[ccp4bb] Senior Scientist (Protein Engineer) position at ModeX Therapeutics (Weston, MA, USA)

2023-11-08 Thread Yuri Iozzo
Hi everyone,
I am looking for an experienced protein engineer to join my group.

Please, apply on the website, but also send me a copy of your CV.
Senior Scientist (Structural Biology) in Natick, Massachusetts | Careers at 
Modex Therapeutics 
(icims.com)<https://careers-modex.icims.com/jobs/4126/senior-scientist-%28structural-biology%29/job>

Job description:
Senior Scientist (Protein Engineering)
Company
ModeX is a clinical-stage biopharmaceutical company developing next-generation 
multispecific antibodies and vaccines for cancer and infectious disease. 
ModeX's modular antibody platforms unite the power of multiple biologic 
components in a single molecule to create multispecific antibodies with greater 
versatility and potency to fight complex disease than traditional approaches. 
Our pipeline includes candidates against both solid and hematological tumors as 
well as several of the world's most pressing viral threats. Our founding team 
includes globally recognized medical innovators with proven track records of 
delivering breakthroughs for patients.
Job Summary
ModeX is looking for an experienced protein engineer with strong background in 
structural biology, protein generation, liability mitigation and design. This 
role mainly focuses on facilitating multiple projects through early engineering 
interventions during the candidate selection and development. Occasional 
outsourcing of X-ray and cryo-EM structure solving efforts is expected as well 
as managing connections with several CROs.
Key accountability and responsibilities include:

  *   Project analysis and making pro-active engineering initiatives,
  *   Rational engineering and software-assisted engineering,
  *   Antibody design including format selection, linkers, mutations, liability 
removal,
  *   Structure generation with AF2 and structure analysis,
  *   Managing structural biology CROs,
  *   Structure solving through outsourcing and analysis of results,
  *   Molecular dynamics and analysis of results,
  *   Supporting multiple projects at a time.
Key qualifications:

  *   M.Sc. or Ph.D. in chemistry, biology, or other relevant discipline,
  *   Minimum 2 years of prior industry experience (the hiring manager will 
consider postdoc years in lieu of industry experience),
  *   Strong hands-on protein design and engineering skills,
  *   Experience with protein production and purification,
  *   Solid background in structural biology with a publication record,
  *   Proficiency with protein design, engineering, and structural biology 
software (PyMol, Chimera, Coot, Schrodinger etc),
  *   Excellent presentation skills.


Best,
Yuri
___
Yuri Iozzo, PhD (eqv), Associate Director of Digital Biology
ModeX Therapeutics
20 Riverside Rd, Weston, MA 02493
E: yuri.io...@modextx.com<mailto:yuri.io...@modextx.com>
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[ccp4bb] Senior Scientist (Protein Engineer) position at ModeX Therapeutics (Weston, MA, USA)

2023-11-08 Thread Yuri Iozzo
Hi everyone,
I am looking for an experienced protein engineer to join my group.

Please, apply on the website, but also send me a copy of your CV.
Senior Scientist (Structural Biology) in Natick, Massachusetts | Careers at 
Modex Therapeutics 
(icims.com)<https://careers-modex.icims.com/jobs/4126/senior-scientist-%28structural-biology%29/job>

Job description:
Senior Scientist (Protein Engineering)
Company
ModeX is a clinical-stage biopharmaceutical company developing next-generation 
multispecific antibodies and vaccines for cancer and infectious disease. 
ModeX's modular antibody platforms unite the power of multiple biologic 
components in a single molecule to create multispecific antibodies with greater 
versatility and potency to fight complex disease than traditional approaches. 
Our pipeline includes candidates against both solid and hematological tumors as 
well as several of the world's most pressing viral threats. Our founding team 
includes globally recognized medical innovators with proven track records of 
delivering breakthroughs for patients.
Job Summary
ModeX is looking for an experienced protein engineer with strong background in 
structural biology, protein generation, liability mitigation and design. This 
role mainly focuses on facilitating multiple projects through early engineering 
interventions during the candidate selection and development. Occasional 
outsourcing of X-ray and cryo-EM structure solving efforts is expected as well 
as managing connections with several CROs.
Key accountability and responsibilities include:

  *   Project analysis and making pro-active engineering initiatives,
  *   Rational engineering and software-assisted engineering,
  *   Antibody design including format selection, linkers, mutations, liability 
removal,
  *   Structure generation with AF2 and structure analysis,
  *   Managing structural biology CROs,
  *   Structure solving through outsourcing and analysis of results,
  *   Molecular dynamics and analysis of results,
  *   Supporting multiple projects at a time.
Key qualifications:

  *   M.Sc. or Ph.D. in chemistry, biology, or other relevant discipline,
  *   Minimum 2 years of prior industry experience (the hiring manager will 
consider postdoc years in lieu of industry experience),
  *   Strong hands-on protein design and engineering skills,
  *   Experience with protein production and purification,
  *   Solid background in structural biology with a publication record,
  *   Proficiency with protein design, engineering, and structural biology 
software (PyMol, Chimera, Coot, Schrodinger etc),
  *   Excellent presentation skills.


Best,
Yuri
___
Yuri Iozzo, PhD (eqv), Associate Director of Digital Biology
ModeX Therapeutics
20 Riverside Rd, Weston, MA 02493
E: yuri.io...@modextx.com<mailto:yuri.io...@modextx.com>
[A picture containing logo  Description automatically generated]

THE INFORMATION CONTAINED IN THIS COMMUNICATION AND ANY ATTACHMENTS HERETO IS 
CONFIDENTIAL, MAY BE ATTORNEY-CLIENT PRIVILEGED, AND IS INTENDED ONLY FOR THE 
PERSONAL AND CONFIDENTIAL USE OF THE ADDRESSEE(S). IF THE READER OF THIS 
MESSAGE IS NOT AN INTENDED RECIPIENT, OR AN AGENT THEREOF, YOU ARE HEREBY 
NOTIFIED THAT ANY REVIEW, USE, DISSEMINATION, DISTRIBUTION, OR COPYING OF THIS 
COMMUNICATION OR ANY ATTACHMENT HERETO IS STRICTLY PROHIBITED. IF YOU HAVE 
RECEIVED THIS MESSAGE IN ERROR, PLEASE NOTIFY US IMMEDIATELY BY E-MAIL, AND 
DELETE THE ORIGINAL MESSAGE..



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[ccp4bb] Off Topic- Fe-S electron transfer

2013-10-01 Thread Yuri Pompeu
Dear Community, 

I apologize for the off topic question but it is hard to resist since so many 
of our colleagues are incredibly knowledgeable.

I am looking for a way to block or even remove the 2Fe-2S cluster in my enzyme. 
This cluster is involved in transferring electron from the Alpha to the Beta 
subunit and I wish to block this for an experiment. 
Does anyone know of a reagent or procedure that is known to do this (elegance 
is optional)? I first thought of EDTA but I don't think it will work given the 
covalent character of the Fe-S bonds.

