Dear All,
I am trying to obtain the pairwise Ca-distances between corresponding residues
of two antibody light chains. CCP4 Superpose can output the distances in the
log file, but the numbers seem to be wrong when examed by eye. Is there a way
to calculate the pairwise distance between two pdb?
Dear All,
I am looking for a way to calculate the size of a protein cavity which is
occupied by a loop from a ligand protein. The goal is to see what's the maximum
length of peptide allowed in this cavity.
Thanks,
Tongqing
Tongqing Zhou, Ph.D.
Staff Scientist
Structural Biology Section
Vaccin
"link"
>>> each sequence with a run of 20 or so alanines i.e. sequence A
>>> followed by AAAA ... sequence B
>>> sequence C.
>>>
>>> There may well be a more elegant solution - but I'm fairly sure this
>>
Dear All,
I am trying to use Arp/wArp to build an antibody-antigen complex with 1.65 A
data, there are three chains (heavy, light chains of antibody and the antigen)
in the complex, my question is how to put the sequences in the *.pir file so
that it still identifies different chains. It looks
I would recommend Qiagen's ProComplex and JCSG+, and Emerald's Precipitant
Synergy.
- Original Message -
From: Ho Leung Ng [mailto:h...@hawaii.edu]
Sent: Thursday, November 17, 2011 07:23 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Protein-Protein Complex Screening
There is at l
You can also try to crosslink before transferring to cryo.
From: Filip Van Petegem
To: CCP4BB@JISCMAIL.AC.UK
Sent: Wed Oct 26 13:19:16 2011
Subject: Re: [ccp4bb] cryo protection
Hello Leonard,
one thing to test is whether transferring your crystals to a drop co
Dear CCP4bb,
We are trying to get some detailed interface information from an
antibody:antigen complex, PDBePISA used to have an option to select atomic
level details, now the new web interface only gives residue level information.
Is there a way to run PISA (in the CCP4 package) with a differe
We have no problem with encryption on Windows 7 here at NIH
- Original Message -
From: Harry
To: CCP4BB@JISCMAIL.AC.UK
Sent: Wed Aug 17 18:23:21 2011
Subject: Re: [ccp4bb] Computer encryption matters
Hi John
My Mac laptop has been encrypted according to MRC rules for several
years a
Dear CCP4 community,
I have few conserved water-mediated interactions in different antibody:antigen
complexes and I want to get a list of those. It's hard to keep track by eye
inspection. Is there a program that can perform such kind of job? PISA does a
nice job on interfaces by ignores water.
y and Infectious Diseases shall not accept
liability for any statements made that are sender's own and not expressly made
on behalf of the NIAID by one of its representatives.
**
-Original Message-----
From: Zhou, Tongqing (NIH/VRC
tives.
**
Zhou, Tongqing (NIH/VRC) [E] wrote:
> Dear All,
>
>
>
> I am trying to set up a dual boot system on a new Dell laptop factory
> installed with 64-bit Windows 7 professional.
>
>
>
> Model: De
Dear All,
I am trying to set up a dual boot system on a new Dell laptop factory installed
with 64-bit Windows 7 professional.
Model: Dell Latitude E6410
OS: Windows 7 Professional
MEM: 8G
CPU: Corei7
HD: 500GB
I first shrank the HD with Win7 to give ~250GB space to the new OS, I then
installed
er's own and not expressly made
on behalf of the NIAID by one of its representatives.
**
-Original Message-
From: Eleanor Dodson [mailto:c...@ysbl.york.ac.uk]
Sent: Tuesday, June 15, 2010 4:46 AM
To: Zhou, Tongqing (NIH/VR
Hi Everyone,
I have some problem in refining a structure. The data goes to 2.4A (with some
30% completeness at 2.15A), the structure was solved by MR with Phaser,
refinement was done with Phenix, but the r and r-free are now staying at 26%
and 32%, even with all possible waters and missing frag
Hi All,
I am wondering anyone is looking into GPU computing on structural refinement? I
see VMD supports GPU computing already, how about other programs such as CCP4
and Phenix
Thanks,
Tongqing
Tongqing Zhou, Ph.D.
Staff Scientist
Structural Biology Section
Vaccine Research Center, NIAID
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