I am planning to buy a linux workstation for crystallography. It seems that Dell does not offer workstations with linux right now. Any good experience to recommend? Thank you! Jie Liu

[ccp4bb] Help Please!

to fix it? I am anxiously waiting for your help! Best regards Jie Liu

[ccp4bb] Software for optimizing drug molecules

on? I would like to have a general idea before going further. Any input will be greatly appreciated. Have a good weekend! Jie Liu PHRI/NJMS/UMDNJ

[ccp4bb] Please help with Raster3D (linux version)

Dear All I tried to make a stereo picture using Raster3D installed on a linux box with the following command: stereo3d -tiff xxx.tif xxx.r3d but got an error message: stereo3d: normal3d seems to be OK stereo3d: rendering left eye view stereo3d: rendering right eye view stereo3d: joining left

[ccp4bb] Postdoctoral position in protein crystallography

send a CV and a list of two references to li...@umdnj.edu Thank you. Jie Liu, Ph.D. PHRI/NJMS/UMDNJ

[ccp4bb] Postdoctoral Position

A postdoctoral position in protein crystallography is available in Dr. Min Lu’s lab at Public Health Research Institute Center, New Jersey Medical School, University of Medicine and Dentistry of New Jersey. Our research mainly focuses on the three-dimensional structures and biological

[ccp4bb] Software for predicting potential disulfide cross-linking sites?

to CYS in order to introduce an intermolecular disulfide bond to stabilize the biological assembly? Your input is greatly appreciated! Jie Liu

Re: [ccp4bb] clapham, or ccp4 6.1.0 release

for such a bundle or we should start to struggle with the compilation right now? Thanks for your attention. Jie Liu Charles Ballard wrote: Dear All as we continue our journey up the A65 (towards the heart of Yorkshire) we are pleased to announce the release of Clapham (or 6.1.0). This is available form

Re: [ccp4bb] Sulfate ion on 2-fold axis - Garib?

I've played around for a while, also read the manual and googled the internet, but just couldn't find a way to set up the restraints to the symmetry related atoms in Refmac5. Could anyone please kindly advice me how to do that? Thank you!!! Jie Eleanor Dodson wrote: It needs Garib to answer

[ccp4bb] Sulfate ion on 2-fold axis

Dear all I have a sulfate ion sitting on a 2-fold axis. Should I put in pdb file one S atom with occu=0.5 and two O atoms with occu=1, or should I put one S and four O atoms all with occu=0.5? Thanks for your inputs. Jie

Re: [ccp4bb] Calculating vertical offset of helices

wondering if there is an existing program? Thanks! Jie Edward Berry wrote: Since Jie Liu is talking about coiled coils and heptad repeat, I think what may be needed is the displacement along the bundle axis. So an expression for the best bundle axis line, and then the projection of different

[ccp4bb] Calculating vertical offset of helices

Dear CCP4ers: Does anyone know an existing program to calculate the lateral displacement---the vertical offset, measured as a fraction of the the heptad repeat---of neighboring helices in coiled coils or helix bundles, either parallel or antiparallel? Your input is greatly appreciated. Have a