Thank you


[ccp4bb] Off Topic- Cystine Detection

2013-02-06 Thread Yuri Pompeu
Dear All,
I am trying to probe the existence of a disulfide bond on the surface of my 
protein.
I have attempted Ellman´s and my results were not as clear as I would have 
hoped for.
I am not a sulfur/cysteine chemist and would appreciate the advice on what 
experiments to try!
Thanks a bunch
YAP


[ccp4bb] How to merge data from 2 separate sections of same crystal

2012-12-10 Thread Yuri Pompeu
hello everyone,
I have collected data on a problematic crystal. (first mistake...)
Images spanning phi angles 45-80 look ok and usable, also images 229-279 are 
usable (index well and merge well too).
How can I combine the 2 separate .mtz files from Mosflm when I scale them?
Attempts to process them in the same session keep maling the program crash!
Thank you very much


Re: [ccp4bb] How to merge data from 2 separate sections of same crystal

2012-12-10 Thread Yuri Pompeu
Thanks for all the suggestions on and off BB.
I used the GUI Sort/Reindex to combine 6 sections then ran Pointless and Scala.
Got a data set to 2.6A Rmerge 0.12 (0.06 inner shell) and solved it in C2221.
It is a good night!
Cheers,


[ccp4bb] To cryo or not to cryo...

2012-11-30 Thread Yuri Pompeu
Dear community,
I have what seems to be a pretty decent single crystal that grew from a screen 
set up 2 weeks ago.
I am trying to reproduce it but so far I have not succeeded. I am however 
afraid the crystal that did form will start to deteriorate. So this brings me 
to dilemma, I feel like I should try and mount this crystal and shoot it. But 
since I only have 1 sample, I do not want to mess this up...  I am inclined to 
try cryo conditions, but I am afraid the addition of a cryo such as glycerol 
could destroy the little guy. 
The crystal formed in 30% PEG 4000, 0.1M NaCitrate pH5.6 and 0.2M NH4AcO, I 
wonder if this is a cryo condition already?
Any suggestions would be appreciated.

best,


[ccp4bb] B-iso vs. B-aniso

2012-09-17 Thread Yuri Pompeu
Dear community,

The protein model I am refining has 400 amino acids (3320 atoms).
Some real quick calculations tell me that to properly refine it 
anisotropically, I would need 119,520 observations. Given my unit-cell 
dimension and space-group it is equivalent to about a 1.24 A complete data set.
However, I have had a couple of cases where anisotropic B-factor refinement 
significantly improved R-work and R-free, while maintaining a reasonable gap 
for lower resolution models (1.4-1.5 A, around 70,000 reflections). What is the 
proper way of modelling the B-factors?
Any thoughts and/or opinions from the community are welcome.
Cheers, 


[ccp4bb] Ligand geometry obs. vs. ideal

2012-09-12 Thread Yuri Pompeu
Hi everyone,
I am trying to show that a ligand underwent catalysis during a soaking 
experiment.
One of the things I would like to show is the geometry of the ligand, bond 
angles/lengths, dihedrals, etc...
One of my models has a hi-res of 1.18A and the ligand density is really clear 
and complete. 
What is the best way to refine the ligand unrestrained and then generate 
measurements?
Also, the idea is to finally compare to ideal geometry. How should I generate 
these values (any softwares in mind)?
ANy idea is welcome.
Thanks a lot


Re: [ccp4bb] Evaluating crystallogarphic experiment

2012-08-20 Thread Yuri Pompeu
Thanks for all the replies {off list}.
Now it's wait and hope that this crystallization experiment is succesful.



Re: [ccp4bb] Optimizing xtals conditions

2012-08-14 Thread Yuri Pompeu
Shoot the existing crystals. Who says you will need optmization? lol


Re: [ccp4bb] Ferredoxin Containing Crystal Bleaching

2012-07-20 Thread Yuri Pompeu
Actually with haeme, and or flavin containing enzymes it is known for the 
cofactor to undergo reduction.
There is a recent JACS paper that explores these changes as a function of X-ray 
exposure.
(2012) J.Am.Chem.Soc. 134: 2823-2834
Excellent work done in part at Allen Orville's X6A
As far as quality of your data goes, unless your crystal is suffering from 
radiation damage (they all do!) from those free electrons/radicals
then your data should not be affected by the bleaching.
HTH.
Yuri


Re: [ccp4bb] FE-Sulfur proteins

2012-07-12 Thread Yuri Pompeu
Hi Jan,
I wonder if the protein has a hexaHis tag. I recently was working on a Fe-S 
containing protein and noticed significant aggregation/precipitation. After I 
cleaving the His tag, the enzyme seems stable for days in the same buffer.
HTH,
Yuri


Re: [ccp4bb] Questions on unknown density?

2012-06-19 Thread Yuri Pompeu
Hi,
Without looking at your model/maps it is difficult to make a really educated 
guess.
By looking at the single screen shot you attach, I would say it could be a 
couple of different things, in order of likelihood based on a single screenshot 
(at whatever level of confidence this assures):
1-Zn coordinate to His, and some waters around it.
2-Phosphorylation of the His. Is this expected or known for this enzyme? 
Although I dont really see nice tetrahedral geometry, and I dont know that you 
really would at your resolution.
3-Alternate His side chain conformation. I cant really say if this fits your 
density with just that one screen shot. It doesnt really look like it to me.
I would inspect distances and angles for each of the scenarios presented above 
and then build a model that makes good chemical and physical sense.

Hope his helps.
yuri



[ccp4bb] Protein-Ligand Binding Energetics

2012-06-19 Thread Yuri Pompeu
Hi everyone,
I have several protein-ligand crystal structures of different ligands bound to 
a combination of mutants of the same enzyme.
I wanted to look at the energetics of these complexes based on the crystal 
structures.
Is there a program or suite of programs that could calculate DeltaG of complex 
formation, given the high resolution crystal structures. 
I would be looking for a trend, and possibly an explanation for why some 
mutations do not seem to form a complex.
Thanks for your input.
Yuri


[ccp4bb] Off-topic Thrombin cleavage

2012-05-23 Thread Yuri Pompeu
Dear community,
I am trying to cleave a hexaHis tag from my protein prior to crystallization.
As I was setting up my digestion, my protein started to precipitate as soon as 
I added the recommended thrombin buffer.
My question is, if anyone has encountered this, how well does it cleave without 
thrombin buffer?
or even, without the CaCl2? Any other buffer/conditions known to work?
thanks in advance


[ccp4bb] .CBF raw images in iMOSFLM- error

2012-04-11 Thread Yuri Pompeu
Hello everyone,

I am trying to process ###.cbf raw images (BNL X25) using the iMOSFLM utility 
and I get the following error message:
Distance has refined to an unreasonable value
This causes the program to freeze and  not open the rest of the frames.
Also it is not picking up the X and Y beam positions.
It looks to me like its just simply not reading the image file HEADER properly.
Anyone has encountered this before and has any ideas on how to get around/fix 
this?
Thanks a lot!
Yuri



[ccp4bb] Error in Scala

2012-04-06 Thread Yuri Pompeu
Hi everyone,
Sorry for the newbie type problems, but I am just starting to use ccp4 for data 
processing.
Here is my problem.
After I index and integrate my images using iMOSFLM, I end up with the .mtz 
files that contains, AIUI, unmerged reflections.
Next I should try to merge and scale experimental intensities, using SCALA.
I am getting an error saying:
 Giving up
Scala:  Negative Scales 
task failed.

Anything obvious I am missing? 
thanks a lot.


[ccp4bb] MOSFLM- Image compatibility

2012-04-05 Thread Yuri Pompeu
Can MOSFLM work with image files of type .x (BNL X6A) ? I am having no luck...
I know it can do .cbf (BNL X25) for instance.
Thanks a lot


Re: [ccp4bb] MOSFLM- Image compatibility

2012-04-05 Thread Yuri Pompeu
thanks for kindly pointing that out. (despite the level of stupidity on my part)
Those were not the raw imgs... They were denzo output files. Its been a while.


