Re: [ccp4bb] Iphone app to display protein models

[Takanori Nakane]

Dear Shiva,


I was wondering if there is any IOS5 based app to display protein models,
which are not in public database, on Iphone.


Just yesterday, Dr. Ishitani at Tokyo university released
Cuemol for iOS.
http://itunes.apple.com/us/app/cuemol/id496236710?ls=1&mt=8

Although not free, iMolview is a nice viewer, too.
http://www.molsoft.com/iMolview.html

Best regards,

Takanori Nakane

P.S. For Android users, I am developing NDKmol.
https://market.android.com/details?id=jp.sfjp.webglmol.NDKmol

Re: [ccp4bb] Ligand chirality error

[Herman . Schreuder]

Dear Debajyoti,
 
The way I check the chirality is to compare the fitted compound with the
structural formula. In coot, I rotate the ligand such that it has the
same orientation as in the formula and check that the "out of plane"
group goes in the right direction. However, it happens quite often that
the chirality of the bound compound is not the chirality the chemist
thinks it has, or the chirality is not known. In that case, I refine
both enantiomers and look which one fits best. Things to look for are
distorted bond angles, poor fitting and small positive and negative
blobs of difference density (green and red blobs in coot with default
settings).
 
To change the chirality, you have to edit the cif dictionary which
contains the description of your compound. In the dictionaries I use you
have to change the  _chem_comp_chir.volume.sign from positiv to negativ
or vice versa.
 
Good luck!
Herman
 





From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On
Behalf Of Debajyoti Dutta
Sent: Friday, January 27, 2012 8:25 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Ligand chirality error



Hi all,

How to check the presence of improper chirality of a fitted
ligand. Is there any way to get rid of such error.

All suggestions are welcome. Thanks in advance.

sincerely
Debajyoti


  
Follow Rediff Deal ho jaye!
  to get exciting offers in your city everyday. 

Re: [ccp4bb] Ligand chirality error

[Paul Emsley]

On 27/01/12 07:25, Debajyoti Dutta wrote:




How to check the presence of improper chirality of a fitted ligand.


With Coot,  Validate -> Incorrect Chiral Volumes


Is there any way to get rid of such error.


Extensions -> Modelling -> Invert this Chiral Centre.


Paul.

Re: [ccp4bb] Ligand chirality error

[Herman . Schreuder]

Hi Paul,

Does this also update the cif dictionary, or stays the change inside
coot?

Best,
Herman 

-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
Paul Emsley
Sent: Friday, January 27, 2012 10:28 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Ligand chirality error

On 27/01/12 07:25, Debajyoti Dutta wrote:
>
>
>
> How to check the presence of improper chirality of a fitted ligand.

With Coot,  Validate -> Incorrect Chiral Volumes

> Is there any way to get rid of such error.

Extensions -> Modelling -> Invert this Chiral Centre.


Paul.

Re: [ccp4bb] Ligand chirality error

[Paul Emsley]

On 27/01/12 09:45, herman.schreu...@sanofi.com wrote:


Does this also update the cif dictionary, or stays the change inside
coot?


It stays within Coot. It does not update the cif dictionary - IMHO, that 
would be a Bad Thing - maybe you are just experimenting.


It creates new set of restraints under a new name (comp-id) and renames 
the residue accordingly [1].


You can write out the new restraints:  Edit -> Restraints -> Save as 
mmCIF...


Paul.

[1] Incidentally, some of us developers would like wwPDB to reserve a 
set of comp-ids so that we can do this safely without bumping into 
comp-ids for which a dictionary already exists.

Re: [ccp4bb] Iphone app to display protein models

[Simone Nenci]

Dear Shiva

> There is an app called Molecules for displaying models but that utilizes 
> coordinates from RCSB and pubchem. 

