[ccp4bb] Faculty Position, Structural Biology, University at Buffalo

2023-10-04 Thread Andrew Gulick
The Department of Structural Biology at the University at Buffalo, part of the 
Jacobs School of Medicine and Biomedical sciences, is recruiting for faculty 
positions in the department at UB. This is a great opportunity to be a part of 
the growth here in Buffalo.

New York State, SUNY, and UB are currently making a solid investment in faculty 
recruitment and a number of other departments (both in the Med School and in 
Chemistry) are currently recruiting. For the ’23-’24 academic year, we have ~15 
new faculty who have just joined the basic science departments in the School of 
Medicine and another round of hiring is underway for Fall of 2024.

Please feel free to forward the posting or the link to our position to any 
qualified candidates. As part of a medical school, we’re particularly 
interested in people who apply Structural Biology tools and methods to 
important biomedical problems and who can potentially interact with faculty in 
other departments.

UB Jobs Posting Site*

https://www.ubjobs.buffalo.edu/postings/38319

(*The Department of Structural Biology made one hire last year. As the posting 
has remained open for the second round this year, the website still says FY 
2022-2023. We may or may not be able to get that updated – administrative red 
tape and all – but the link above is correct)

Best wishes,
Andrew


--
Andrew M. Gulick, 
Ph.D.
Professor
Department of Structural Biology
Jacobs School of Medicine and Biomedical Sciences
University at Buffalo
955 Main Street, Room 5152
Buffalo, New York 14203-1121
office: 716-829-3696
email: amgul...@buffalo.edu
web: Gulick Lab




To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/


[ccp4bb] COOT: Rotate/Translate Fragment tool

2023-06-15 Thread Andrew Gulick
When using the COOT (0.9.8.5 EL) on a Mac, the behavior appears to have changed 
for manually rotating a fragment (Rotate/Translate Zone/Chain Molecule tool)

When activated, the pop-up window allows me to use the sliders to rotate or 
translate. That works as advertised.

However, I used to be able to hold down the Control key (on Mac OS) and then 
use the LeftMouse to make the same minor adjustments to the rotation and 
translation. On current version, if I do that, it appears that rather than the 
center of rotation being the last atom chosen, the center of rotation is 
somewhere else (it is not the center of mass of the fragment). Thus, using 
Control-Mouse causes the fragment to fly off as it is rotating around some 
distant origin rather than the molecule itself.

Edit > Settings > Rotate Translate Zone Mode > provides two options (about 
fragment center and about second clicked atom) and neither seems to help.

Again, this tool works fine using the slider bars. Additionally, Control – 
LeftMouse ON an atom to move an atom works fine. It is just the Control – 
LeftMouse NOT ON an atom in an effort to rotate the entire fragment that is 
problematic.

Is there a setting to return this to operational.

Thanks for any suggestions.
Andy





To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/


[ccp4bb] Research Scientist at Hauptman-Woodward Institute

2017-08-29 Thread Andrew Gulick
Please see the posting below for an independent investigator at the 
Hauptman-Woodard Institute. Please direct any questions or applications to the 
opportun...@hwi.buffalo.edu email address.
Best wishes,
Andrew

--
Andrew M. Gulick, Ph.D.
-
Hauptman-Woodward Institute and
Dept. of Structural Biology, SUNY at Buffalo
700 Ellicott St Buffalo, NY 14203
--

The Hauptman-Woodward Medical Research Institute (HWI) invites applications for 
a full time Research Scientist in the areas of structural, computational, or 
molecular biology.  The Institute seeks exceptional faculty candidates who will 
direct an independently funded research program in important areas of human 
biology, health or disease.

A startup package will be provided to each individual hired.  Candidates are 
expected to have a Ph.D. or equivalent in a relevant field and a strong record 
of scientific productivity.  The position is open to candidates at the junior 
faculty level but senior level candidates will also be considered.

HWI is celebrating its 60th year as an independent research institute and 
expects to make several new hires over the next few years. Located in Buffalo, 
New York, HWI is at the heart of the growing Buffalo-Niagara Medical Campus and 
partners with the University at Buffalo, Roswell Park Cancer Institute, and the 
Kaleida Health System. It also has links to industry, houses a gene to 
structure company, HarkerBIO, and operates the IMCA-CAT beamline at the 
Advanced Photon Source.