Re: [ccp4bb] negative difference density around sulphur and oxygen atoms

2012-04-04 Thread Yuri Pompeu
could it be that the scattering table would be slightly different for the 
sulfur atoms at the collected wavelength?
Are they Cys or Met residues? if Cys is there a possibility of oxidation to the 
disulfides?


Re: [ccp4bb] weird--No protein expression using pET30a

2012-03-18 Thread Yuri Pompeu
Hello,
Probably a stupid comment on my part, but anyways, make sure your strain has a 
T7 polymerase! (I have forgotten before).
And I agree with the last idea that sometimes it is worth to just start from 
scratch. New construct new vector. It may simply just work.
HTH,
Yuri


Re: [ccp4bb] Membrane Protein Crystallization Plates

2012-02-27 Thread Yuri Pompeu
Thanks for all the replies.
I will try a couple of different plates/set-ups. My favorite will be the one 
that gives me a crystal ;)


[ccp4bb] Membrane Protein Crystallization Plates

2012-02-25 Thread Yuri Pompeu
Hello Everyone,
I am considering the purchase of crystallization plates for membrane proteins.
I would love to hear what some of the community thinks or has experienced with 
these.
Particulalrly the monoolein and monoolein/cholesterol coated plates ( I am not 
sure I can mention the vendor here but it should not matter)
So fire away. Is it worth it? Any succes stories? Bad experiences?
I appreciate the input
Best,
Yuri


Re: [ccp4bb] Soaking Kinase Crystals with ATP analogues

2012-02-01 Thread Yuri Pompeu
Maybe someone has suggested this already... If so, I am re-enforcing it. 
If the cracking is coming from actual molecular movement induced by binding 
(and not other reason like differing ionic strength in your soaking conditions) 
you could try setting up some co-crystallization and (hopefully)
grow some enzyme-substrate complex crystals...
hth
yuri


Re: [ccp4bb] Problem with getting Rfree and Rf down

2012-01-23 Thread Yuri Pompeu
Hi Sam, 
some obvious questions:
1-Space group right? ( i´d say so from your R values...)
2-Is your data good throughout all of the 180 frames? whats Rsym if take only 
100?
3-how good/complete is model? Missing parts, residues, base pairs??
4-evaluate your refinement strategy...
HTH


[ccp4bb] writing scripts-off topic

2012-01-23 Thread Yuri Pompeu
Hello Everyone,
I want to play around with some coding/programming. Just simple calculations 
from an input PDB file, B factors averages, occupancies, molecular weight, so 
forth...
What should I use python,C++, visual basic?
thanks


[ccp4bb] Protein Fold Motifs- off-topic

2012-01-20 Thread Yuri Pompeu
Hello Everyone,
Does anyone know of a quick (yet somewhat reliable) sort of cheat-sheet/quick 
reference sheet with the more common folds with an illustrative example?


Re: [ccp4bb] Protein Fold Motifs- off-topic

2012-01-20 Thread Yuri Pompeu
Thanks guys


Re: [ccp4bb] Molecular Transform Superimposed on a Dataset

2012-01-13 Thread Yuri Pompeu
to echo Tim's question:
If by pattern you mean the position of the spots on the film, I dont think they 
would change based on the complexity of the macromolecule being studied. As far 
I know it, the position of the spots are dictated by the reciprocal lattice 
points
(therefore the real crystal lattice) (no?)
The intensity will, obviously, vary dramatically...
ps. Very interesting (cool) images James!!!


Re: [ccp4bb] on the electronic density of several maps

2012-01-13 Thread Yuri Pompeu
Fenghui,
What is your resolution? If your having trouble distinguishing between pro and 
leu I am guessing it is 
worse than 2.8 A. 
You may not be able to model side chains confidently with lower resolution 
data. You may have to make a call
on wether or not to model side chains, and if your model is interesting enough 
to pursue even without side chains.


Re: [ccp4bb] live streaming of ccp4 study weekend

2012-01-06 Thread Yuri Pompeu
I also had some trouble streaming live. 
So I am going to go ahead and also suggest/ask please that the video files be 
made available for subscribers and/or all academic users.
Cheers,


Re: [ccp4bb] Structure Determination combining X-ray Data and NMR

2012-01-06 Thread Yuri Pompeu
First thing I would try to shoot more crystals. Easy way out. I once struggled 
with a 2.7A data set for weeks only to find out I had a 1.5A diffracting 
crystal taking a bath in some storage buffer right next to my bench. 
You mention you have at this point you are looking at 25% rotamer outliers. I 
wonder if at 3.2A if you really have density for these side chains. You may be 
trying to fit these side chains in very weak unreliable (e.g. noise) electron 
density. As Ed Pozharski suggested, omitting these may be the right thing to do.
How certain are you of your space group and how did you generate you Rfree test 
set. You should have RworkRfree after refining your model.
HTH
Yuri 


Re: [ccp4bb] Structure Determination combining X-ray Data and NMR

2012-01-06 Thread Yuri Pompeu
correction:
 You should NOT have RworkRfree


Re: [ccp4bb] MERGING THREE DATASETS

2011-12-22 Thread Yuri Pompeu
I was actually trying to do the same thing. I have to data sets processed in 
p21 that I would like to merge as one contains higher resolution data. They 
were processed and merged using the HKL suite. So I have the two .sca files
I guess the first step for me would be to create  a fake unmerged set of both 
using Combat, as suggested by prof. Dodson and others.  Practically speaking, 
do I accomplish that by changing the space group to P1 while keeping my cell 
dimensions constant in combat? 
Thanks a lot


Re: [ccp4bb] Jrh correction Re: [ccp4bb] Mg or water?

2011-12-16 Thread Yuri Pompeu
In my personal opinion, whatever that is worth, I would question why you are 
modelling a Mg2+ ion if you are having to go through some trouble to prove it 
is there. If you dont see octahedral coordination to waters and or Asp/Glu it 
probably is not a Mg.
HTH


Re: [ccp4bb] PHENIX vs REFMAC refinement had me fooled

2011-12-12 Thread Yuri Pompeu
Hi Ed, 
I just had a chance of looking at your comment more closely.
You are right it only uses PHIC if in refmacs set up you choose to refine with 
prior phase information -AFAIU.
So what exactly is the info contained in the output refmacX.mtz besides map 
coefficients for COOT? If it is not just the raw xray data Fo, is it Fc only, 
or Fc that are filled in for missing Fo?
I guess I am not really sure. I was under the impression that model´s PHIC 
would cause the problems, if they were present.
Best,


Re: [ccp4bb] PHENIX vs REFMAC refinement had me fooled

2011-12-11 Thread Yuri
Precisely, one should not use it! I have seen people do it either 
because they dont fully understand what is going on or are not at all 
familiar with the documentation.
In phenix the output .mtz contains Fo plus x% Rfree flag=1, so one may 
try and do this for refmac because of one of the two above mentioned 
reasons (or both)


On Sun, 11 Dec 2011 20:41:48 -0500, Ed Pozharski wrote:

On Sun, 2011-12-11 at 05:28 +, Yuri Pompeu wrote:
In refmac however the newly generated refmacX.mtz file contains 
phase

info as PHIC calculated from your model. Using this for subsequent
rounds of refinement results in terrific looking maps as they are 
now

biased (even more so) by the input model.