You can also import your structure directly from itunes in pdb format
iMolview is not free but is very nice (better than Molecules :-)

cheers
Simone 

On Jan 27, 2012, at 8:00 AM, Shiva Bhowmik wrote:

> Dear All,
> 
> I was wondering if there is any IOS5 based app to display protein models, 
> which are not in public database, on Iphone. There is an app called Molecules 
> for displaying models but that utilizes coordinates from RCSB and pubchem. 
> 
> Thanks,
> 
> Shiva  



Simone Nenci
-
Dipartimento di Biologia e Biotecnologia
Università di Pavia
Via Ferrata 8, 27100 Pavia
Italy
Tel. +39-0382-985535/985534
Fax +39-0382-528496
Web www.unipv.it/biocry

Re: [ccp4bb] Iphone app to display protein models

[Opher Gileadi]

Molsoft has a free application:

http://www.molsoft.com/iMolview.html 

Re: [ccp4bb] Coot on an SGI

[Michael Strickler]

As someone stuck maintaining an SGI for a user who resolutely refuses to
abandon Showcase or Ribbons for IRIX, I sympathize with those cases
where one simply has to get an old computer system to work.

Anyway, we don't have the relevant library file in our freeware
directories either.  However, the last version of UCSF Chimera to
support IRIX, version 1.3, supplies libgcc_s.so.1.  We are using a
symbolic link libgcc_s.so --> libgcc_s.so.1 to run Coot 0.3.3 (not Coot
0.0.33, which runs only on Babbage analytical engines).  Chimera 1.3 is
still available from the UCSF Chimera download page:

http://www.cgl.ucsf.edu/chimera/download.html

as long as you are able to agree to their non-commercial software
license agreement.

Regards,

-- 
Michael Strickler, Ph.D.
Research Specialist
Richards Center for Structural Biology
Yale University
260 Whitney Ave, 355C JWG
PO Box 208114
New Haven, CT 06520-8114

Re: [ccp4bb] No diffraction

[Joe Watts]

1. Try room temperature mounts (as suggested by others)
2. Expose the hell out of the crystal (5 min) on home source or go synchrotron 
3. Run your protein through another column (ion exchange) even if it looks pure
4. Try an additive screen
5. Try limited proteolysis or methylation

6. If none of theat works, clone the same protein from another 
organism/strain/variant, ad try again

Re: [ccp4bb] Coot on an SGI

[Clayton, Gina]

I second Michael's situation.  I am stuck with getting the old SGI system to 
work in this  case - . So many thanks for the info Michael I will let you know 
if that works out. 

Hi Bill I have not seen the Zalman for sale at the price you give of $270. I 
looked around a while ago for a good price but I think the cost was around 
$500. 

Best
Gina

On Jan 27, 2012, at 6:44 AM, Michael Strickler wrote:

> As someone stuck maintaining an SGI for a user who resolutely refuses to
> abandon Showcase or Ribbons for IRIX, I sympathize with those cases
> where one simply has to get an old computer system to work.
> 
> Anyway, we don't have the relevant library file in our freeware
> directories either.  However, the last version of UCSF Chimera to
> support IRIX, version 1.3, supplies libgcc_s.so.1.  We are using a
> symbolic link libgcc_s.so --> libgcc_s.so.1 to run Coot 0.3.3 (not Coot
> 0.0.33, which runs only on Babbage analytical engines).  Chimera 1.3 is
> still available from the UCSF Chimera download page:
> 
> http://www.cgl.ucsf.edu/chimera/download.html
> 
> as long as you are able to agree to their non-commercial software
> license agreement.
> 
> Regards,
> 
> -- 
> Michael Strickler, Ph.D.
> Research Specialist
> Richards Center for Structural Biology
> Yale University
> 260 Whitney Ave, 355C JWG
> PO Box 208114
> New Haven, CT 06520-8114


Dear Gina:

I think Coot 0.0.33 originated sometime early in the Nixon administration, and 
I finally parted with my SGIs a few years ago, so am not in a good position to 
advise.  I seem vaguely to remember some non-canonical naming of the files.  
What happens if you make a symbolic link from the one you have to the one that 
is required?