Candidates are encouraged to develop academic and potentially industrial 
collaborations.  Interested candidates should send, as a single PDF file, a 
complete curriculum vitae, a statement of research accomplishments, an outline 
of future research plans, and arrange for three letters of recommendation to be 
sent separately to: Search Committee, Hauptman-Woodward Institute, 700 Ellicott 
Street, Buffalo, NY 14203, or by Email to opportun...@hwi.buffalo.edu.

HWI is an equal opportunity employer.


[ccp4bb] Research Scientist at Hauptman-Woodward Institute, Buffalo, USA

2017-08-29 Thread Andrew Gulick
Please see the posting below for an independent investigator at the 
Hauptman-Woodard Institute. Please direct any questions or applications to the 
opportun...@hwi.buffalo.edu email address.
Best wishes,
Andrew

--
Andrew M. Gulick, Ph.D.
-
Hauptman-Woodward Institute and
Dept. of Structural Biology, SUNY at Buffalo
700 Ellicott St Buffalo, NY 14203




Re: [ccp4bb] precipitation after storage

2010-11-08 Thread Andrew Gulick
We routinely use a P200 to pipette drops of protein directly into a small Dewar 
of liquid nitrogen. The protein forms small BB's with a volume of approximately 
30 micro-L each. Pipette slowly, allowing the drops to freeze solid before 
adding the next one. The frozen BB's can be picked up with forceps or a slotted 
spoon and stored in a cryovial in the -80 freezer. For future experiments, you 
can thaw only what you need. I have only seen one protein that couldn't recover 
from this and could only be crystallized prior to freezing.

A systematic study of this procedure is described in Deng et al.
 http://www.ncbi.nlm.nih.gov/pubmed/14684931

--Andrew




On 11/5/10 3:40 PM, Eric Karg harvard...@yahoo.com wrote:

Dear all,

I'm working on a protein which starts to precipitate after 3-4 days of storage 
at 4 degrees or room temperature. The storage buffer contains 300 mM NaCl 
because at lower salt concentrations it also tends to precipitate. Different 
buffers and adding glycerol did not help although this was not done in a 
systematic way. Has anyone had similar experiences? Any suggestions to overcome 
this problem?

Thanks in advance!

Eric



--
Andrew M. Gulick, Ph.D.
---
(716) 898-8619
Hauptman-Woodward Institute
700 Ellicott St
Buffalo, NY 14203
---
Hauptman-Woodward Institute
Dept. of Structural Biology, SUNY at Buffalo

http://www.hwi.buffalo.edu/Faculty/Gulick/Gulick.html
http://labs.hwi.buffalo.edu/gulick


Re: [ccp4bb] Cys-Lysine Side chain Interaction

2010-07-19 Thread Andrew Gulick
Hello John,

We had just such an issue a year or so ago and I posed the same question to
the BB. The density that I observed, and the CCP4bb discussion, can be found
at:

   http://labs.hwi.buffalo.edu/gulick/cyslys.html
   http://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg06092.html

I was advised to try metals and a variety of oxidation states for the
Cysteine. None of which refined satisfactorily. Ultimately, I believe that
what we captured was a thiocarbamate or a thiouronium. We modeled the link
as such, and have published the density and our best efforts at modeling
this in

Shah, M. B., Ingram-Smith, C., Cooper, L. L., Qu, J., Meng, Y., Smith, K.
S., and Gulick, A. M. (2009) The 2.1A crystal structure of an Acyl-CoA
synthetase from Methanosarcina acetivorans reveals an alternate acyl binding
pocket for small branched acyl substrates. Proteins 77, 685-698.

The Deposited PDB is 3ETC. The paper also describes a few references for
chemical precedent.

Good luck.
Andrew
-- 
Andrew M. Gulick, Ph.D.
---
(716) 898-8619
Hauptman-Woodward Institute
700 Ellicott St
Buffalo, NY 14203
---
Hauptman-Woodward Institute
Dept. of Structural Biology, SUNY at Buffalo

http://www.hwi.buffalo.edu/Faculty/Gulick/Gulick.html
http://labs.hwi.buffalo.edu/gulick




On 7/16/10 4:00 PM, John R. Horton jrho...@emory.edu wrote:

 Hello!
 