PHIC won't be used in refinement unless you specify it, so this can't
happen if you just use the refmac output mtz.  AFAIU, the reason the
output mtz should never be used in subsequent refinement is because 
the
Fo's are modified.  I never understood why one would even have an 
idea
of using the output mtz as a new input.  Maybe you can explain this 
to

me at last.

Cheers,

Ed.


--
Yuri Pompeu


Re: [ccp4bb] PHENIX vs REFMAC refinement had me fooled

2011-12-10 Thread Yuri Pompeu
PHENIX has an otpion under the reflection editor program that will create R 
flags that are compatible with ccp4 programs.
Another point worth mentioning is in phenix.refine it is appropriate to use the 
data.mtz files generated each round of refinement, as these are the raw data 
plus the Rfree flags. In refmac however the newly generated refmacX.mtz file 
contains phase info as PHIC calculated from your model. Using this for 
subsequent rounds of refinement results in terrific looking maps as they are 
now biased (even more so) by the input model.


Re: [ccp4bb] Efficient way of showing residue conservation-thank you everyone

2011-12-08 Thread Yuri

On Thu, 8 Dec 2011 09:19:57 +, Mads Gabrielsen wrote:

I believe Charlie Bond's ALINE
(http://crystal.bcs.uwa.edu.au/px/charlie/software/aline/) will let 
you
make a nicely coloured sequence alignement, and then write out a 
Pymol

script which will colour the surface by conservation.

Mads
--
Mads Gabrielsen, PhD
Institute of Infection, Immunology and Inflammation
College of Medical, Veterinary and Life Sciences
University of Glasgow

Room B216 /L303
GBRC
120 University place
G12 8TA


Phone: 0141 3307264 / 6180

E-mail: mads.gabriel...@glasgow.ac.uk





On 08/12/2011 05:26, Yuri Pompeu yuri.pom...@ufl.edu wrote:

I once saw a figure showing the protein as surface, but instead of 
having

it coloured by atom type
or potential, it was shown by percent conservation in the family.
Something like red highly conserved, all the way to white, not 
conserved

at all...
Now, I assume the figure was done by uploading aligned sequnces of
several members of a family, and the colouring
the generated surface accordingly.
Does anyone know a way to do this more elegantly than what I tried 
doing?
ps. I quit colouring them manually after I remebered my protein was 
407

aa long...


--
Yuri Pompeu


[ccp4bb] Efficient way of showing residue conservation

2011-12-07 Thread Yuri Pompeu
I once saw a figure showing the protein as surface, but instead of having it 
coloured by atom type
or potential, it was shown by percent conservation in the family. Something 
like red highly conserved, all the way to white, not conserved at all...
Now, I assume the figure was done by uploading aligned sequnces of several 
members of a family, and the colouring
the generated surface accordingly. 
Does anyone know a way to do this more elegantly than what I tried doing?
ps. I quit colouring them manually after I remebered my protein was 407 aa 
long...


Re: [ccp4bb] ccp4 on Win7 'clipper::Message_fatal'-Solved

2011-12-06 Thread Yuri

Seems to be working now.
I wish the error message was a little more indicative of the actual 
problem for the not-so-intelligent like myself!

(which turned out to have a simple fix here)
That could have saved some time, and spared you from looking into 
something this obvious!

Thank you for the help!

On Tue, 6 Dec 2011 16:33:14 +, andrey.lebe...@stfc.ac.uk wrote:

Yes, you are right, both -hklin and -mtzin are valid option keys.

I have reproduced your error message.
The problem is in the command line option -colout yap-ii-77-73.

Now I must check what happens on Linux.
Meanwhile a quick fix for you: use no more than 10 characters in the 
box

Modifier to append to column labels.

Does this recipe work for you?

Andrey

On 6 Dec 2011, at 14:51, Yuri wrote:

The thing is, I did not run any command myself. I was using the GUI. 
So the command was written for me.
Thats why I thought it was really odd that this may be a wrong 
command.

Obviuosly the GUI for RedHat works.

Best,


On Tue, 6 Dec 2011 13:14:36 +, andrey.lebe...@stfc.ac.uk wrote:

Hi Yuri

Perhaps you have used incorrect command line keys.

I have installed ccp4 using Marcins script on my Windows 7 Virtual 
Box.

Then I used ccp4i to run ctruncate with my test case.
Run  Run  View Com File showed the following command:
ctruncate -mtzin
C:/Users/andrey/Desktop/HemH_tutorial/test_scala1.mtz -mtzout
C:/Ccp4Temp/HemH_4_1_mtz.tmp -colin /*/*/\[IMEAN,SIGIMEAN\]
-colano /*/*/\[I(+),SIGI(+),I(-),SIGI(-)\]

This is different from yours (-mtzin, not -hklin):
ctruncate -hklin C:/Ccp4Temp/oye1_77-73_3_1_mtz.tmp -hklout 
C:/Ccp4Temp/oye1_77-73_3_3_mtz.tmp -colin 
/*/*/\[IMEAN,SIGIMEAN\] -colano 
/*/*/\[I(+),SIGI(+),I(-),SIGI(-)\] -colout yap-ii-77-73 -nres 400




Please try using ccp4i or try -mtzin instead of -hklin.
Does it work?

Andrey

On 6 Dec 2011, at 01:24, Yuri Pompeu wrote:


Dear Developers,
I was trying to get ccp4 up and running on a Windows7 pc, and even 
though the installation proceeds smoothly,

I cant get any task to finish succesfully.
Below is what the log file has to say about it.
I saw someone having trouble with the windows install as well. I 
have the installation packaged posted by Marcin installed.

Thanks for any help

* Information from CCP4Interface script

***
The program run with command: ctruncate -hklin 
C:/Ccp4Temp/oye1_77-73_3_1_mtz.tmp -hklout 
C:/Ccp4Temp/oye1_77-73_3_3_mtz.tmp -colin 
/*/*/\[IMEAN,SIGIMEAN\] -colano 
/*/*/\[I(+),SIGI(+),I(-),SIGI(-)\] -colout yap-ii-77-73 -nres 400

has failed with error message
CCP4MTZfile - internal error

This application has requested the Runtime to terminate it in an 
unusual way.
Please contact the application's support team for more 
information.
terminate called after throwing an instance of 
'clipper::Message_fatal'


***


#CCP4I TERMINATION STATUS 0 CCP4MTZfile - internal error  This 
application has requested the Runtime to terminate it in an unusual 
way. Please contact the application's support team for more 
information. terminate called after throwing an instance of 
'clipper::Message_fatal'

#CCP4I TERMINATION TIME 05 Dec 2011  20:19:00
#CCP4I MESSAGE Task failed


--
Yuri Pompeu


--
Yuri Pompeu


[ccp4bb] ccp4 on Win7 'clipper::Message_fatal'

2011-12-05 Thread Yuri Pompeu
Dear Developers,
I was trying to get ccp4 up and running on a Windows7 pc, and even though the 
installation proceeds smoothly, 
I cant get any task to finish succesfully.
Below is what the log file has to say about it.
I saw someone having trouble with the windows install as well. I have the 
installation packaged posted by Marcin installed.
Thanks for any help