As I recall, coot on an SGI (at least on my R1, which I think has a 
processor almost as fast as that in my generation A iPod touch) was impossibly 
slow.  By contrast, I can run the very latest svn revision of coot in stereo on 
a $270 Zalman monitor attached to a $600 mac mini.

I'm sorry this doesn't answer your question, but I think an ancient version of 
coot on an ancient computer will just be a world of hurt.

-- Bill

William G. Scott
Professor
Department of Chemistry and Biochemistry
and The Center for the Molecular Biology of RNA
228 Sinsheimer Laboratories
University of California at Santa Cruz
Santa Cruz, California 95064
USA
NOTICE: This email message is for the sole use of the intended recipient(s) and 
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[ccp4bb] Reasoning for Rmeas or Rpim as Cutoff

[Jacob Keller]

Dear Crystallographers,

I cannot think why any of the various flavors of Rmerge/meas/pim
should be used as a data cutoff and not simply I/sigma--can somebody
make a good argument or point me to a good reference? My thinking is
that signal:noise of >2 is definitely still signal, no matter what the
R values are. Am I wrong? I was thinking also possibly the R value
cutoff was a historical accident/expedient from when one tried to
limit the amount of data in the face of limited computational
power--true? So perhaps now, when the computers are so much more
powerful, we have the luxury of including more weak data?

JPK


-- 
***
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
email: j-kell...@northwestern.edu
***

Re: [ccp4bb] Reasoning for Rmeas or Rpim as Cutoff

[Jacob Keller]

Clarification: I did not mean I/sigma of 2 per se, I just meant
I/sigma is more directly a measure of signal than R values.

JPK

On Fri, Jan 27, 2012 at 11:47 AM, Jacob Keller
 wrote:
> Dear Crystallographers,
>
> I cannot think why any of the various flavors of Rmerge/meas/pim
> should be used as a data cutoff and not simply I/sigma--can somebody
> make a good argument or point me to a good reference? My thinking is
> that signal:noise of >2 is definitely still signal, no matter what the
> R values are. Am I wrong? I was thinking also possibly the R value
> cutoff was a historical accident/expedient from when one tried to
> limit the amount of data in the face of limited computational
> power--true? So perhaps now, when the computers are so much more
> powerful, we have the luxury of including more weak data?
>
> JPK
>
>
> --
> ***
> Jacob Pearson Keller
> Northwestern University
> Medical Scientist Training Program
> email: j-kell...@northwestern.edu
> ***



-- 
***
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
email: j-kell...@northwestern.edu
***

Re: [ccp4bb] Iphone app to display protein models

[Shiva Bhowmik]

Dear CCP4-users,

Thank you all for your suggestions. Below is the compiled list of
suggestions for Iphone apps to display models:

1. Import structure directly from itunes in pdb format view in iMolview
(not free).
2. Cuemol for iOS: http://itunes.apple.com/us/**app/cuemol/id496236710?ls=1&;
**mt=8 
3. Jolecule, web based: http://jolecule.appspot.com/

An app for android users under development: NDKmol.
https://market.android.com/**details?id=jp.sfjp.webglmol.**NDKmol

Cheers,

Shiva

On Fri, Jan 27, 2012 at 3:38 AM, Opher Gileadi
wrote:

> Molsoft has a free application:
>
> http://www.molsoft.com/iMolview.html
>

[ccp4bb] 3 Letter for 1'-deoxyribofurnaose-5'-phosphate?

[James Stroud]

Hello All,

Do any of you RNA structural biologists know what is the 3 letter code for 
1'-deoxyribofurnaose-5'-phosphate (abasic site in RNA)? I found that the 
1'2'-dideoxy is 3DR, but could not find a lead on the 1'-deoxy. I scoured 
HIC-UP to no avail, which I think is the most comprehensive hetero-compound 
library.

