Dear all, is there a way to "automatically" patch up the missing atoms in
the residues that otherwise are properly defined in a PDB entry. For
example, an Arginine is defined as Arginine but only has the beta carbon on
the side chain.
In Coot I could use the Extensions/Modeling/Residues with Missi
al Residues...
I'm using WinCoot 0.8.9.2 EL.
Sorry if I have missed anything obvious. Thanks for your helps, -yong
On Sat, May 23, 2020 at 9:30 PM Paul Emsley
wrote:
> On 23/05/2020 20:18, Yong Tang wrote:
> > Dear all, is there a way to "automatically" patch up the mis
Dear all,
I'm wondering if you have personal experiences with an antiparallel
homodimerization motif that I may use to add to my target protein for
homodimerization. I was thinking along the lines of a helix or beta sheet
(or hairpin) that is capable of antiparallel homodimerization.
For the inte
Dear all,
We are currently looking into setting up some inexpensive and personal
"incubators" for crystallization at a stable temperature of ~25C. I
was told that a couple of years back there was an active discussion on
the forum about making some house-hold items into such an incubator,
more spe
Dear all,
I sent this enquiry a couple of days ago unintentionally under another
thread. I got the only response from Artem suggesting Koolatron and
would like to try my luck again today to see if you would be able to
offer more ideas. Thanks! -yong
We are currently looking into setting up some
RE: Removal of bacterial chaperone Hsp70 contaminant from recombinant
protein preparation
Dear all,
I have a protein expressed at 37C for 3 hours in BL21 DE3 and purified
with sub-stoichiometric amount of apparent Hsp70 contaminant even
after exhaustive affinity (GST-fusion or His-tagged), ion-e
Deal all, thank you for all the wonderful helping tips. A quick test
of ATP-Mg at 2mM at 37C for 2 hours had proved ineffective in my case
so now I'm thinking of trying the other protocols that you had offered
as listed below. Many thanks and have a wonderful week! -yong
Original Question
RE: Rem
Dear all, just a super dummy question: I treated a protein with
trypsin, found the protein being degraded into two well-define
fragments, ran a sizing column to find them co-elute, sent the peak
fraction for mass-spec, got the two masses. Now here is the question -
is there any program readily ava
ptidecutter/
3) http://bioinformatics.genomicsolutions.com/PawsDL.html
4) http://www.expasy.ch/tools/findpept.html
Subject: (bigger) fragment identification of limited proteolysis w/ mass-spec
----
From: Yong Tang <[EMAIL PROTECTED]>
Dear all, just a super dummy question: I treated a prote
James, for a LN container like this I don't think people would even consider
putting these plastic things into the autoclave for pasteurization. I had
used these at GM-CA [EMAIL PROTECTED] more than once and always wish to have
one in
the lab - less ice formation on the rim, hence in the liquid in
could not re-enable loggraph popup.
Can someone tell me what setting I need to change to have the old style
loggraphs popup ? .
Thanks
Yong
--
Yong Tang
.."
(file
"/home/yong.tang/ccp4_root/ccp4-6.4.0/share/ccp4i/loggraph/loggraph.tcl"
line 2324)
invoked from within
"source [file join $env(CCP4I_TOP) loggraph loggraph.tcl]"
(file
"/home/yong.tang/ccp4_root/ccp4-6.4.0/share/ccp4i/bin/loggraph.tcl" line 83)
Hi there I have a quick question about coot. I'm using Coot 0.8-pre EL
(revision 5001). I just realize that the sequence display is limited to
somewhere around 2245... The structure that I am looking at has the
starting residue number larger that 2245 so the whole sequence is not shown
in Draw/Sequ
or
> with pdbset. This, however, would break the reasonable custom that
> residue number should match the biological sequence number, so don't
> forget to rerenumber upon deposition.
>
> Regards,
> Tim
>
> On 10/09/2014 08:36 PM, Yong Tang wrote:
> > Hi there I have
Dear all, I have no access to Moleman now but I need to compile a
statistics table for a structure, more specifically, for its atom numbers
(protein/ligand/water), B factors, RMS deviations etc. Is there an
alternative program for that in the CCP4 suite? Thank you in advance for
your help, -yong
Dear all,
I downloaded the latest mac version of CCP4 suite for installation on a new
Mac (macOS Big Sur Version 11.5.2). The package was downloaded using
Chrome. After unpacking and moving the folder to its destination
/Applications/ccp4-7.1, the set up using
./BINARY.setup
gives error messages
st checked, the CCP4i and coot are now running as expected.
I really would like to copy the whole BB to express my gratitude - kudos,
Charles, -yong
Yong Tang, Ph.D.
Director, Structure Biology
ENSEM Therapeutics
200 Boston Ave, Suite 1875
Medford, MA 02155
yong.t...@ensemtx.com
P.S. I followed
Dear all,
Do we have tutorials suitable for beginners to follow from Molecular
Replacement to model building and refinement, all the way up to water and
ligand inclusion?
I remember in the old days there were "case studies" that one could
download and follow through in Coot/Refmac - I have troubl
Dear all, I'm interested in considering the SERp but it seems that the
server is no longer accepting queries.
https://services.mbi.ucla.edu/SER/
Any replacement server/software for the same analysis?
Many thanks, -yong
To
Dear all, I'm interested in considering the SERp but it seems that the
server is no longer accepting queries.
https://services.mbi.ucla.edu/SER/
Are you aware of any replacement server/software for such analysis?
Many thanks, -yong
###
Dear all, I'm interested in considering the SERp but it seems that the
server is no longer accepting queries.
https://services.mbi.ucla.edu/SER/
Are you aware of any replacement server/software for such analysis?
Many thanks, -yong
>
Dear all, happy summer!
I searched in many ways but could not find relevant references easily
so I'm hoping you could help.
For TSA assays on a Cys-containing protein (drug target) that has just gone
through a covalent adduction reaction with a compound carrying a Michael
acceptor covalent warhea
Dear all,
Taking a random PDB entry 8hbk as an example, at one point of time, we have
access to a phase file called 8hbk_phases.mtz under the download section in
https://www.rcsb.org/structure/8hbk However that option doesn't seem to be
available anymore in general.
I do understand PDBe offers
ture/66ead31f2c751d5c77fbb706>*
What a great community to be in - I'm grateful, -yong
On Tue, Jan 14, 2025 at 9:37 AM Yong Tang wrote:
> Dear all,
>
>
> Taking a random PDB entry 8hbk as an example, at one point of time, we
> have access to a phase file called 8hbk_
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