* Information from CCP4Interface script
***
The program run with command: ctruncate -hklin 
C:/Ccp4Temp/oye1_77-73_3_1_mtz.tmp -hklout 
C:/Ccp4Temp/oye1_77-73_3_3_mtz.tmp -colin /*/*/\[IMEAN,SIGIMEAN\] -colano 
/*/*/\[I(+),SIGI(+),I(-),SIGI(-)\] -colout yap-ii-77-73 -nres 400  
has failed with error message
CCP4MTZfile - internal error

This application has requested the Runtime to terminate it in an unusual way.
Please contact the application's support team for more information.
terminate called after throwing an instance of 'clipper::Message_fatal'
***


#CCP4I TERMINATION STATUS 0 CCP4MTZfile - internal error  This application has 
requested the Runtime to terminate it in an unusual way. Please contact the 
application's support team for more information. terminate called after 
throwing an instance of 'clipper::Message_fatal'
#CCP4I TERMINATION TIME 05 Dec 2011  20:19:00
#CCP4I MESSAGE Task failed


[ccp4bb] Software for showing crystal packing

2011-12-02 Thread Yuri Pompeu
Hello everyone,
Whats a good software for showing crystal packing and unit cell, axes , etc...
I know pymol and coot will do it but would love to hear other 
possibilities/ideas.
Cheers,


Re: [ccp4bb] Anomalous signal for chlorides

2011-11-25 Thread Yuri Pompeu
Hi Boaz, 
Yes indeed, the phosphate group of the molecule looks quite beautiful at 1.17A 
and it has a really big peak 18sigma!
Is there a utility for calculating anomalous maps, or is it simply an option in 
the refinement program?


[ccp4bb] Merging with CAD fails

2011-11-05 Thread Yuri Pompeu
Hello,
I am trying to merge two data sets on from 28 to 2.3 A 99% comlpeteness
with another one from 26 to 1.95A 82% completeness.
I keep getting an error saying Duplicate labels in the output file.
I am sure its something simple but I cannot seem to figure it out
Any ideas?
Thanks


Re: [ccp4bb] Merging with CAD fails

2011-11-05 Thread Yuri

Thanks for the help.
I believe option 3 describes my situation the best.
I am looking into it now...
Best,
Yuri

On Sat, 05 Nov 2011 16:38:11 -0400, Ed Pozharski wrote:

If you post the cad input file, it should be easy to pinpoint the
problem.  As  it stands, you are either:

1) Including Miller indices as merged columns - they get done
automatically, so if you specify them, you get the duplicate labels
2) You actually do have the same name for the two columns in the 
output

- thus duplicate labels
3) You may be thinking that cad can merge two datasets into one - it
can't.  CAD just takes columns from two or more files and puts them 
into
one.  What you are trying to do requires scaling/merging of two 
datasets

- you should look at scala for that.

HTH,

Ed.


--
Yuri Pompeu


Re: [ccp4bb] MR - small coiled coil, 1.65A = 1.000 solutions, all of them wrong

2011-11-02 Thread Yuri Pompeu
Hi Napo,

i am sorry if you already answered this, why are so sure your solutions are 
wrong?
Your maps do not look that bad. What kind of R's do you get?
Are you not happy with the packing of your coils?



[ccp4bb] NCS 2-fold perpendicular to crystal 2-fold

2011-10-28 Thread Yuri Pompeu
Hello Everyone,
I have data sets that scaled fairly welll in C2 2 21, but intensity statistics 
suggested twinning. 
I was able to solve the structure in P1 21 1 (Rwork0.19/Rfree0.24 at 2.3A) with 
OK looking maps.
I notice that I have 2-fold NCS that is paralell to the crystallographic A 
axis, perpendicular to my crystallographic 2-fold B axis.
Can anyone ellaborate on the effect of this on the data (indexing/scaling and 
refining)?

Best,




Re: [ccp4bb] Weird blob appears

2011-10-27 Thread Yuri Pompeu
Jacob,
By simply looking at the figures you show, it does look like you have some type 
of long, maybe polymeric, molecule bound.
With that being said:
1- It is in the symmetry axis so maybe be a little noisy there
2-If you are in doubt about it being real or not check the density and how it 
fits into your protein and (symm. related neighbours of course). If the desity 
appears to be in position for some real interactions- i.e, there are some peaks 
at H-bond distances of polar groups etc...- it may be real. If its all random 
and through your protein atoms, probably not
Keep in mind alternate conformers
HTH


Re: [ccp4bb] COOT not connected to PHENIX

2011-10-25 Thread Yuri

I installed the version with python embedded in coot
And it works!!
Thanks a lot!!

On Tue, 25 Oct 2011 11:41:38 -0700, Nathaniel Echols wrote:

On Tue, Oct 25, 2011 at 11:40 AM, Yuri yuri.pom...@ufl.edu wrote:

Now here comes the stupid question...
How do I fix it?
Install a different coot version or is it something in my 
architecture?


Install a different Coot.  If you're downloading from Paul Emsley's
page, you need a package with python in the file name.  I have no
idea whether the Linux binaries distributed by CCP4 have Python or 
not

(the Mac version definitely does).

-Nat


--
Yuri Pompeu


Re: [ccp4bb] help me after several refmac

2011-10-13 Thread Yuri Pompeu
Echoing whats been said:
1- Are you sure your crystal really is in C 2 2 21? If so How good is your data 
(completeness, Rmerge, etc...)
2-Could have twinning? I recently just got done working on a structure that 
could be scaled in C 2 2 21 but turned out to really be an almost perfect P21 
twin.
(of course in monoclinic there are certain conditions for twinning...)
3- How good is your model, is it complete, all the waters? Missing protein or 
DNA?
 HTH

Yuri


Re: [ccp4bb] Refinement with twinned data question

2011-10-02 Thread Yuri
  

1-So for my case, I should try and generate Rfree flags, in the
higher apparent C 2 2 21 and not the real P 1 21 1, correct?
2-I noticed
that if I used the output PHIC FOM data, the maps looked awesome! Too
good almost... 

Thanks a lot 

On Sun, 2 Oct 2011 12:07:22 +0100, Garib
N Murshudov wrote: 

 Dear Yuri 
 1) For twin refinement refmac
internally changes free reflections so that twin related reflections
belong to the same class (twin or working). However it would be good to
generate free reflections in higher space group that would include twin
and space group symmetries. 
 2) You should always use original data
for refinement. Never use output from refmac for next round of
refinement. Output mtz file is representation of model. 
 regards 

Garib 
 
 On 2 Oct 2011, at 03:27, Yuri wrote: 
 
 Dear all,
 I
have some questions about the correct protocol for refinement of twinned
data (0.46)
 
 1- How do I ensure that my Rfree set is generated
properly?
 
 2-I noticed that if I enable intensity based twin
refinement, refmac estimates the correct twin fraction
 law -h,-k,h+l.
But for subsequent refinement rounds should I keep using the raw
intensity mtz file or
 the newly generated mtz with PHIC and FOM
information?
 
 Thank you
 -- 
 Yuri Pompeu
 
 Garib N
Murshudov 
 Structural Studies Division 
 MRC Laboratory of Molecular
Biology 
 Hills Road 
 Cambridge 
 CB2 0QH UK
 Email:
ga...@mrc-lmb.cam.ac.uk [1] 
 Web http://www.mrc-lmb.cam.ac.uk [2]

--

Yuri Pompeu
  

Links:
--
[1] mailto:jen...@mrc-lmb.cam.ac.uk
[2]
http://www.mrc-lmb.cam.ac.uk/


[ccp4bb] Refinement with twinned data question

2011-10-01 Thread Yuri

Dear all,
I have some questions about the correct protocol for refinement of 
twinned data (0.46)


1- How do I ensure that my Rfree set is generated properly?

