Hi,
Thanks, I think the problem is with the EDS server as I tried numerous pdb
files (not just the 3TVN) and none of them worked so far.
Shya
On Wed, Aug 8, 2012 at 5:47 PM, Paul Emsley wrote:
> On 08/08/12 21:39, Shya Biswas wrote:
>
>> Hi all,
>>
>> I was trying to g
Hi all,
I was trying to get maps using the *fetch PDB and Map using EDS option* in
coot, however the map would not open I am using coot version 0.6.2 was
wondering if anybody else had similar problems and how to fix this, the
following is the error message I get. It used to work fine with a previo
Hi all,
I have a dataset that I scaled in p212121 with cell dimension a=28.9 b=67.1
and c=93.5 however I do not get a right MR solution with this. So I went
back and scaled it in p222 space group and asked phaser to find the right
spacegroup solution for it, this time phaser gave me the right solu
Hi,
Try modeling a zinc close to the histidine and then do one round of
refinement the density will improve close to that area, generally a zinc
ion coordinated to histidine also has a water molecule close to the zinc.
HTH,
Shya
On Tue, Jun 19, 2012 at 5:47 AM, Lianying Jiao wrote:
> Dear all,
>
files. I just tried, it took 5 minutes to
> calculate them on my mac.
>
> Pavel
>
> On Wed, May 9, 2012 at 9:08 AM, Shya Biswas wrote:
>
>> Hi all,
>> I am having trouble generating a pdb and cif file from the following
>> smiles string:
>> O=C(C[N+]23CN1CN(CN(C
The following seems to work with phenix:
O=C(C[N@+]23CN1CN(CN(C1)C2)C3)c45c45
Shya
On Wed, May 9, 2012 at 12:15 PM, Bosch, Juergen wrote:
> Is that your molecule ?
>
> On May 9, 2012, at 12:08 PM, Shya Biswas wrote:
>
> O=C(C[N+]23CN1CN(CN(C1)C2)C3
,
Shya
On Wed, May 9, 2012 at 12:55 PM, Paul Emsley wrote:
> On 09/05/12 17:08, Shya Biswas wrote:
>
>> Hi all,
>> I am having trouble generating a pdb and cif file from the following
>> smiles string:
>> O=C(C[N+]23CN1CN(CN(C1)C2)C3)**c45c45
>>
&g
Hi all,
I am having trouble generating a pdb and cif file from the following smiles
string:
O=C(C[N+]23CN1CN(CN(C1)C2)C3)c45c45
Prodrg fails to run when i draw the molecule in JME editor was wondering if
anyone knows a better program which does this kind of job.
thanks in advance,
shya
the transform to apply to that solution
> in pdbset to get the solution in the "standard" setting? Or is it easier
> to just repeat the MR?
> eab
>
> Shya Biswas wrote:
>
>> Hi Matt,
>> It worked really well in HKL 2000 reindex option, sorry about the
>>
Hi Matt,
It worked really well in HKL 2000 reindex option, sorry about the confusion
before, I wanted hkl to lhk. as you pointed out the second one gave me what
I wanted.
thanks,
Shya
On Mon, May 7, 2012 at 4:47 PM, Matthew Franklin wrote:
> On 5/7/12 4:09 PM, Shya Biswas wrote:
>
>
Hi,
My case is old b is changed to c (scenario 2 as you explained) or hkl is
changed to hlk. Thanks for the help
Shya
On Mon, May 7, 2012 at 4:33 PM, Ethan Merritt wrote:
> On Monday, May 07, 2012 01:09:25 pm Shya Biswas wrote:
> > Hi all,
> > I was wondering if anyone knows how
Hi all,
I was wondering if anyone knows how to convert the P21221 to P21212
spacegroup in HKL2000. I scaled the data set in P21212 in HKL 2000 but I
got a correct MR solution in P21221 spacegroup. I have a script file that
runs with scalepack but was wondering if there is an easier way to do it
wit
Hi all,
I was wondering if anyone had problems with drawing molecule using JME
editor in PRODRG? If yes then how do I fix it? I could not draw molecule in
the JME editor in the PRODRG webpage recently and JAVA is already installed
in my computer.
thanks,
Shya
Hi,
Did you try using a different column like Superose 6? This column works
well to separate large molecular weight proteins including oligomers.
Ideally if your solution is not cloudy (coming out of void volume) those
are not aggregates those might be oligomers.
HTH,
Shya
On Tue, Feb 21, 2012 at
sorry totally misunderstood your question, however if you can ship your
protein i can always try to setup a tray for you.
Shya
On Fri, Nov 18, 2011 at 9:34 AM, xaravich ivan wrote:
> Hi,
> I apologize in advance as it is not a ccp4 related question, but over the
> years, CCP4bb is synonymous with
Hi,
I am routinely using the gryphon robot from Art Robbins.This instrument can
dispense 0.02microlitre at minimum. Your drops can dry out if you use such
low volumes you have to be really fast. You can set up 0.2 to 0.1 micro
litre drops using this for 96 well plates however the instrument needs t
Hi Francis,
Once I had asked Pavel Afonine the same questions and these were his
suggestions but most of these can be implemented in phenix...
I guess there is no general/unified procedure to do this, and in most of
cases the tools and outcomes vary case by case.
Some general points:
- Removing p
Hi Eric,
Once you merge the ligand coordinates to your model and do one round of
refinement, the next time you open up coot and try using the real space
refinement it never works (even if you import cif dictionary of your ligand)
so not sure if its a problem with coot. Did anyone else had similar
p
Hi,
I was wondering if anyone knows what HKL 2000 does? Does it merge all
partials and treat it as one, because often times I noticed with increase in
partials the redundancy increases.
Shya
On Fri, Jul 15, 2011 at 1:24 PM, James Holton wrote:
> At the risk of asking a question to which I shou
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