 I am working on a structure that has continuous density from a Lys Nz atom to
 a Cys Sg; these are ~2.9A from each other.  I would consider this a H-bond;
 however, the 2fo-fc density does not run straight from atom to atom in this
 1.9A structure.  At an apx right angle, with the line joining these two atoms
 being the hypotenuse, there is aspherical fo-fc density ~2.1A from the Cys Sg
 and ~1.7A from the Lys Nz as if another atom sits between these two atoms.
 The modeled side chains fit the density very well.  No other atoms are close
 by to be ligands so I ruled out an ion.
 
 I'd appreciate any thoughts any of you may have...thanks!
 
 John Horton
 Emory University



Re: [ccp4bb] Identifying an unknown ligand

2009-04-02 Thread Andrew Gulick
My money is on:

Dithiothreitol or dithioerythritol.

Any chance they are in there? If not and you believe this copurified with
your protein, than I'd guess erythritol or threitol.

(I didn't bother trying to gauge the stereochemistry from your picture)

Cheers
Andy



On 4/2/09 1:38 PM, Abhinav Kumar abhin...@slac.stanford.edu wrote:

 Hi,
 
 I am refining a structure and have a region of unmodeled density into
 which I am trying to fit a ligand. The identity of the ligand is not
 obvious, so I modeled a bunch of dummy atoms into the density.
 Could you please have a look at the map and pdb files and help me
 identify this ligand?
 
 Please see http://smb.slac.stanford.edu/~abhinavk/UNL/unl.html
 
 Thanks 
 Abhinav 
 
 Stanford Synchrotron Radiation Laboratory
 Joint Center for Structural Genomics
 Mail Stop 99 
 Phone: (650) 926-2992
 Fax: (650) 926-3292

-- 
Andrew M. Gulick, Ph.D.
---
(716) 898-8619
Hauptman-Woodward Institute
700 Ellicott St
Buffalo, NY 14203
---
Hauptman-Woodward Institute
Dept. of Structural Biology, SUNY at Buffalo

http://www.hwi.buffalo.edu/Faculty/Gulick/Gulick.html
http://labs.hwi.buffalo.edu/gulick


Re: [ccp4bb] generating omit maps

2008-12-10 Thread Andrew Gulick
Let me also follow up on this point. I also agree that the ligand should be
added very late in the refinement/model-building procedure. I also encourage
people in  my group to create a subdirectory BEFORE_LIGANDS into which
they put the current PDB and map (or mtz) files prior to adding the ligand.
Putting it into a separate directory avoids accidentally deleting it if you
tidy up your modeling files at some later state.

Come publication time, include in your manuscript the map generated at this
stage prior to inclusion of the ligand. It is sometimes not as pretty but it
gives the reader a honest view of your ligand density.

Cheers,
Andy

-- 
Andrew M. Gulick, Ph.D.
---
(716) 898-8619
Hauptman-Woodward Institute
700 Ellicott St
Buffalo, NY 14203
---
Hauptman-Woodward Institute
Dept. of Structural Biology, SUNY at Buffalo

http://www.hwi.buffalo.edu/Faculty/Gulick/Gulick.html
http://labs.hwi.buffalo.edu/gulick


On 12/10/08 10:41 AM, Mischa Machius [EMAIL PROTECTED]
wrote:

 Kathleen - The easiest way is to simply remove the ligand from the
 coordinates and refine for a few cycles. Whether that is particularly
 meaningful is another question. Better would be to remove the ligand
 coordinates, shake the remaining coordinates (i.e., randomly
 displace them by a small amount), and then refine. Even better,
 perhaps, would be to calculate a simulated-annealing omit map, but
 AFAIK, you can't use CCP4 for that. IMHO, the best option is to not
 include the ligand in the model-building and refinement processes
 until all of the protein(s), solvent molecules, etc. have been
 properly modeled. I personally tend to include ligands only at the
 very end of the modeling/refinement process, unless there is really no
 ambiguity. This strategy will minimize any model bias from the ligand,
 and it will give you an omit map by default (until you actually
 include the ligand). Best - MM
 
 --
 --
 Mischa Machius, PhD
 Associate Professor
 Department of Biochemistry
 UT Southwestern Medical Center at Dallas
 5323 Harry Hines Blvd.; ND10.214A
 Dallas, TX 75390-8816; U.S.A.
 Tel: +1 214 645 6381
 Fax: +1 214 645 6353
 
 
 
 On Dec 10, 2008, at 9:30 AM, Kathleen Frey wrote:
 
 Hi Everyone,
 
 Can anyone tell me a relatively easy way to generate an omit density
 map for a ligand? I know that CNS can do this, but I was wondering
 if there's a CCP4 related program to generate omit maps.
 