2-I noticed that if I enable intensity based twin refinement, refmac 
estimates the correct twin fraction
law -h,-k,h+l. But for subsequent refinement rounds should I keep using 
the raw intensity mtz file or

the newly generated mtz with PHIC and FOM information?

Thank you
--
Yuri Pompeu


[ccp4bb] Ramachandran Restraints in refmac

2011-09-30 Thread Yuri Pompeu
Hello everyone,
I am refining a structure to 2.4A with 2-fold NCS and twinned.
Maps look ok and Rfree is 0.27however as I start checking my validations I 
notice that after refinemnt 
my geomtry gets significantly worse. especially the rama plot. Initially I have 
2 outliers and I end up with 32 (5%)!!!
I played with the Xray weight term but alll it helped me with was rmsd 
bond/angles, rama is still messing up...
Can I impose some ramachadran restraints or maybe have a reference model?

best,


Re: [ccp4bb] Apparent twinning in P 1 21 1

2011-09-29 Thread Yuri Pompeu
After I ran DETWIN with the estimated 0.46 alpha, my completeness for the 
detwinned data is now down to 54%!!!
Is this normal behavior? (I am guessing yes since the lower symmetry untwinned 
dat is P1 21 1)


Re: [ccp4bb] Apparent twinning in P 1 21 1

2011-09-29 Thread Yuri

I am refining in phenix twin law h,-k,-h-l.
Without twinning I was around 0.36 Rfree and 0.25 with twinning.
I am noticing however that my Rgap keeps increasing slowly... (little 
concerned now its at 8% - 0.18-0.26 - to 2.4A)
Maps look decent for 2.4A I have a lot of clashes however some are just 
bad waters though. phenix does not do real space when twinning is 
enabled.

Any ideas here?

thank you much

On Thu, 29 Sep 2011 10:25:17 -0400, Phil Jeffrey wrote:

Yuri,

Detwinning relies on having both twin-related reflections present to
calculate either/both of the the de-twinned data values.  Therefore 
it

magnifies incompleteness depending on where your missing data is with
respect to the twin operator.

I'd recommend against trying to do this with a twin fraction close to
0.5.  From the DETWIN docs:

Itrue(h1) = ((1-tf)*iTw(h1) -tf*iTw(h2)) / (1-2tf)

i.e. tf = twin fraction, so 1/(1-2tf) becomes a large number and it's
multiplying a weighted term of the form: (iTw(h1) - iTw(h2)) which
becomes a very small number as the twin fraction approaches 0.5.  The
latter difference can easily be less than sigma(I), and so the
signal/noise of your data plummets.

Better to use REFMAC and phenix.refine's abilities to compensate for
the twin fraction directly in refinement and leave your data as it 
is.


Phil Jeffrey
Princeton


On 9/29/11 10:03 AM, Yuri Pompeu wrote:
After I ran DETWIN with the estimated 0.46 alpha, my completeness 
for the detwinned data is now down to 54%!!!
Is this normal behavior? (I am guessing yes since the lower symmetry 
untwinned dat is P1 21 1)


--
Yuri Pompeu


Re: [ccp4bb] Apparent twinning in P 1 21 1

2011-09-29 Thread Yuri
  

I am now realizing that! I have been refining with twin law
enabled, its been somewhat succesful. 

I have been using phenix and now
getting ready to try refmac... 

regards 

On Thu, 29 Sep 2011 15:23:13
+0100, Garib N Murshudov wrote: 

 Why do you detwin? It would not be
normal procedure if you have twinning. Molecular replacement programs
usually do not have much problem with twinned data and refinement
programs can deal with them more or less properly. 
 when you detwin
then errors are increased (As far as I remember proportional to
1/(1-2alpha), if alpha is 0.46 then errors will increase more than 10
times). Moreover it is very likely that twin and pseudo rotation are
close to each other and estimated twin fractions may not be accurate. 

regards 
 Garib 
 
 On 29 Sep 2011, at 15:03, Yuri Pompeu wrote: 


 After I ran DETWIN with the estimated 0.46 alpha, my completeness
for the detwinned data is now down to 54%!!!
 Is this normal behavior?
(I am guessing yes since the lower symmetry untwinned dat is P1 21 1)


 Garib N Murshudov 
 Structural Studies Division 
 MRC Laboratory of
Molecular Biology 
 Hills Road 
 Cambridge 
 CB2 0QH UK
 Email:
ga...@mrc-lmb.cam.ac.uk [1] 
 Web http://www.mrc-lmb.cam.ac.uk [2]

--

Yuri Pompeu
  

Links:
--
[1] mailto:jen...@mrc-lmb.cam.ac.uk
[2]
http://www.mrc-lmb.cam.ac.uk/


Re: [ccp4bb] Apparent twinning in P 1 21 1 (refmac)

2011-09-29 Thread Yuri Pompeu
after 1 round of refmac rigid body and restrained refinement with twin law 
(estimated alpha 0.47)
I am looking at 0.25 -0.29 Rwork Rfree and overall FOM 0.72.
I also defined NCS restraints...


[ccp4bb] Apparent twinning in P 1 21 1

2011-09-27 Thread Yuri Pompeu
Hello everyone,
I have a 2.3A data set that could be scaled in C 2 2 21  and P 1 21 1 
Intensity statistics tests indicate twinning (pseudo-merohedral h,-k,-h-l in P 
1 21 1)
I find a good MR solution and when I try to refine it with the twin law I get 
fairly good maps and decent Rs 21-28%. I can see features tha were not in the 
search model
Which leads me to think that this a valid solution. The one thing that bothers 
me however is the fact that my beta angle in P 1 21 1 is 104 (not close to 90) 
and that the geometry gets worse after refinement?
Any suggestions?
cheers


Re: [ccp4bb] Apparent twinning in P 1 21 1

2011-09-27 Thread Yuri Pompeu
These papers describe something similar to what I see.
Acta Cryst. (2001). D57, 1829-1835
Acta Cryst. (2009). D65, 388-392


[ccp4bb] Direct method solution at 1.15A

2011-09-23 Thread Yuri Pompeu
Hello everyone,
I have a data set 99% completeness to 1.15A
This is a 400 amino acid long protein and it has 7 Met (Sulfur peaks around 
20sigma)
And a tightly bound phosphate (P peak around 22sigma)
Could I try and solve this directly or is it crazy idea?
If so what program should I try?

thanks 
Yuri



Re: [ccp4bb] Direct method solution at 1.15A

2011-09-23 Thread Yuri Pompeu
I solved the structure using molecular replacement. Those sigmas are simply 
from my sigmaa 2mFo-DFc maps.
I was wondering if I could try and solve sort of like small molecules are


Re: [ccp4bb] Structure problem

2011-09-14 Thread Yuri Pompeu
Just echoing what has been said.
I would make sure you have the right space group.
It may be worthwhile tyring to find a MR solution in different space groups 
with different compositions.
Another imporatant thing is how complete is your model?
Do you have all the protein and DNA modeled in? How many waters (you should see 
plenty at 1.5 A)
How good is the difference map?
These are all things that should be checked before panic sets in

Cheers


Re: [ccp4bb] COOT on CentOS 6 (x86_64)

2011-09-12 Thread Yuri Pompeu
Hi Paul,
I am running the centos5 build. After a couple of yum installs it seems to be 
happy...

