Hi Jessica,
there is a flag -t, which you should give in the command line to set the
number of threads. eg shelxd -t4 name
Best wishes,
Isabel
--
ICREA Res. Prof. Isabel Usón
Crystallographic Methods
Department of Structural Biology (“Maria de Maeztu” 2014 Unit of Excellence),
Molecular Biolo
Hi all,
Thank you for the excellent advice. I think I have found what I am looking
for.
To James, I am currently not using a queuing system and I am just launching
jobs directly on a shared GPU machine. Soon I will move to a PBS cluster,
which should help with all of this.
Thanks again!
Cheers,
Hi Jessica,
like most shelx programs, there is a little help message when started
without command line options. The option
'-tN' sets the number of CPUs to N. If I remember correctly, SHELXD
also respects the environment variable OMP_NUM_THREADS.
Best,
Tim
On Wed, 16 Mar 2022 17:21:38 -0700 Jes
Most cluster queueing systems have a way to limit such things. Which one
are you using?
You can also set the environment variable OMP_NUM_THREADS to tell SHELXD
to limit its CPU usage. You do this with either:
setenv OMP_NUM_THREADS 10
or
export OMP_NUM_THREADS=10
on the command line before
PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] SHELXD - Limit Number of CPUs?
Hi all,
I am wondering if there is a way to limit the number of CPUs that can be used
by SHELXD. It seems that this program uses all that are available until it hits
the NTRY you specified or it finds a .fin file. Is
Hi all,
I am wondering if there is a way to limit the number of CPUs that can be
used by SHELXD. It seems that this program uses all that are available
until it hits the NTRY you specified or it finds a .fin file. Is there a
way to limit its CPU and MEM usage? I am running this on a large cluster
On Tue, 1 Mar 2022 18:06:34 +0800, fu wrote:
>Dear Colleagues,
>I have two question.
>The first question is, in SHELXD, they use XPREP to calculate the
> correlation coefficient(CCano) between the signed anomalous differences at
> different wavelengths? What’s the meaning? And how to ca
The diagonal elements of the scale matrix are 1/a, 1/b and 1/c for orthogonal
cells. It converts orthogonal coordinates to fractional. There should be more
info on the rcsb.org website or in the ccp4 documentation e.g. for pdbset.
Cheers, Jon.C.
Sent from ProtonMail mobile
Original Me
Hi Fu,
"The SCALEn (n = 1, 2, or 3) records present the transformation from the
orthogonal coordinates as contained in the entry to fractional
crystallographic coordinates." (please see here
https://www.wwpdb.org/documentation/file-format-content/format33/sect8.html)
"The self-correlation co
Hi Tim,
Thanks a lot for your suggestion! I tried different versions later, and I
found that the newest version doesn't work, but an old version works... I
have no idea what is wrong, but anyway it is working now, and it is related
to version...
Thank you so much,
Chen
On Wed, May 13, 2015 at 3:
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Dear Chen,
the fact that you differentiate between mp and non-mp version of
shelxd makes me assume you have a rather old version of shelxd
installed. Can you try again with the latest version of shelxd and
report if the (or any) error persists?
Best
Just an update. If I run shelxd from the command line the same error
appears. However, if I change the shelxd to the mp version, the command
line works but the hkl2map still doesn't work. I am more confused now.
Your input is greatly appreciated!
Best,
Chen
On Tue, May 12, 2015 at 5:11 PM, Chen
Hi all,
I encountered a problem with shelxd (in hkl2map gui) installed in a flash
drive running 32 bit Ubuntu OS.
The error message is:
OMP: Error #29: Unable to set OMP thread stack size to 268435456
OMP:System error #12: Cannot allocate memory
OMP:Hint: Try decreasing OMP_STACKSIZE
The $OMP_ST
@JISCMAIL.AC.UK] on behalf of Monica Mittal
[monica.mitta...@gmail.com]
Sent: Tuesday, April 22, 2014 3:13 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] shelxd
Dear all
I am naive in phasing experiments. CAn anyone please guide how to do the
following:
In a S-SAD for SHELXD searches, try various high
Dear Monica,
if you are new to phasing I recommend you first use the ``standard''
values in shelx c/d/e, either using one of my tutorials or, even better,
the GUI hkl2map, available at http://webapps.embl-hamburg.de/hkl2map/.
If your native data are about 2A or better, and your structure is a
pro
Dear all
I am naive in phasing experiments. CAn anyone please guide how to do the
following:
In a S-SAD for *SHELXD* searches, try various high-resolution cutoffs for
example 2.5 to 5 Å in steps of 0.1 Å. Based on these attempts, use a
high-resolution cutoff at for example 3.8 Å for substructure
The pseudo-free CC in SHELXE is not a very decisive figure of merit. By
far the best way is to run the autotracing (e.g. with -a5) and to look
at the CC for the trace against the native data. A value of more than
25% is almost always solved.
George
On 12/06/2011 10:02 PM, Tiruttani Subhramany
Hi
I forgot to mention the ShelxE beta results in the previous mail
P43212 with 15 sites: Mean FOM = 0.669 , Pseudo-free CC = 69.59 %
P43 with 36 sites: Mean FOM = 0.674, Pseudo-free CC = 70.19 %
P212121 with 36 sites: Mean FOM = 0.689 Pseudo-free CC = 72.08 %
thank you
With regards
uday
--
SHELXD does not use the solvent content. However since you know how many
seleniums it found and presumably know how many methionines are in the
sequence, you can use that to estimate the number of molecules is the
asymmetric unit. Note that an N-terminal selenomethionine is often
disordered and
hi
I have a 2.9 ang selenomet MAD data set integrated in four space groups P4,
P422, P222 and C222
i had to integrate in all the four space groups as I was stuck in refining the
model in P422
by using shelxD I found solution in P43, P43212 and p212121 but not in C222
the CC all/weak for them
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Hi Paul,
I just checked and did notice that coot (version 0.6.2) does not crash
anymore in the presence of two 'END' cards in the .hat-file.
I am sorry for mis-blaming coot.
Cheers,
Tim
On 11/14/2011 04:39 PM, Paul Emsley wrote:
> On 11/11/11 13:18
On 11/11/2011 11:31 AM, Andre Godoy wrote:
Hello everyone.
I'm a begginer in crystallography, especially in EP and I'm trying to solve a structure
by SAD. Right now I'm trying to solve the substructure on shelxD by running hkl2map, but
I'm finding hard to chose between solutions. So I'm asking
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Dear Andre,
as a rule of thumb you should cut the resolution for shelxd in SAD where
the anomalous selfCC as reported by shelxc drops below 30%. The second
important figure is a correct solvent content for shelxe, but only
really if you do not use the
Hello everyone.
I'm a begginer in crystallography, especially in EP and I'm trying to solve a
structure by SAD. Right now I'm trying to solve the substructure on shelxD by
running hkl2map, but I'm finding hard to chose between solutions. So I'm
asking, what should by my solution criteria (CCall
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