 Thanks,
 Kathleen


Re: [ccp4bb] Problem with crystallization of Se-Met labeled protein

2008-05-28 Thread Andrew Gulick
Consider also the possibility that your SeMet protein differs from the
native protein by something other than the sulfur -- selenium. Growing your
cells in different conditions may induce different host proteins that could
modify your protein.  (Often we use rich media for native protein production
and minimal media of some flavor for SeMet)

We had an example of this, (EJ Drake, Chem Biol, 13, 409) where growing the
cells in minimal media (low iron, being the relevant factor) induced a host
siderophore biosynthetic pathway that post-translationally added a cofactor
to our recombinant protein. We only figured out why we couldn't crystallize
the SeMet protein after we finally solved the structure (by a low homology
molecular replacement) and saw that the site of cofactor addition was buried
against a symmetry related molecule. Adding the 350Da cofactor at this
position likely prevented the SeMet crystals from growing.

Bottom line, if there is any chance of a post-translational modification,
make sure your growth conditions are as similar to native protein expression
as possible. A methionine auxotroph may be preferred over metabolic
inhibition in this case.

Andy



On 5/27/08 5:11 PM, Joe Smith [EMAIL PROTECTED] wrote:

 Dear all,
 Sorry for an off-topic query.
 I have been unable to crystallize a Se-met containing protein (8 Met
 in 206 amino acids) in the native crystallization condition ( 0.1 M
 Tris pH 8.5, 1.2 M K-Na-tartrate; Theoretical pI of protein is 8.4).
 As expected, solubility of Se-Met containing protein is little less
 than the wild type. Other than seeding, i don't know what else I
 should try for obtaining a Se-met crystal for phasing. Can I mutate
 some of the exposed Met  (based on secondary structure prediction and
 homologous structure) to Ala as I feel I don't really need 8 Se for
 phasing 208 aa long polypeptide. I want to know what generally one
 should do when Se-Met containing proteins fail to crystallize.
 Thanks in advance.
 Joe
 PS: Since, protein contains 3 Cys residues.. I am also planning to try
 my luck with heavy atom compounds containing Hg.

-- 
Andrew M. Gulick, Ph.D.
---
(716) 898-8619
Hauptman-Woodward Institute
700 Ellicott St
Buffalo, NY 14203
---
Senior Research Scientist
Hauptman-Woodward Institute
Dept. of Structural Biology, SUNY at Buffalo

http://www.hwi.buffalo.edu/Faculty/Gulick/Gulick.html
http://labs.hwi.buffalo.edu/gulick


[ccp4bb] Density Joining Cysteine and Lysine Side chains

2008-05-22 Thread Andrew Gulick
Greetings.

I'm wondering if anyone has ever seen something like this. I have a 2.1 A
data set (synchrotron data) that is nearing completion. I see density that
appears to join a cysteine side chain to a lysine (30 residues away from
each other in primary sequence). There is a picture of the density here.

http://labs.hwi.buffalo.edu/gulick/cyslys.html

I have modeled this in as a Cysteine sulfenic acid (Side chain is Cb-Sg-OH)
and refined. There remains a bit of positive Fo-Fc density above the oxygen
and the lysine N and sulfenic acid hydroxyl are 1.8A away.

I have some other crazy ideas but haven't been able to find any precedent in
the literature. Any thoughts on what this might be or if anyone has seen
something similar would be greatly appreciated.
Andy





-- 
Andrew M. Gulick, Ph.D.
---
(716) 898-8619
Hauptman-Woodward Institute
700 Ellicott St
Buffalo, NY 14203
---
Senior Research Scientist
Hauptman-Woodward Institute
Dept. of Structural Biology, SUNY at Buffalo

http://www.hwi.buffalo.edu/Faculty/Gulick/Gulick.html
http://labs.hwi.buffalo.edu/gulick


Re: [ccp4bb] Tag, you're in! Flag, V5, etc

2008-02-07 Thread Andrew Gulick
If circumstances require a C-terminal tag, the intein system from New
England Biolabs has worked very well for us.  The pTYB1 plasmid encodes a
fusion between your protein of interest, a viral intein (think protein
intron) and a chitin binding domain.  The fusion adsorbs to a chitin resin
and all other proteins are washed away.  The intein is engineered to not
catalyze protein ligation but rather to release the protein in a
thiol-directed manner.  To cleave your protein from the fusion, simply add
DTT, plug the column, and incubate overnight.  The next day, push your
unbound protein off the column: native protein with no tag residues left!
The CBD-intein remain bound to the resin

You don't get a lot of protein (5-10mg is more common than 50mg) and it is
diluted to the volume of your column.  On the other hand, it is pure enough
to go right into trials upon concentration.