Except I cannot maximize the window for some reason.
Thanks for the reply.

Yuri


[ccp4bb] COOT on CentOS 6 (x86_64)

2011-09-11 Thread Yuri Pompeu
Hello everyone,
Could anyone tell me (or point me to) how to get COOT running on CentOS6 64-bit?
It doesnt launch due to failed dependencies, it requires packages that CentOS6 
has replaced...
At least that is what it looks like to me...
Cheers,


Re: [ccp4bb] EDS server

2011-09-02 Thread Yuri Pompeu
A simple way to validate real space density fit is to look at it under 
validate---density fit anlysis in COOT.
I think even the GUI of phenix.refine at the end of a run the results give a 
list of all residues that are under the user-definied RSCCoeficient.
With those two tools you should be able to see what you need to see


Re: [ccp4bb] Trying to digest PISA results

2011-09-01 Thread Yuri Pompeu
This is regarding Ethan´s point, particularly:
  2) the protein has crystallized as a monomer even though it
  [sometimes] exists in solution as a dimer.  The interface
  seen in the crystal is not the real dimer interface and
  thus the PISA score is correct.
I see the same exact interface in a crystal of a close homologue that belongs 
to a different space group (hexagonal vs tetragonal system)


[ccp4bb] Trying to digest PISA results

2011-08-31 Thread Yuri Pompeu
I was playing around with PDBe PISA and came across the following:
For pdb entry 1OYA. The most promising interface has an area bury of around 
720A^2 and DeltaG of -10.6Kcal/mol. sym_op(y,x,-z+1) and CSS of 0.039!   
Assembly analysis says it has no strong indications that point to stable 
quaternary structure.
This protein has been extensively studied and determined to be a dimer.
Entry 3RND is the same protein with one single conservative mutation deep in 
the active site.
They align with a RMSD of 0.3 A, 99.8% sequence identity. Superposition and 
inspection of the regions that contact 
the adjacent monomer shows they are basically identical.
The interface here shows Area bury of 760 A^2 and DeltaG = -6.6Kcal/mol. sym_op 
(-y,-x,-z-1/2) CSS=0.00 !
 Assembly analysis basically says no stable oligomers form. This enzyme also is 
 dimer according to gel filtration.
Could anyone ellaborate on this please, if they feel like they have the time...
Cheers


[ccp4bb] Temperature Factor statistics

2011-08-30 Thread Yuri Pompeu
Quick newbie question, 
After i get my output file from baverage containing the average b-factor and 
rms by residues,
How can I calculate and display the average (and or mean) B-factors?
Is there a way of calculating it by protein, ligands and solvent separately?
thank you


Re: [ccp4bb] Sequence Alignment Question- Thank you everyone

2011-08-19 Thread Yuri

Thanks everyone, for the help.

--
Yuri Pompeu


[ccp4bb] Sequence Alignment Question

2011-08-18 Thread Yuri

Hello Everyone,
A little off topic but, what is a good way to show (publication 
quality) multiple sequence alignment?
I am trying to show conserved regions in related proteins from 
different organisms.

Thank you
--
Yuri Pompeu


[ccp4bb] PyMol plugin

2011-08-14 Thread Yuri Pompeu
I installed the plugin superSym  but when I triesd to run it, ended up with the 
following message:
  File 
/home/local/UFAD/yuri.pompeu/Desktop/PHENIX_installation/phenix-installer-dev-833/phenix-dev-833/pymol/modules/pmg_tk/PMGApp.py,
 line 156, in initialize_plugins
__builtin__.__import__(mod_name)
  File 
/home/local/UFAD/yuri.pompeu/Desktop/PHENIX_installation/phenix-installer-dev-833/phenix-dev-833/pymol/modules/pmg_tk/startup/SuperSymPlugin12.py,
 line 18, in ?
 Color: map_colour defined as [ 0.000, 0.500, 1.000 ].
 Color: iso_diff_map_colour defined as [ 0.000, 1.000, 0.250 ].
quit(Oops! SuperSym requires cctbx and numeric python to function. Please 
install these.)
 
I then installed cctbx+Python bundle from http://cci.lbl.gov/cctbx_build/ and 
sourced it.
I still get the same result in PyMol though..
Does anyone know what to do?
Thank you for your time
Best,
Yuri


Re: [ccp4bb] PyMol plugin

2011-08-14 Thread Yuri Pompeu
Jurgen,
I was able to make the picture i wanted the poor man´s way.
I saved the symmetry coordinates in COOT and open all of them as objects 
independently.
I just wanted to know what else I need to do to get the plugins going. I have 
tried two differents ones with no success.


Re: [ccp4bb] PyMol plugin

2011-08-14 Thread Yuri Pompeu
Yes I just tried symex and it is a LOT faster... especially with 12 symm 
operators...
yes I want to show crystal packing, but I know SuperSym can show the three axis 
and fancy representations of unit cells, etc...


Re: [ccp4bb] Symmetry Related molecules

2011-08-05 Thread Yuri

Thank you all,
Best

On Fri, 05 Aug 2011 09:19:55 +0200, Thomas Holder wrote:

On 08/05/2011 05:22 AM, Albert Guskov wrote:

have a look at SuperSym plugin for pymol
http://www.pymolwiki.org/index.php/SuperSym


Or the Supercell script. It has less features than SuperSym but does
not require cctbx module.

http://pymolwiki.org/index.php/Supercell

Cheers,
  Thomas


--
Yuri Pompeu


[ccp4bb] Mixed Iso/Aniso in refmac5

2011-08-04 Thread Yuri Pompeu
Hello everyone,
How does refmac5 pick atoms for B-factor refinement, particularly with the 
mixed option enabled?
I dont see a place for entering a manual selection, eg resname FMN...
Thank you


[ccp4bb] Symmetry Related molecules

2011-08-04 Thread Yuri
Whats the best way to visualize all the symmetry related molecules, I 
know COOT will show them as backbone.

I was looking for publication quality images...PyMol maybe?
thank you for suggestions

--
Yuri Pompeu


Re: [ccp4bb] Newbie Installation Question- Solved

2011-08-02 Thread Yuri
  

I can launch the program after installing the newest package from
the Website 

Thank you all, 

yuri 

On Mon, 1 Aug 2011 17:01:47 +,
ronan.kee...@stfc.ac.uk wrote: 

 Dear Yuri, 
 
 Are you still
encountering problems with this? I've made the changes to the CCP4
download site so that the path to the tcltk distribution is set
correctly on installation. You might want to download the latest version
from our website again if you are still having problems. 
 
 Let me
know if you need help. 
 
 Best wishes, 
 
 Ronan 
 
 Ronan Keegan

 
 CCP4 Group 
 
 FROM: CCP4 bulletin board
[mailto:CCP4BB@JISCMAIL.AC.UK] ON BEHALF OF Yuri
 SENT: 30 July 2011
01:02
 TO: ccp4bb
 SUBJECT: Re: [ccp4bb] Newbie Installation Question

 
 I downloaded the package for RHEL5. My default shell is sh. But I
can change environments. I have progrmas that I must run in tcsh. 
 

I tried sourcing sh and csh setups. With the csh setup, after I changed
the PATH in the ccp4.setup file (originally set to usr/local/bin), I
type ccp4 and I get no error. I am a bit at loss 
 
 with the sh setup
I tried sourcing and I get a command not found message, which leads me
to think I am not succeding in sourcing it. 
 
