[ccp4bb] phenix.refine error

ame with the link as an additional argument. How could I solve this problem? Thank you so much! All the best! ******** Yamei Yu State Key Laboratory of Biotherapy／Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University,

[ccp4bb] unknown densities

method to detect what it is? Thanks! Best wishes! yamei Yamei Yu State Key Laboratory of Biotherapy／Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University,Chengdu,610041, P.R.China Tel: 15882013485 Email: ymyux

[ccp4bb] how to get a reflection cid file from PDB

error message. Where is the reflection cif files located in PDB? How to get the original diffraction data from PDB? Thank you so much for your help! Best wishes! Yamei Yu Sichuan University,Chengdu,610041, P.R.China Tel: 15882013485 Email: ymyux

Re: [ccp4bb] moleman2 install problem

Hi Tim, Thank you! yes, I download it through ftp from xray.bmc.uu.se I got it from pub/gerard/xutil_osx I couldn’t find usf_osx_bin/moleman2 Does anyone know how to find it ? Thanks! Yamei Yu State Key Laboratory of Biotherapy／Collaborative

Re: [ccp4bb] moleman2 install problem

much! Yamei Yu State Key Laboratory of Biotherapy／Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University,Chengdu,610041, P.R.China Tel: 15882013485 Email: ymyux...@gmail.com ymyux...@163.com

[ccp4bb] moleman2 install problem

) Could you tell me how to solve this problem? Thank you so much! Best wishes! yamei Yamei Yu State Key Laboratory of Biotherapy／Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University,Chengdu,610041, P.R.China Tel

Re: [ccp4bb] twin or untwinned

Thanks all for your comments! Yamei Yu On Jul 5, 2014, at 5:10 AM, Nat Echols wrote: > On Thu, Jul 3, 2014 at 7:50 AM, Nat Echols wrote: > On Thu, Jul 3, 2014 at 6:53 AM, Dirk Kostrewa > wrote: > yes - unfortunately,

[ccp4bb] Rfree set for twinned data

Hi all, Is there anything that needed to pay attention to while choosing Rfree set for twinned data set? Or we can choose Rfree set randomly as untwined data set? Thanks! Best wishes! Yamei Yu

[ccp4bb] twin or untwinned

twin or no twin? Please find the log file of phenix.xtrage in attachment. Thank you so much for your suggestion! Yamei Yu

[ccp4bb] a warning message from XDS (IDXREF)

RRECT" STEP BY SPECIFYING ALTERNATIVE SETS OF UNIT CELL BASIS VECTORS: UNIT_CELL_A-AXIS= -25.024 -66.429 -28.634 UNIT_CELL_B-AXIS= 20.919 22.359 -70.153 UNIT_CELL_C-AXIS= 157.798 -70.095 24.714 Thanks so much! **** Yamei Yu

[ccp4bb] install coot in mac through fink

Hi All I'm trying to install a coot for my new Mac. I followed the instructions from http://scottlab.ucsc.edu/~wgscott/xtal/wiki/index.php/Fink_for_10.9 when I execute the command :sudo apt-get install coot I got two errors: Get:23 http://psbmini.ucsc.edu stable/main gcc48-shlibs 4.8.2-1001 [33.0M

[ccp4bb] fink problem

Hi all, I use this command "fink -y install coot" to install coot but I got the following error message "arch: /usr/bin/perl5.10.0 isn't executable" Then I check the folder /usr/bin/ I don't have perl5.10.0 I only have perl5.10 how to solve this problem? Thanks! yamei

[ccp4bb] calculate buried area between antibody and antigen

Hi all, Is there an easy way to calculate the buried areas between antibody and antigen for all these complexes in PDB database? Or is there a good reference have such number? I found an old reference (published in 1990) reported this number but as more an more structures deposited into the PDB d

[ccp4bb] Is there a protein that it could interact with different proteins by the same part?

HI all, We know one protein can interact with different partners by different domains or different parts. Is there a protein that it could interact with different proteins by the same part (maybe the same part but in different conformations?)? Thank you in advance!! yamei

[ccp4bb] Parrot versus prime-and-switch-phasing

Hi all, To decrease model bias from molecular replacement we can either use Parrot or prime-and-switch-phasing. What's the difference between these two programs? Which one is better? Thank you very much! Yamei Yu

Re: [ccp4bb] coot and probe clash

Thanks! I download the executable probe and reduce and add them to .coot. Now it works well. Thank you very much! 2010/2/8 William G. Scott > On Feb 8, 2010, at 2:07 PM, Nathaniel Echols wrote: > > > On Mon, Feb 8, 2010 at 1:51 PM, William G. Scott < > wgsc...@chemistry.ucsc.edu > >> wrote: > >

[ccp4bb] coot and probe clash

Hi all, I have installed coot 0.6.1 in my Mac OS X 10.6. But the Prove chashes button in validate is grey. How to get 'Probe clashes" work in coot? Thank you very much! yamei

[ccp4bb] problem of imosflm in ccp4

Hi all, I use fink to install ccp4-6.1.2 on my Mac OS X 10.6. All programs in ccp4 works well except imosflm. when I run it, it gives me the following error message" Top level CCP4 directory is /sw64/share/xtal/ccp4-6.1.2 Using CCP4 programs from /sw64/share/xtal/ccp4-6.1.2/bin MOSDIR is /Use

[ccp4bb] how to show double conformation in PyMol

Hi all, There is a 10 residues loop in my structure which has two conformations, how could I show the double conformations at the same time in ribbon or cartoon model in PyMol? Thanks! yamei