If I knew what the 3 and R stood for in "3DR" I could probably guess. I'm 
pretty sure the "D" stands for the 2' deoxy.

Thank you for any help!

James

Re: [ccp4bb] Iphone app to display protein models

[Jonathan Winger]

On Jan 26, 2012, at 11:00 PM, Shiva Bhowmik wrote:

> Dear All,
> 
> I was wondering if there is any IOS5 based app to display protein models, 
> which are not in public database, on Iphone. There is an app called Molecules 
> for displaying models but that utilizes coordinates from RCSB and pubchem. 
> 
> Thanks,
> 
> Shiva  

Just for the sake of accuracy, Molecules can view custom pdb files as well:

from http://www.sunsetlakesoftware.com/molecules
Custom molecule structures can also be downloaded to the device from any 
publicly available web server. The location of these structures can either be 
manually specified in the application, or custom URLs, such as 
molecules://www.sunsetlakesoftware.com/sites/default/files/neonPump.pdb.gz , 
can be clicked on within Safari or Mail on the device. This will launch 
Molecules and have it start downloading the file at that address.

On iPad, molecular structures can now be dragged into the application directly 
using iTunes by going to the Applications tab, scrolling down to the bottom, 
and clicking on the Molecules icon.

Re: [ccp4bb] 3 Letter for 1'-deoxyribofurnaose-5'-phosphate? - SOLVED!

[James Stroud]

Hello All,

Two people named Rob told me that the the 3 letter code is "N".

   http://ligand-expo.rcsb.org/reports/N/N/index.html

Coincidentally, the old 3 letter name is "ROB".

Thank you for your help!

James




> On Fri, Jan 27, 2012 at 2:38 PM, James Stroud  wrote:
>> Hello All,
>> 
>> Do any of you RNA structural biologists know what is the 3 letter code for 
>> 1'-deoxyribofurnaose-5'-phosphate (abasic site in RNA)? I found that the 
>> 1'2'-dideoxy is 3DR, but could not find a lead on the 1'-deoxy. I scoured 
>> HIC-UP to no avail, which I think is the most comprehensive hetero-compound 
>> library.
>> 
>> If I knew what the 3 and R stood for in "3DR" I could probably guess. I'm 
>> pretty sure the "D" stands for the 2' deoxy.
>> 
>> Thank you for any help!
>> 
>> James

[ccp4bb] BioSAXS beamtime available

[Richard Gillilan]

Dear BioSAXS users,

Beamtime at MacCHESS will be available during the Spring running period (March 
7-March 27) for BioSAXS.

To apply for time, please submit an online express-mode proposal at 
http://express.chess.cornell.edu/EM_form.php

Under "Choice of experimental technique" specify "Other
In the box provided  for "Special experimental and facility needs" type 
"standard BioSAXS".

Please also send me an email  when you submit your express mode form: 
r...@cornell.edu

To insure a successful visit, please carefully follow the sample preparation 
guidelines and other information given on our BioSAXS web link: 
http://www.macchess.cornell.edu/MacCHESS/bio_saxs.html

 News --

BioSAXS Essentials III, the introductory SAXS minicourse for biologists is open 
for registration! Have your students apply soon, the course is already rapidly 
filling up ... only 4 more slots left: 
http://www.chess.cornell.edu/BioSAXS%20course/Registration/register02242012.html

MacCHESS has purchased two Pilatus 100K-S detectors which are dedicated 
exclusively to BioSAXS. The first detector is now in full-time operation for 
users at F2 station. We have also purchased an AKTA Purifier size-exclusion 
chromatography (SEC) system for use at the F2 beamline. If your samples seem to 
aggregate rapidly after preparation, or you think you may have a mixture, you 
may want to investigate on-site SEC. If you are interested, contact me (Richard 
Gillilan) directly for details.

--

We look forward to an exciting Spring running period and hope you can join us!

Best

Richard Gillilan
MacCHESS