 Someone mentioned
something about some files are not readable... 
 
 I tried running the
executables in the /bin directory but nothing happens... 
 
 Thank you

 
 On Fri, 29 Jul 2011 13:53:49 -0700, Iain Kerr wrote: 
 
 What
is the output when you try to launch ccp4i ? Are there any error
messages ? Problems with Tcl/Tk will usually return an error about not
being able to locate a specific library.
 
 Can you launch the
programs independent of the GUI ? eg. if you go to where the executables
are (CCP4/ccp4-6.2.0/bin)
 
  ./mtzdump
 
 You should see some
output giving the program version etc. and a list of keyword options. If
so, the installation is probably OK and as Ed suggested it could be an
environment problem. Why don't you outline the specific steps you've
taken so far during installation and environment set up - what shell are
you using ? did you download the source code or binaries ? what Tcl/Tk
version are you using and where did you get it from ?
 
 I can help
with this, off the board and then if we find a solution you can post it
on the BB.
 
 Iain
 
 On 7/29/2011 12:37 PM, Yuri wrote: 
 

I tried that too ... no success 
 
 On Fri, 29 Jul 2011 15:28:58
-0400, Ed Pozharski wrote: 
 
 On Fri, 2011-07-29 at 20:08 +0100,
Yuri wrote: 
 
 Dear all, 
 I have just downloaded and installed
the ccp4-6.2.0. 
 It says all I should do next is source the
/setup-scripts/csh/ccp4.setup file... I have done that, but I cannot
launch the program... 
 Any help is welcome...(it is probably
something really stupid on my part...) 
 Best, 
 
 It is most
likely that your default shell is bash and you are trying to 
 source
tsch script, which naturally fails. 
 Try /setup-scripts/sh/ccp4.setup
instead.
 
 -- 
 
 Yuri Pompeu

-- 
Yuri Pompeu
  

[ccp4bb] Newbie Installation Question

2011-07-29 Thread Yuri
Dear all,
I have just downloaded and installed the ccp4-6.2.0. 
It says all I should do next is source the /setup-scripts/csh/ccp4.setup 
file... I have done that, but I cannot launch the program...
Any help is welcome...(it is probably something really stupid on my part...)
Best,


Re: [ccp4bb] Newbie Installation Question

2011-07-29 Thread Yuri

I tried that too ... no success



On Fri, 29 Jul 2011 15:28:58 -0400, Ed Pozharski wrote:

On Fri, 2011-07-29 at 20:08 +0100, Yuri wrote:

Dear all,
I have just downloaded and installed the ccp4-6.2.0.
It says all I should do next is source the 
/setup-scripts/csh/ccp4.setup file... I have done that, but I cannot 
launch the program...
Any help is welcome...(it is probably something really stupid on my 
part...)

Best,



It is most likely that your default shell is bash and you are trying 
to

source tsch script, which naturally fails.
Try /setup-scripts/sh/ccp4.setup instead.


--
Yuri Pompeu


Re: [ccp4bb] Newbie Installation Question

2011-07-29 Thread Yuri
  

yes, I noticed the default was TCLTK /usr/local/bin. I think it
should be /usr/local/username.../tcltkplusplus/bin 

Even after editing
this it doesnt launch. the command not found message is gone though 

On
Fri, 29 Jul 2011 22:02:22 +0200, Wei-Chun Kao wrote: 

 Hi, 
 where
did you install CCP4? from the path of your setup-script it seems like
to be in the root (/) ? It looks like the problem I posted some days
before but probably being buried in the middle of the other thread.
Since it's more related to this topic so I paste it again, hoping that
it can solve your question. 
 I recently found the problem that after
finishing the installation of CCP4-6.2.0 on RHEL5, if the installation
destination is not the default path (/usr/local/), the ccp4.setup for
csh wouldn't take the customized TCLTK path correctly. No matter if I
used sh or csh to install the CCP4 package. This would result in
programs using wish failed to start (e.g., ccp4i) from csh. Perhaps it's
also related to the issue in this thread. 
 
 The way to solve this
problem is to manually edit the ccp4.setup for csh and correct the TCLTK
path. If you have no idea you can just copy the correct one in the
ccp4.setup for sh. 
 Wei-Chun 
 
 On Fri, Jul 29, 2011 at 9:08 PM,
Yuri wrote:
 
 Dear all,
 I have just downloaded and installed the
ccp4-6.2.0.
 It says all I should do next is source the
/setup-scripts/csh/ccp4.setup file... I have done that, but I cannot
launch the program...
 Any help is welcome...(it is probably something
really stupid on my part...)
 Best,
 
 -- 
 
 Wei-Chun Kao, MSc.

 TEL: +49-761-203-5277 
 Institute for Biochemistry and Molecular
Biology 
 Albert-Ludwigs-Universitaet Freiburg im Breisgau 

Stefan-Meier-Str. 17 
 D-79104 Freiburg im Breisgau 
 Germany

--

Yuri Pompeu
  

Links:
--
[1] mailto:yuri.pom...@ufl.edu


Re: [ccp4bb] Newbie Installation Question

2011-07-29 Thread Yuri
  

I downloaded the package for RHEL5. My default shell is sh. But I
can change environments. I have progrmas that I must run in tcsh. 

I
tried sourcing sh and csh setups. With the csh setup, after I changed
the PATH in the ccp4.setup file (originally set to usr/local/bin), I
type ccp4 and I get no error. I am a bit at loss 

with the sh setup I
tried sourcing and I get a command not found message, which leads me
to think I am not succeding in sourcing it. 

Someone mentioned
something about some files are not readable... 

I tried running the
executables in the /bin directory but nothing happens... 

Thank you


On Fri, 29 Jul 2011 13:53:49 -0700, Iain Kerr wrote: 

 What is the
output when you try to launch ccp4i ? Are there any error messages ?
Problems with Tcl/Tk will usually return an error about not being able
to locate a specific library.
 
 Can you launch the programs
independent of the GUI ? eg. if you go to where the executables are
(CCP4/ccp4-6.2.0/bin)
 
 ./mtzdump
 
 You should see some output
giving the program version etc. and a list of keyword options. If so,
the installation is probably OK and as Ed suggested it could be an
environment problem. Why don't you outline the specific steps you've
taken so far during installation and environment set up - what shell are
you using ? did you download the source code or binaries ? what Tcl/Tk
version are you using and where did you get it from ?
 
 I can help
with this, off the board and then if we find a solution you can post it
on the BB.
 
 Iain
 
 On 7/29/2011 12:37 PM, Yuri wrote: 
 
 I
tried that too ... no success 
 
 On Fri, 29 Jul 2011 15:28:58
-0400, Ed Pozharski wrote: 
 
 On Fri, 2011-07-29 at 20:08 +0100,
Yuri wrote: 
 
 Dear all, 
 I have just downloaded and
installed the ccp4-6.2.0. 
 It says all I should do next is source
the /setup-scripts/csh/ccp4.setup file... I have done that, but I cannot
launch the program... 
 Any help is welcome...(it is probably
something really stupid on my part...) 
 Best,
 
 It is most
likely that your default shell is bash and you are trying to 
 source
tsch script, which naturally fails. 
 Try
/setup-scripts/sh/ccp4.setup instead.

-- 
Yuri Pompeu