At least that's been our experience.
Andy
(No affiliation with NEB)

On 2/7/08 4:33 PM, James Whisstock [EMAIL PROTECTED]
wrote:

 Hiya
 
 We usually add all N-terminal tags with a TeV cleavable linker.  C-terminal
 tags always seem a pain to remove cleanly, because most highly specific
 recognition sequences (such as TeV) take advantage of P rather than P'
 specificity so you are usually left with a five (or so) residue tail.
 Actually has anyone any neat tricks for C-terminal tag removal?
 
 J
 


-- 
Andrew M. Gulick, Ph.D.
---
(716) 898-8619
Hauptman-Woodward Institute
700 Ellicott St
Buffalo, NY 14203
---
Senior Research Scientist
Hauptman-Woodward Institute

Assistant Professor
Dept. of Structural Biology, SUNY at Buffalo

http://www.hwi.buffalo.edu/Faculty/Gulick/Gulick.html
http://labs.hwi.buffalo.edu/gulick


Re: [ccp4bb] How to refine a structure with ATP and AMP and pyrophosphate sharing the same density in CCP4i?

2008-01-18 Thread Andrew Gulick

In the best case, you would know something about the enzyme bound
equilibrium constant between the two ligand mixtures (see, for example, TM
Larsen et al Biochemistry 35, 4349).  That would give you a good sense of
how to model the occupancies of the active site ligands.

Unfortunately, in many cases, the on-enzyme equilibrium constant is not
known and we are left with mixtures of ligands in the active site.  I
believe that there is no single correct way to then model your structure and
(as with many topics) you¹ll get multiple opinions:  You can refine the
³predominant² ligand and acknowledge extra difference density that is likely
due to other ligands, you can refine a 50/50 mixture and allow the B-values
to accommodate some of the differences, or you can refine some other mixture
(although I personally am less comfortable with claiming a 35/65 % mixture
of your ligands).  

As you note, the addition of an extra oxygen is not really going to
dramatically alter your R-factors so you cannot rely on that to determine
the ³correct² model.  I think that what you have described is appropriate.
It is now important to provide enough information so that your readers can
judge any biochemical interpretations that you make.

Best wishes,
Andy

-- 
Andrew M. Gulick, Ph.D.
Hauptman-Woodward Institute

On 1/18/08 3:09 PM, Sun Tang [EMAIL PROTECTED] wrote:

 Hello everyone,
   
 I have a structure of intermediate state in which about half amount of ATP
 decomposed to AMP and pyrophosphate. The ATP and AMP + pyrophosphate have
 little difference in conformation, sharing the same electron density.
   
 I just gave them different residue ID and did the TLS and restrained
 refinement in CCP4i. It is hard to tell from the R-factor because they are
 only a very small part of the whole structure. Can anyone tell whether it is
 the correct way to do?
 
 Any suggestions are greatly appreciated.

 Thank you very much!

 Sincerely,

 Sun Tang
   
 



[ccp4bb] carving up maps (was re: pymol help)

2007-10-29 Thread Andrew Gulick
I'd be curious to know if there is any consensus in the community with using
the carve command for showing maps.  I have never felt comfortable showing
density within a cutoff radius of a particular residue or--even worse--a
ligand, and felt the figures should display the extraneous bits as well.
The burden was on the crystallographer to find an appropriate view (slab,
sigma, etc...) to display the map.

The Bobscript manual appears to agree with me on this one as it states:

http://www.strubi.ox.ac.uk/bobscript/doc24.html
If your density is good then you will just have density over residue 999,
but if things are not so hot then you may want to cheat and just draw the
bits of density near to the selected atoms.

Just curious,
Andy
-- 
Andrew M. Gulick, Ph.D.
---
(716) 898-8619
Hauptman-Woodward Institute
700 Ellicott St
Buffalo, NY 14203
---
Senior Research Scientist
Hauptman-Woodward Institute

Assistant Professor
Dept. of Structural Biology, SUNY at Buffalo

http://www.hwi.buffalo.edu/Faculty/Gulick/Gulick.html
http://labs.hwi.buffalo.edu/gulick


On 10/29/07 4:40 AM, Stefan Schmelz [EMAIL PROTECTED] wrote:

 Dear Yanming,
 
 To show pretty density of a model you have to import a ccp4 density
 map and display it around your ligand. The simplest solution is using
 ccp4 and tick the box Generate weighted difference maps files in CCP4
 format when running Refmac5 (one  or two cycles  are enough).  Specify
 names for FWT and DelFwt maps and rename the maps afterwards to *.ccp4.
 This renamed map (e.g. fwt.ccp4) can be opened in pymol. To show density
 around our ligand you can use the following command:
 
 isomesh map, name_of_fwtmap, 1.0, ligand, carve=1.8
 
 (map = greats an object name map, name_of_fwtmap = name of your map,
 1.0 = Sigma level, carve=1.8 = width map is displayed around your
 ligand
 
 This will allow you to show a pretty electron density map around your
 ligand without any chemical info of the ligand.
 
 
 Stefan Schmelz
 
 
 Yanming Zhang wrote:
 Hi, all,
 
 I want to make a pymol figure wich can show the pretty density of a
 ligand. But we don't want to show  the detailed chemical info of the
 ligand. If I use a large enough sphere_scale for the ligand, the
 chemical info will be hidden but the density map will be disrupted. If
 I use a smaller sphere_scale, the density looks great but the chemical
 info of the ligand will be visible. How should I overcome this dilemma?
 Thank you very much for your help.
 Yanming


[ccp4bb] Coot and Density Fit Analysis

2007-09-07 Thread Andrew Gulick
Can someone tell me what the number is that appears with each residue above
the bar in the COOT Density Fit Analysis graph?



I have a structure with good data (resolution=2.3A, Rmerge=5%) but a high
Wilson B of ~60.  The structure refines reasonably well; we've gotten the
Rfactor to 18% and Rfree to 22%.  It's a previously determined structure
(with new ligands) so we know there is no gross mis-tracing.

If I perform the Density Fit Analysis in COOT, I get a poor looking plot
with significant numbers of red and orange bars.  Hovering over a bar gives
the residue and a number that is pretty low (seldom above 0.7) and in
several places there are long stretches of residues that appear fine in the
density where the number in this plot is 0.3.

I see from the documentation and prior CCP4bb postings that perhaps this
results from poor scaling and that I can change the colors of the bars with
the (set-residue-density-fit-scale-factor X) command.  If I use the
recommended scale factor (1/4*sigma), the bars get redder.  Doing so also
changes the colors and the size of the bars but not the number that appears
above each bar.  

My question then is what is the number that appears in this plot?  Is it a
correlation coefficient?  I have calculated the per residue correlation
coefficients with the CORRELATE program and see much more reasonable values.

Thanks for any suggestions.
Andy


-- 
Andrew M. Gulick, Ph.D.
---
Hauptman-Woodward Institute
---


[ccp4bb] Sorting on residue number in Coot

2007-07-05 Thread Andrew Gulick
I am building a new structure that was partially fit with RESOLVE.  Various
lengths of chain are properly numbered (where RESOLVE identified a match)
and the unplaced polyalanine peptides are numbered 801-806, 811-823,
831-835, etc...  

When I have identified the correct sequence for a stretch of polyalanine, I
can renumber it with Coot very nicely.  However, after renumbering several
stretches it becomes necessary to output a PDB, edit the file to order the
renumbered residues, then restart coot with the edited file.  This is
especially necessary when two stretches should actually be joined.

Perhaps I've missed it but does a feature exist in Coot to sort the PDB file
by residue number (keeping chains separate)?  If not, might it be a
desirable feature to include a sort button with the renumber feature so
that the PDB file can be re-ordered?   I realize I could use a sort command
in UNIX however that would be complicated by the presence of multiple chains
and splitting up the PDB by chain could be as tedious as manually editting.
Any other easy work-around suggestions from anyone?

Many thanks
Andy


-- 
Andrew M. Gulick, Ph.D.
---
(716) 898-8619
Hauptman-Woodward Institute
700 Ellicott St
Buffalo, NY 14203
---
Research Scientist
Hauptman-Woodward Institute

Assistant Professor
Dept. of Structural Biology, SUNY at Buffalo

http://www.hwi.buffalo.edu/Faculty/Gulick/Gulick.html
http://labs.hwi.buffalo.edu/gulick